Starting phenix.real_space_refine on Sun Aug 24 22:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkc_27487/08_2025/8dkc_27487.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 14730 2.51 5 N 4027 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23282 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1813 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1813 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "C" Number of atoms: 9356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9356 Classifications: {'peptide': 1184} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1124} Chain breaks: 1 Chain: "D" Number of atoms: 9457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 9457 Classifications: {'peptide': 1201} Link IDs: {'CIS': 2, 'PTRANS': 48, 'TRANS': 1150} Chain breaks: 1 Chain: "E" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 843 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Time building chain proxies: 4.70, per 1000 atoms: 0.20 Number of scatterers: 23282 At special positions: 0 Unit cell: (129.05, 171.77, 171.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4437 8.00 N 4027 7.00 C 14730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 815 " - pdb=" SG CYS D 896 " distance=2.00 Simple disulfide: pdb=" SG CYS D 815 " - pdb=" SG CYS D 899 " distance=2.07 Simple disulfide: pdb=" SG CYS D 896 " - pdb=" SG CYS D 899 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 918.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5510 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 37 sheets defined 38.0% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 33 through 48 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.628A pdb=" N ILE A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.874A pdb=" N GLU A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.865A pdb=" N ALA A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 removed outlier: 3.643A pdb=" N THR B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.928A pdb=" N ALA B 160 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 231 removed outlier: 4.304A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 49 through 58 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.700A pdb=" N SER C 352 " --> pdb=" O ASN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 382 through 398 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 416 through 442 removed outlier: 3.555A pdb=" N GLN C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.788A pdb=" N LEU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 454' Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.800A pdb=" N SER C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 506 through 510 Processing helix chain 'C' and resid 572 through 576 removed outlier: 4.141A pdb=" N GLU C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 576' Processing helix chain 'C' and resid 639 through 651 Processing helix chain 'C' and resid 670 through 676 removed outlier: 3.526A pdb=" N SER C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 825 through 831 removed outlier: 4.140A pdb=" N ASP C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 913 through 942 Processing helix chain 'C' and resid 954 through 964 removed outlier: 4.157A pdb=" N SER C 964 " --> pdb=" O ILE C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 4.273A pdb=" N SER C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1019 Processing helix chain 'C' and resid 1083 through 1086 Processing helix chain 'C' and resid 1092 through 1105 Processing helix chain 'C' and resid 1120 through 1131 Processing helix chain 'C' and resid 1167 through 1171 removed outlier: 3.533A pdb=" N ASP C1170 " --> pdb=" O MET C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1210 removed outlier: 3.665A pdb=" N VAL C1204 " --> pdb=" O GLY C1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1222 Processing helix chain 'C' and resid 1226 through 1240 Processing helix chain 'C' and resid 1249 through 1260 removed outlier: 3.622A pdb=" N LYS C1260 " --> pdb=" O LEU C1256 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.702A pdb=" N ARG D 77 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.524A pdb=" N VAL D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.762A pdb=" N PHE D 113 " --> pdb=" O HIS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 222 through 241 removed outlier: 3.756A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.878A pdb=" N VAL D 251 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.530A pdb=" N LEU D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 297 removed outlier: 3.514A pdb=" N ASP D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 321 Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.822A pdb=" N TYR D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.685A pdb=" N ARG D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 429 Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.610A pdb=" N PHE D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 542 through 552 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 604 through 619 Processing helix chain 'D' and resid 619 through 642 removed outlier: 3.693A pdb=" N GLY D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 653 through 676 removed outlier: 4.004A pdb=" N ASP D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 661 " --> pdb=" O ASP D 657 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 664 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 665 " --> pdb=" O GLN D 661 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 666 " --> pdb=" O GLU D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 710 removed outlier: 3.770A pdb=" N VAL D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 710 " --> pdb=" O GLN D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'D' and resid 769 through 803 removed outlier: 4.039A pdb=" N TYR D 796 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.526A pdb=" N ARG D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 876 Processing helix chain 'D' and resid 896 through 901 removed outlier: 3.715A pdb=" N TYR D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY D 901 " --> pdb=" O ALA D 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 901' Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 927 through 930 Processing helix chain 'D' and resid 1127 through 1136 Processing helix chain 'D' and resid 1205 through 1214 removed outlier: 4.109A pdb=" N ILE D1209 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing helix chain 'D' and resid 1214 through 1233 Processing helix chain 'D' and resid 1238 through 1250 removed outlier: 4.652A pdb=" N PHE D1242 " --> pdb=" O ASN D1238 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D1245 " --> pdb=" O HIS D1241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D1247 " --> pdb=" O GLU D1243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D1248 " --> pdb=" O VAL D1244 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D1249 " --> pdb=" O ILE D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1276 removed outlier: 4.455A pdb=" N GLU D1273 " --> pdb=" O ASP D1270 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D1274 " --> pdb=" O LYS D1271 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D1276 " --> pdb=" O GLU D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1345 Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1357 through 1369 removed outlier: 3.623A pdb=" N VAL D1361 " --> pdb=" O GLU D1357 " (cutoff:3.500A) Processing helix chain 'D' and resid 1376 through 1384 Processing helix chain 'D' and resid 1389 through 1393 removed outlier: 3.985A pdb=" N LEU D1393 " --> pdb=" O GLY D1390 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 26 through 57 Processing helix chain 'E' and resid 70 through 81 Processing helix chain 'E' and resid 84 through 96 removed outlier: 3.526A pdb=" N ILE E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 4.675A pdb=" N THR A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 189 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.758A pdb=" N GLU A 143 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 57 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER A 145 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.539A pdb=" N VAL A 153 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 172 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.248A pdb=" N ILE B 21 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 204 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS B 23 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 202 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU B 25 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET B 200 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS B 27 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LEU B 198 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 189 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 187 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B 196 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 185 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 198 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 183 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET B 200 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 181 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 202 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 179 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR B 204 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 177 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.816A pdb=" N LYS B 58 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 145 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 56 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.712A pdb=" N GLU B 108 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS B 133 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 110 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.693A pdb=" N VAL B 153 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 172 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.869A pdb=" N ILE C 10 " --> pdb=" O ALA C1112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.590A pdb=" N TYR C 74 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 98 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE C 76 " --> pdb=" O PRO C 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 95 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 123 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 97 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 121 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 99 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP C 119 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 101 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 117 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 103 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C 115 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 105 " --> pdb=" O PHE C 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.270A pdb=" N SER C 145 " --> pdb=" O SER C 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'C' and resid 152 through 160 removed outlier: 4.170A pdb=" N HIS C 160 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR C 164 " --> pdb=" O HIS C 160 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 167 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC1, first strand: chain 'C' and resid 559 through 560 removed outlier: 3.687A pdb=" N ASP C 618 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 580 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 601 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 719 removed outlier: 6.275A pdb=" N ARG C 699 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 688 " --> pdb=" O ARG C 699 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AC4, first strand: chain 'C' and resid 756 through 757 Processing sheet with id=AC5, first strand: chain 'C' and resid 1138 through 1139 removed outlier: 7.660A pdb=" N ILE C 783 " --> pdb=" O SER C1060 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C1062 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 785 " --> pdb=" O ILE C1062 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ILE C1079 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 768 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU C1081 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 770 " --> pdb=" O LEU C1081 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR C1155 " --> pdb=" O TYR C 771 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 813 through 814 removed outlier: 3.593A pdb=" N GLY C 813 " --> pdb=" O THR C 810 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU C 809 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE C1029 " --> pdb=" O GLU C 809 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 893 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 851 removed outlier: 6.826A pdb=" N LEU C 885 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 854 through 855 Processing sheet with id=AC9, first strand: chain 'C' and resid 1173 through 1175 removed outlier: 3.672A pdb=" N SER D 363 " --> pdb=" O ARG C1175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 16 through 17 Processing sheet with id=AD2, first strand: chain 'D' and resid 30 through 33 removed outlier: 8.018A pdb=" N HIS D 100 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU D 33 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N HIS D 102 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 99 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.543A pdb=" N VAL D 266 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 561 through 569 Processing sheet with id=AD6, first strand: chain 'D' and resid 821 through 823 Processing sheet with id=AD7, first strand: chain 'D' and resid 826 through 828 removed outlier: 3.768A pdb=" N LEU D 826 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 834 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN D 828 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL D 832 " --> pdb=" O GLN D 828 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 1151 through 1152 Processing sheet with id=AD9, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.277A pdb=" N ILE D1179 " --> pdb=" O ARG D1163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1253 through 1258 removed outlier: 6.570A pdb=" N THR D1331 " --> pdb=" O VAL D1256 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5801 1.33 - 1.46: 5143 1.46 - 1.58: 12582 1.58 - 1.71: 0 1.71 - 1.83: 149 Bond restraints: 23675 Sorted by residual: bond pdb=" N ILE D 883 " pdb=" CA ILE D 883 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N VAL D 574 " pdb=" CA VAL D 574 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" N VAL D 370 " pdb=" CA VAL D 370 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.15e+00 bond pdb=" N GLU D 572 " pdb=" CA GLU D 572 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.21e-02 6.83e+03 8.95e+00 bond pdb=" N ARG D 884 " pdb=" CA ARG D 884 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.34e-02 5.57e+03 8.20e+00 ... (remaining 23670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 31196 2.77 - 5.55: 680 5.55 - 8.32: 94 8.32 - 11.10: 12 11.10 - 13.87: 3 Bond angle restraints: 31985 Sorted by residual: angle pdb=" N VAL D1287 " pdb=" CA VAL D1287 " pdb=" C VAL D1287 " ideal model delta sigma weight residual 111.88 104.22 7.66 1.06e+00 8.90e-01 5.22e+01 angle pdb=" CA TYR D 635 " pdb=" CB TYR D 635 " pdb=" CG TYR D 635 " ideal model delta sigma weight residual 113.90 125.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" N LEU C1259 " pdb=" CA LEU C1259 " pdb=" C LEU C1259 " ideal model delta sigma weight residual 111.28 104.31 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 113.71 107.79 5.92 9.50e-01 1.11e+00 3.88e+01 angle pdb=" CB LYS A 181 " pdb=" CG LYS A 181 " pdb=" CD LYS A 181 " ideal model delta sigma weight residual 111.30 97.43 13.87 2.30e+00 1.89e-01 3.64e+01 ... (remaining 31980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13118 17.62 - 35.23: 1177 35.23 - 52.85: 180 52.85 - 70.47: 44 70.47 - 88.08: 30 Dihedral angle restraints: 14549 sinusoidal: 6000 harmonic: 8549 Sorted by residual: dihedral pdb=" CA GLU D 572 " pdb=" C GLU D 572 " pdb=" N LEU D 573 " pdb=" CA LEU D 573 " ideal model delta harmonic sigma weight residual 180.00 102.67 77.33 0 5.00e+00 4.00e-02 2.39e+02 dihedral pdb=" CB CYS D 815 " pdb=" SG CYS D 815 " pdb=" SG CYS D 896 " pdb=" CB CYS D 896 " ideal model delta sinusoidal sigma weight residual -86.00 -5.38 -80.62 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CA GLU D1310 " pdb=" C GLU D1310 " pdb=" N ASN D1311 " pdb=" CA ASN D1311 " ideal model delta harmonic sigma weight residual -180.00 -137.60 -42.40 0 5.00e+00 4.00e-02 7.19e+01 ... (remaining 14546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2991 0.073 - 0.146: 595 0.146 - 0.219: 44 0.219 - 0.292: 6 0.292 - 0.364: 2 Chirality restraints: 3638 Sorted by residual: chirality pdb=" CB ILE B 173 " pdb=" CA ILE B 173 " pdb=" CG1 ILE B 173 " pdb=" CG2 ILE B 173 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA LEU C1259 " pdb=" N LEU C1259 " pdb=" C LEU C1259 " pdb=" CB LEU C1259 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA TYR E 93 " pdb=" N TYR E 93 " pdb=" C TYR E 93 " pdb=" CB TYR E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3635 not shown) Planarity restraints: 4161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 635 " 0.046 2.00e-02 2.50e+03 3.11e-02 1.93e+01 pdb=" CG TYR D 635 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR D 635 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 635 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 635 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 635 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 635 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 635 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D1279 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP D1279 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP D1279 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG D1280 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 187 " -0.025 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 187 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 187 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 187 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 187 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 187 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 187 " -0.004 2.00e-02 2.50e+03 ... (remaining 4158 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 465 2.60 - 3.17: 22878 3.17 - 3.75: 36299 3.75 - 4.32: 49379 4.32 - 4.90: 76270 Nonbonded interactions: 185291 Sorted by model distance: nonbonded pdb=" OG SER A 107 " pdb=" O LYS A 136 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR C1155 " pdb=" OD1 ASN D 646 " model vdw 2.034 3.040 nonbonded pdb=" OG SER C 825 " pdb=" OD1 ASP C 827 " model vdw 2.086 3.040 nonbonded pdb=" NE2 GLN B 85 " pdb=" OE2 GLU D 544 " model vdw 2.088 3.120 nonbonded pdb=" NH1 ARG E 101 " pdb=" O MET E 102 " model vdw 2.101 3.120 ... (remaining 185286 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 'A' selection = chain 'B' } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 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 : 0.007 0.462 23679 Z= 0.426 Angle : 1.020 19.553 31991 Z= 0.568 Chirality : 0.056 0.364 3638 Planarity : 0.006 0.080 4161 Dihedral : 14.110 88.085 9030 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.23 % Favored : 87.57 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.82 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.14), residues: 2936 helix: -0.97 (0.16), residues: 970 sheet: -1.15 (0.28), residues: 302 loop : -2.62 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 912 TYR 0.074 0.003 TYR D 635 PHE 0.063 0.003 PHE A 187 TRP 0.022 0.003 TRP D 422 HIS 0.008 0.002 HIS D 806 Details of bonding type rmsd covalent geometry : bond 0.00652 (23675) covalent geometry : angle 1.00776 (31985) SS BOND : bond 0.02937 ( 3) SS BOND : angle 11.64548 ( 6) hydrogen bonds : bond 0.15502 ( 898) hydrogen bonds : angle 7.82203 ( 2514) Misc. bond : bond 0.46165 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.771 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: A 19 ASP cc_start: 0.9119 (t70) cc_final: 0.8845 (t70) REVERT: A 200 MET cc_start: 0.7540 (ttp) cc_final: 0.7284 (ttm) REVERT: B 96 ASP cc_start: 0.9339 (p0) cc_final: 0.9027 (p0) REVERT: B 140 LEU cc_start: 0.9497 (mt) cc_final: 0.9184 (mt) REVERT: C 645 MET cc_start: 0.8100 (mtm) cc_final: 0.7298 (tmm) REVERT: C 789 MET cc_start: 0.8423 (mmm) cc_final: 0.8126 (mmm) REVERT: C 1090 MET cc_start: 0.7646 (mpp) cc_final: 0.7159 (mmt) REVERT: C 1148 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 1161 PHE cc_start: 0.7980 (t80) cc_final: 0.7319 (t80) REVERT: C 1194 PHE cc_start: 0.7231 (m-10) cc_final: 0.6789 (m-80) REVERT: C 1255 LEU cc_start: 0.8977 (tt) cc_final: 0.8684 (mt) REVERT: D 185 ASP cc_start: 0.9405 (m-30) cc_final: 0.9178 (t0) REVERT: D 477 ASP cc_start: 0.6995 (m-30) cc_final: 0.6683 (m-30) REVERT: D 479 MET cc_start: 0.8712 (mmm) cc_final: 0.8395 (mmm) REVERT: D 519 MET cc_start: 0.7825 (mpp) cc_final: 0.7407 (mpp) REVERT: D 602 LEU cc_start: 0.8386 (tt) cc_final: 0.8141 (tt) REVERT: D 721 MET cc_start: 0.8171 (tmm) cc_final: 0.7509 (tmm) REVERT: E 46 LYS cc_start: 0.9253 (pptt) cc_final: 0.8979 (pptt) REVERT: E 78 TYR cc_start: 0.9112 (t80) cc_final: 0.8901 (t80) REVERT: E 84 LYS cc_start: 0.8859 (mttt) cc_final: 0.8202 (mttp) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1534 time to fit residues: 62.1426 Evaluate side-chains 189 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN C 989 HIS C1257 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 672 GLN D 828 GLN ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.127477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.094089 restraints weight = 94802.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096938 restraints weight = 47865.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.098761 restraints weight = 31823.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.099906 restraints weight = 24763.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.100599 restraints weight = 21294.359| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 23679 Z= 0.253 Angle : 0.883 14.225 31991 Z= 0.464 Chirality : 0.052 0.239 3638 Planarity : 0.006 0.076 4161 Dihedral : 7.479 84.918 3213 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.27 % Favored : 88.62 % Rotamer: Outliers : 1.60 % Allowed : 10.56 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.14), residues: 2936 helix: -0.63 (0.15), residues: 985 sheet: -1.27 (0.28), residues: 302 loop : -2.53 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 444 TYR 0.062 0.003 TYR D 635 PHE 0.036 0.002 PHE A 187 TRP 0.015 0.002 TRP C1205 HIS 0.010 0.002 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00567 (23675) covalent geometry : angle 0.87751 (31985) SS BOND : bond 0.01142 ( 3) SS BOND : angle 6.92240 ( 6) hydrogen bonds : bond 0.05925 ( 898) hydrogen bonds : angle 6.64504 ( 2514) Misc. bond : bond 0.00283 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.776 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 15 MET cc_start: 0.6800 (tmm) cc_final: 0.6525 (tmm) REVERT: A 19 ASP cc_start: 0.9083 (t70) cc_final: 0.8833 (t70) REVERT: A 106 ASN cc_start: 0.8754 (t0) cc_final: 0.8204 (t0) REVERT: A 200 MET cc_start: 0.7625 (ttp) cc_final: 0.7382 (ttm) REVERT: B 96 ASP cc_start: 0.9275 (p0) cc_final: 0.8878 (p0) REVERT: B 187 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.5872 (p90) REVERT: B 191 GLN cc_start: 0.8543 (mm110) cc_final: 0.8261 (mm-40) REVERT: C 100 LYS cc_start: 0.8390 (mptt) cc_final: 0.8126 (mmtm) REVERT: C 364 TYR cc_start: 0.9073 (m-80) cc_final: 0.8676 (m-80) REVERT: C 651 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8151 (mtt90) REVERT: C 674 LYS cc_start: 0.8992 (tppt) cc_final: 0.8518 (pttt) REVERT: C 789 MET cc_start: 0.8458 (mmm) cc_final: 0.8102 (mmm) REVERT: D 98 MET cc_start: 0.6880 (mmp) cc_final: 0.6546 (mmp) REVERT: D 479 MET cc_start: 0.8709 (mmm) cc_final: 0.8342 (mmm) REVERT: D 519 MET cc_start: 0.7650 (mpp) cc_final: 0.7331 (mpp) REVERT: D 721 MET cc_start: 0.8283 (tmm) cc_final: 0.7778 (tmm) REVERT: E 46 LYS cc_start: 0.9245 (pptt) cc_final: 0.8887 (pptt) REVERT: E 78 TYR cc_start: 0.9016 (t80) cc_final: 0.8816 (t80) REVERT: E 79 TYR cc_start: 0.7966 (m-80) cc_final: 0.7146 (m-80) REVERT: E 84 LYS cc_start: 0.8860 (mttt) cc_final: 0.8189 (mttp) outliers start: 41 outliers final: 28 residues processed: 240 average time/residue: 0.1446 time to fit residues: 54.1837 Evaluate side-chains 219 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1249 MET Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 43 optimal weight: 0.0170 chunk 280 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN B 231 ASN ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 HIS C1094 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.130017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096643 restraints weight = 94817.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099621 restraints weight = 46923.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101568 restraints weight = 30900.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.102740 restraints weight = 23887.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.103350 restraints weight = 20507.114| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23679 Z= 0.158 Angle : 0.762 12.051 31991 Z= 0.395 Chirality : 0.048 0.240 3638 Planarity : 0.005 0.073 4161 Dihedral : 6.822 82.015 3213 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.25 % Favored : 89.71 % Rotamer: Outliers : 2.54 % Allowed : 13.02 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.15), residues: 2936 helix: -0.18 (0.16), residues: 990 sheet: -1.14 (0.28), residues: 300 loop : -2.32 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1341 TYR 0.030 0.002 TYR D 635 PHE 0.032 0.002 PHE A 187 TRP 0.010 0.002 TRP D 111 HIS 0.012 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00347 (23675) covalent geometry : angle 0.75871 (31985) SS BOND : bond 0.00751 ( 3) SS BOND : angle 5.37972 ( 6) hydrogen bonds : bond 0.04794 ( 898) hydrogen bonds : angle 6.15443 ( 2514) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.617 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 15 MET cc_start: 0.7119 (tmm) cc_final: 0.6832 (tmm) REVERT: A 19 ASP cc_start: 0.9071 (t70) cc_final: 0.8820 (t70) REVERT: A 33 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: A 106 ASN cc_start: 0.8714 (t0) cc_final: 0.8118 (t0) REVERT: B 96 ASP cc_start: 0.9244 (p0) cc_final: 0.8787 (p0) REVERT: B 142 MET cc_start: 0.7366 (pmm) cc_final: 0.7157 (pmm) REVERT: B 187 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6034 (p90) REVERT: C 364 TYR cc_start: 0.9073 (m-80) cc_final: 0.8727 (m-80) REVERT: C 651 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8053 (mtt90) REVERT: C 674 LYS cc_start: 0.9042 (tppt) cc_final: 0.8570 (pttt) REVERT: C 789 MET cc_start: 0.8471 (mmm) cc_final: 0.8243 (mmm) REVERT: C 814 LEU cc_start: 0.9636 (mm) cc_final: 0.9298 (pt) REVERT: C 932 HIS cc_start: 0.9298 (t-90) cc_final: 0.8950 (t70) REVERT: C 1092 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4688 (pt) REVERT: D 98 MET cc_start: 0.6710 (mmp) cc_final: 0.6418 (mmp) REVERT: D 479 MET cc_start: 0.8699 (mmm) cc_final: 0.8294 (mmm) REVERT: D 519 MET cc_start: 0.7616 (mpp) cc_final: 0.7249 (mpp) REVERT: D 721 MET cc_start: 0.8328 (tmm) cc_final: 0.7715 (tmm) REVERT: D 735 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5880 (mp) REVERT: D 1250 MET cc_start: 0.3758 (mtm) cc_final: 0.3541 (mtm) REVERT: E 46 LYS cc_start: 0.9209 (pptt) cc_final: 0.8869 (pptt) REVERT: E 78 TYR cc_start: 0.8964 (t80) cc_final: 0.8730 (t80) REVERT: E 79 TYR cc_start: 0.7918 (m-80) cc_final: 0.7280 (m-80) REVERT: E 84 LYS cc_start: 0.8760 (mttt) cc_final: 0.8198 (mttp) outliers start: 65 outliers final: 31 residues processed: 278 average time/residue: 0.1394 time to fit residues: 61.8241 Evaluate side-chains 234 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1008 ILE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 204 optimal weight: 10.0000 chunk 125 optimal weight: 0.0170 chunk 287 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1337 GLN D1345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.128282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.094856 restraints weight = 93619.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.097777 restraints weight = 46837.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.099635 restraints weight = 30912.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100809 restraints weight = 23922.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101448 restraints weight = 20453.225| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23679 Z= 0.187 Angle : 0.785 20.014 31991 Z= 0.400 Chirality : 0.049 0.401 3638 Planarity : 0.005 0.073 4161 Dihedral : 6.671 78.942 3213 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.49 % Favored : 89.48 % Rotamer: Outliers : 3.17 % Allowed : 15.92 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.15), residues: 2936 helix: -0.14 (0.16), residues: 991 sheet: -1.14 (0.28), residues: 302 loop : -2.33 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 444 TYR 0.034 0.002 TYR D 635 PHE 0.046 0.002 PHE C1210 TRP 0.013 0.002 TRP D 111 HIS 0.015 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00421 (23675) covalent geometry : angle 0.78185 (31985) SS BOND : bond 0.00918 ( 3) SS BOND : angle 4.96904 ( 6) hydrogen bonds : bond 0.04872 ( 898) hydrogen bonds : angle 6.08246 ( 2514) Misc. bond : bond 0.00735 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7214 (tmm) cc_final: 0.6936 (tmm) REVERT: A 19 ASP cc_start: 0.9097 (t70) cc_final: 0.8858 (t70) REVERT: A 33 TYR cc_start: 0.6165 (OUTLIER) cc_final: 0.5083 (m-80) REVERT: A 106 ASN cc_start: 0.8786 (t0) cc_final: 0.8150 (t0) REVERT: B 15 MET cc_start: 0.8526 (tmm) cc_final: 0.8292 (tmm) REVERT: B 96 ASP cc_start: 0.9250 (p0) cc_final: 0.8813 (p0) REVERT: B 187 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.5948 (p90) REVERT: C 330 GLN cc_start: 0.3565 (OUTLIER) cc_final: 0.2874 (mp-120) REVERT: C 364 TYR cc_start: 0.9086 (m-80) cc_final: 0.8700 (m-80) REVERT: C 610 THR cc_start: 0.5130 (OUTLIER) cc_final: 0.4901 (t) REVERT: C 645 MET cc_start: 0.7996 (mtm) cc_final: 0.7514 (mtt) REVERT: C 651 ARG cc_start: 0.8382 (mtt-85) cc_final: 0.8062 (mtt90) REVERT: C 674 LYS cc_start: 0.9092 (tppt) cc_final: 0.8641 (pttt) REVERT: C 789 MET cc_start: 0.8475 (mmm) cc_final: 0.8275 (mmm) REVERT: C 832 LEU cc_start: 0.8713 (tp) cc_final: 0.8480 (tp) REVERT: C 1001 TYR cc_start: 0.9028 (t80) cc_final: 0.8781 (t80) REVERT: C 1041 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: C 1092 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4713 (pt) REVERT: D 98 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6662 (mmp) REVERT: D 111 TRP cc_start: 0.8194 (m100) cc_final: 0.7963 (m100) REVERT: D 338 LYS cc_start: 0.7115 (pttp) cc_final: 0.6878 (pttp) REVERT: D 340 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.5096 (pt) REVERT: D 467 CYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7280 (p) REVERT: D 479 MET cc_start: 0.8703 (mmm) cc_final: 0.8277 (mmm) REVERT: D 519 MET cc_start: 0.7639 (mpp) cc_final: 0.7312 (mpp) REVERT: D 635 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5568 (t80) REVERT: D 721 MET cc_start: 0.8327 (tmm) cc_final: 0.7707 (tmm) REVERT: D 735 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5879 (mp) REVERT: D 1250 MET cc_start: 0.3837 (mtm) cc_final: 0.3462 (mtm) REVERT: D 1379 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: E 46 LYS cc_start: 0.9201 (pptt) cc_final: 0.8940 (pptt) REVERT: E 78 TYR cc_start: 0.8974 (t80) cc_final: 0.8708 (t80) REVERT: E 79 TYR cc_start: 0.8016 (m-80) cc_final: 0.7333 (m-80) REVERT: E 84 LYS cc_start: 0.8775 (mttt) cc_final: 0.8066 (mttp) outliers start: 81 outliers final: 43 residues processed: 264 average time/residue: 0.1423 time to fit residues: 59.5354 Evaluate side-chains 251 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1008 ILE Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 11 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 289 optimal weight: 0.0570 chunk 95 optimal weight: 0.0020 chunk 252 optimal weight: 3.9990 chunk 66 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 overall best weight: 2.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 191 GLN ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 HIS ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1337 GLN D1345 GLN D1363 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.129402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.095968 restraints weight = 92410.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.098932 restraints weight = 46200.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.100813 restraints weight = 30432.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.101979 restraints weight = 23556.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.102622 restraints weight = 20099.937| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 23679 Z= 0.152 Angle : 0.774 23.106 31991 Z= 0.385 Chirality : 0.048 0.306 3638 Planarity : 0.005 0.072 4161 Dihedral : 6.404 75.282 3213 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.01 % Favored : 89.95 % Rotamer: Outliers : 3.32 % Allowed : 17.36 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.15), residues: 2936 helix: -0.04 (0.16), residues: 1003 sheet: -0.90 (0.29), residues: 311 loop : -2.26 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 912 TYR 0.029 0.002 TYR C1001 PHE 0.030 0.002 PHE A 187 TRP 0.011 0.001 TRP D1282 HIS 0.006 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00339 (23675) covalent geometry : angle 0.77118 (31985) SS BOND : bond 0.00869 ( 3) SS BOND : angle 4.61110 ( 6) hydrogen bonds : bond 0.04492 ( 898) hydrogen bonds : angle 5.89815 ( 2514) Misc. bond : bond 0.00844 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7303 (tmm) cc_final: 0.7045 (tmm) REVERT: A 19 ASP cc_start: 0.9113 (t70) cc_final: 0.8876 (t70) REVERT: A 33 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.5099 (m-80) REVERT: A 106 ASN cc_start: 0.8805 (t0) cc_final: 0.8244 (t0) REVERT: B 96 ASP cc_start: 0.9229 (p0) cc_final: 0.8763 (p0) REVERT: C 330 GLN cc_start: 0.3563 (OUTLIER) cc_final: 0.2840 (mp-120) REVERT: C 364 TYR cc_start: 0.9147 (m-10) cc_final: 0.8770 (m-80) REVERT: C 610 THR cc_start: 0.5108 (OUTLIER) cc_final: 0.4893 (t) REVERT: C 642 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8267 (mmm160) REVERT: C 651 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8073 (mtt90) REVERT: C 674 LYS cc_start: 0.9077 (tppt) cc_final: 0.8627 (pttt) REVERT: C 789 MET cc_start: 0.8463 (mmm) cc_final: 0.8184 (mmm) REVERT: C 832 LEU cc_start: 0.8718 (tp) cc_final: 0.8465 (tp) REVERT: C 1041 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6278 (ttm170) REVERT: C 1092 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4588 (pt) REVERT: D 111 TRP cc_start: 0.8226 (m100) cc_final: 0.7999 (m100) REVERT: D 191 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5623 (pt) REVERT: D 467 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7262 (p) REVERT: D 479 MET cc_start: 0.8689 (mmm) cc_final: 0.8244 (mmm) REVERT: D 519 MET cc_start: 0.7639 (mpp) cc_final: 0.7333 (mpp) REVERT: D 635 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.5551 (t80) REVERT: D 637 MET cc_start: 0.8046 (tpp) cc_final: 0.7766 (tpp) REVERT: D 721 MET cc_start: 0.8305 (tmm) cc_final: 0.7711 (tmm) REVERT: D 735 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5834 (mp) REVERT: D 1250 MET cc_start: 0.3433 (mtm) cc_final: 0.3031 (mtm) REVERT: D 1379 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7825 (pp20) REVERT: E 78 TYR cc_start: 0.8933 (t80) cc_final: 0.8647 (t80) REVERT: E 79 TYR cc_start: 0.8029 (m-80) cc_final: 0.7298 (m-80) REVERT: E 84 LYS cc_start: 0.8714 (mttt) cc_final: 0.8137 (mttp) REVERT: E 102 MET cc_start: 0.7062 (mmp) cc_final: 0.5203 (tmm) outliers start: 85 outliers final: 48 residues processed: 280 average time/residue: 0.1449 time to fit residues: 64.3361 Evaluate side-chains 254 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1008 ILE Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 899 CYS Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 161 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 274 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 0.0030 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS C 652 GLN C 799 HIS C1094 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 ASN D1266 GLN E 47 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.126136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.092615 restraints weight = 94848.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095417 restraints weight = 48368.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.097197 restraints weight = 32217.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.098318 restraints weight = 25117.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.098912 restraints weight = 21565.196| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23679 Z= 0.254 Angle : 0.835 15.250 31991 Z= 0.429 Chirality : 0.051 0.431 3638 Planarity : 0.005 0.073 4161 Dihedral : 6.647 69.588 3213 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.65 % Favored : 88.32 % Rotamer: Outliers : 3.79 % Allowed : 18.03 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.15), residues: 2936 helix: -0.25 (0.16), residues: 1003 sheet: -1.03 (0.29), residues: 299 loop : -2.38 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 150 TYR 0.045 0.002 TYR D 635 PHE 0.031 0.002 PHE A 187 TRP 0.009 0.002 TRP D 422 HIS 0.007 0.001 HIS D 806 Details of bonding type rmsd covalent geometry : bond 0.00573 (23675) covalent geometry : angle 0.83224 (31985) SS BOND : bond 0.01142 ( 3) SS BOND : angle 4.93278 ( 6) hydrogen bonds : bond 0.05386 ( 898) hydrogen bonds : angle 6.14897 ( 2514) Misc. bond : bond 0.00473 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 198 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7240 (tmm) cc_final: 0.6983 (tmm) REVERT: A 19 ASP cc_start: 0.9133 (t70) cc_final: 0.8909 (t70) REVERT: A 33 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.4715 (m-80) REVERT: A 106 ASN cc_start: 0.8949 (t0) cc_final: 0.8399 (t0) REVERT: B 96 ASP cc_start: 0.9230 (p0) cc_final: 0.8787 (p0) REVERT: B 142 MET cc_start: 0.7342 (pmm) cc_final: 0.6953 (pmm) REVERT: B 187 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6159 (p90) REVERT: C 330 GLN cc_start: 0.3334 (OUTLIER) cc_final: 0.2601 (mp-120) REVERT: C 364 TYR cc_start: 0.9175 (m-10) cc_final: 0.8806 (m-80) REVERT: C 610 THR cc_start: 0.5347 (OUTLIER) cc_final: 0.5123 (t) REVERT: C 651 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.8173 (mtt90) REVERT: C 789 MET cc_start: 0.8535 (mmm) cc_final: 0.8319 (mmm) REVERT: C 832 LEU cc_start: 0.8713 (tp) cc_final: 0.8499 (tp) REVERT: C 1041 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6390 (ttm170) REVERT: C 1092 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.4693 (pt) REVERT: D 215 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7475 (ppt90) REVERT: D 447 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7574 (tp) REVERT: D 467 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7197 (p) REVERT: D 479 MET cc_start: 0.8722 (mmm) cc_final: 0.8341 (mmm) REVERT: D 497 MET cc_start: 0.9163 (mtp) cc_final: 0.8740 (mtp) REVERT: D 519 MET cc_start: 0.7660 (mpp) cc_final: 0.7290 (mpp) REVERT: D 721 MET cc_start: 0.8362 (tmm) cc_final: 0.7679 (tmm) REVERT: D 735 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5954 (mp) REVERT: D 1250 MET cc_start: 0.3887 (mtm) cc_final: 0.3168 (mtm) REVERT: D 1357 GLU cc_start: 0.8689 (tp30) cc_final: 0.8225 (tm-30) REVERT: D 1379 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7938 (pp20) REVERT: E 78 TYR cc_start: 0.9020 (t80) cc_final: 0.8718 (t80) REVERT: E 79 TYR cc_start: 0.7972 (m-80) cc_final: 0.7250 (m-80) REVERT: E 84 LYS cc_start: 0.8955 (mttt) cc_final: 0.8280 (mttp) outliers start: 97 outliers final: 62 residues processed: 272 average time/residue: 0.1461 time to fit residues: 62.6422 Evaluate side-chains 257 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 184 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 892 LYS Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1262 LEU Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 27 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 282 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 24 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 HIS ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 HIS ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1266 GLN E 26 ASN E 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.126211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.092612 restraints weight = 94824.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.095432 restraints weight = 48328.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.097232 restraints weight = 32199.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.098361 restraints weight = 25083.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.098969 restraints weight = 21536.080| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23679 Z= 0.230 Angle : 0.827 14.566 31991 Z= 0.423 Chirality : 0.050 0.263 3638 Planarity : 0.006 0.129 4161 Dihedral : 6.634 63.689 3213 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.27 % Favored : 88.69 % Rotamer: Outliers : 3.83 % Allowed : 18.54 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.15), residues: 2936 helix: -0.30 (0.16), residues: 1004 sheet: -1.08 (0.29), residues: 299 loop : -2.41 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 444 TYR 0.041 0.002 TYR D 635 PHE 0.070 0.002 PHE C1210 TRP 0.008 0.001 TRP C1127 HIS 0.008 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00518 (23675) covalent geometry : angle 0.82471 (31985) SS BOND : bond 0.01085 ( 3) SS BOND : angle 4.90740 ( 6) hydrogen bonds : bond 0.05227 ( 898) hydrogen bonds : angle 6.16602 ( 2514) Misc. bond : bond 0.00528 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 198 time to evaluate : 0.973 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: A 11 ASN cc_start: 0.6117 (t0) cc_final: 0.5845 (t0) REVERT: A 19 ASP cc_start: 0.9154 (t70) cc_final: 0.8943 (t70) REVERT: A 33 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: A 106 ASN cc_start: 0.9066 (t0) cc_final: 0.8604 (t0) REVERT: B 96 ASP cc_start: 0.9211 (p0) cc_final: 0.8762 (p0) REVERT: B 142 MET cc_start: 0.7265 (pmm) cc_final: 0.6833 (pmm) REVERT: B 187 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6159 (p90) REVERT: C 330 GLN cc_start: 0.3587 (OUTLIER) cc_final: 0.2839 (mp-120) REVERT: C 364 TYR cc_start: 0.9220 (m-10) cc_final: 0.8859 (m-80) REVERT: C 642 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8136 (mmm160) REVERT: C 645 MET cc_start: 0.7599 (ptp) cc_final: 0.7071 (mtm) REVERT: C 651 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8106 (mtt90) REVERT: C 789 MET cc_start: 0.8418 (mmm) cc_final: 0.8168 (mmm) REVERT: C 1056 LYS cc_start: 0.9087 (tppp) cc_final: 0.8882 (tppp) REVERT: C 1092 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4721 (pt) REVERT: D 191 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5632 (pt) REVERT: D 215 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7471 (ppt90) REVERT: D 447 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7491 (tp) REVERT: D 467 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7163 (p) REVERT: D 479 MET cc_start: 0.8728 (mmm) cc_final: 0.8329 (mmm) REVERT: D 497 MET cc_start: 0.9178 (mtp) cc_final: 0.8725 (mtp) REVERT: D 519 MET cc_start: 0.7656 (mpp) cc_final: 0.7292 (mpp) REVERT: D 637 MET cc_start: 0.8083 (tpp) cc_final: 0.7762 (tpp) REVERT: D 721 MET cc_start: 0.8354 (tmm) cc_final: 0.7563 (tmm) REVERT: D 735 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5874 (mp) REVERT: D 1250 MET cc_start: 0.3749 (mtm) cc_final: 0.2971 (mtm) REVERT: D 1379 GLU cc_start: 0.8545 (tt0) cc_final: 0.8040 (pp20) REVERT: E 78 TYR cc_start: 0.9057 (t80) cc_final: 0.8738 (t80) REVERT: E 79 TYR cc_start: 0.8021 (m-80) cc_final: 0.7299 (m-80) REVERT: E 84 LYS cc_start: 0.8976 (mttt) cc_final: 0.8278 (mttp) outliers start: 98 outliers final: 67 residues processed: 274 average time/residue: 0.1378 time to fit residues: 60.3414 Evaluate side-chains 263 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 187 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 HIS Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 892 LYS Chi-restraints excluded: chain D residue 899 CYS Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1262 LEU Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 190 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 134 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 chunk 246 optimal weight: 0.9980 chunk 233 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 HIS ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.129586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.096310 restraints weight = 92296.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.099212 restraints weight = 46311.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.101145 restraints weight = 30517.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.102325 restraints weight = 23644.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.102978 restraints weight = 20227.943| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23679 Z= 0.142 Angle : 0.785 20.445 31991 Z= 0.391 Chirality : 0.048 0.285 3638 Planarity : 0.005 0.090 4161 Dihedral : 6.204 57.124 3213 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.32 % Favored : 89.61 % Rotamer: Outliers : 3.13 % Allowed : 19.71 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.15), residues: 2936 helix: -0.05 (0.16), residues: 1008 sheet: -0.85 (0.29), residues: 311 loop : -2.30 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 912 TYR 0.033 0.001 TYR C1001 PHE 0.063 0.002 PHE C1210 TRP 0.012 0.001 TRP D 111 HIS 0.007 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00316 (23675) covalent geometry : angle 0.78277 (31985) SS BOND : bond 0.00832 ( 3) SS BOND : angle 4.62482 ( 6) hydrogen bonds : bond 0.04338 ( 898) hydrogen bonds : angle 5.85520 ( 2514) Misc. bond : bond 0.00774 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.6472 (t0) cc_final: 0.6246 (t0) REVERT: A 19 ASP cc_start: 0.9138 (t70) cc_final: 0.8916 (t70) REVERT: A 33 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.4830 (m-80) REVERT: A 106 ASN cc_start: 0.8977 (t0) cc_final: 0.8386 (t0) REVERT: B 49 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5915 (mm) REVERT: B 66 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5566 (m-80) REVERT: B 96 ASP cc_start: 0.9183 (p0) cc_final: 0.8696 (p0) REVERT: B 142 MET cc_start: 0.7279 (pmm) cc_final: 0.6883 (pmm) REVERT: B 187 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6035 (p90) REVERT: C 330 GLN cc_start: 0.3496 (OUTLIER) cc_final: 0.2748 (mp-120) REVERT: C 364 TYR cc_start: 0.9230 (m-10) cc_final: 0.8881 (m-80) REVERT: C 409 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7170 (mm) REVERT: C 440 MET cc_start: 0.7825 (ttp) cc_final: 0.7587 (ptm) REVERT: C 636 GLU cc_start: 0.6749 (pt0) cc_final: 0.6352 (pm20) REVERT: C 642 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8162 (mmm160) REVERT: C 645 MET cc_start: 0.7432 (ptp) cc_final: 0.7096 (mtm) REVERT: C 789 MET cc_start: 0.8456 (mmm) cc_final: 0.8174 (mmm) REVERT: C 1041 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6366 (ttm170) REVERT: C 1056 LYS cc_start: 0.9032 (tppp) cc_final: 0.8821 (tppp) REVERT: C 1092 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4660 (pt) REVERT: D 111 TRP cc_start: 0.8360 (m100) cc_final: 0.7792 (m100) REVERT: D 191 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5752 (pt) REVERT: D 215 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7273 (ppt90) REVERT: D 340 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5714 (mt) REVERT: D 467 CYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7192 (p) REVERT: D 479 MET cc_start: 0.8695 (mmm) cc_final: 0.8275 (mmm) REVERT: D 721 MET cc_start: 0.8263 (tmm) cc_final: 0.7687 (tmm) REVERT: D 735 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5745 (mp) REVERT: D 1233 GLN cc_start: 0.8891 (mp-120) cc_final: 0.8610 (mm-40) REVERT: D 1250 MET cc_start: 0.3438 (mtm) cc_final: 0.3000 (mtm) REVERT: D 1357 GLU cc_start: 0.8658 (tp30) cc_final: 0.7825 (tm-30) REVERT: D 1379 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8002 (pp20) REVERT: E 26 ASN cc_start: 0.9287 (t0) cc_final: 0.8852 (t0) REVERT: E 46 LYS cc_start: 0.9156 (pptt) cc_final: 0.8862 (pptt) REVERT: E 78 TYR cc_start: 0.9004 (t80) cc_final: 0.8665 (t80) REVERT: E 79 TYR cc_start: 0.7940 (m-80) cc_final: 0.7200 (m-80) REVERT: E 84 LYS cc_start: 0.8927 (mttt) cc_final: 0.8306 (mttp) outliers start: 80 outliers final: 54 residues processed: 284 average time/residue: 0.1444 time to fit residues: 64.9960 Evaluate side-chains 277 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain C residue 1260 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 899 CYS Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 125 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 chunk 292 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 HIS ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1004 HIS C1094 GLN ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.126329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092785 restraints weight = 94929.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.095581 restraints weight = 48419.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.097390 restraints weight = 32303.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.098517 restraints weight = 25200.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.099181 restraints weight = 21617.619| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23679 Z= 0.236 Angle : 0.868 17.910 31991 Z= 0.435 Chirality : 0.051 0.336 3638 Planarity : 0.006 0.096 4161 Dihedral : 6.416 52.665 3213 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.48 % Favored : 88.49 % Rotamer: Outliers : 3.44 % Allowed : 19.87 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.15), residues: 2936 helix: -0.26 (0.16), residues: 1004 sheet: -0.91 (0.29), residues: 309 loop : -2.41 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 444 TYR 0.041 0.002 TYR D 635 PHE 0.068 0.002 PHE C1210 TRP 0.014 0.002 TRP C 178 HIS 0.009 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00535 (23675) covalent geometry : angle 0.86501 (31985) SS BOND : bond 0.01123 ( 3) SS BOND : angle 4.94555 ( 6) hydrogen bonds : bond 0.05211 ( 898) hydrogen bonds : angle 6.11223 ( 2514) Misc. bond : bond 0.00781 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 205 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.6255 (t0) cc_final: 0.5988 (t0) REVERT: A 19 ASP cc_start: 0.9135 (t70) cc_final: 0.8916 (t70) REVERT: A 33 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: A 106 ASN cc_start: 0.9083 (t0) cc_final: 0.8597 (t0) REVERT: B 49 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5812 (mm) REVERT: B 66 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: B 96 ASP cc_start: 0.9213 (p0) cc_final: 0.8746 (p0) REVERT: B 142 MET cc_start: 0.7228 (pmm) cc_final: 0.6788 (pmm) REVERT: B 187 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6152 (p90) REVERT: C 330 GLN cc_start: 0.3365 (OUTLIER) cc_final: 0.2599 (mp-120) REVERT: C 364 TYR cc_start: 0.9270 (m-10) cc_final: 0.8936 (m-80) REVERT: C 409 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7262 (mm) REVERT: C 642 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8126 (mmm160) REVERT: C 645 MET cc_start: 0.7377 (ptp) cc_final: 0.7038 (mtm) REVERT: C 789 MET cc_start: 0.8429 (mmm) cc_final: 0.8156 (mmm) REVERT: C 1041 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6288 (ttm170) REVERT: C 1056 LYS cc_start: 0.9073 (tppp) cc_final: 0.8860 (tppp) REVERT: C 1092 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4644 (pt) REVERT: D 111 TRP cc_start: 0.8413 (m100) cc_final: 0.7811 (m100) REVERT: D 191 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5750 (pt) REVERT: D 215 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7502 (ppt90) REVERT: D 351 PHE cc_start: 0.5333 (m-10) cc_final: 0.5101 (m-10) REVERT: D 467 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7101 (p) REVERT: D 479 MET cc_start: 0.8774 (mmm) cc_final: 0.8329 (mmm) REVERT: D 497 MET cc_start: 0.9162 (mtp) cc_final: 0.8781 (mtp) REVERT: D 519 MET cc_start: 0.7714 (mpp) cc_final: 0.7295 (mpp) REVERT: D 637 MET cc_start: 0.8145 (tpp) cc_final: 0.7871 (tpp) REVERT: D 721 MET cc_start: 0.8392 (tmm) cc_final: 0.7816 (tmm) REVERT: D 735 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5819 (mp) REVERT: D 1250 MET cc_start: 0.3631 (mtm) cc_final: 0.3195 (mtm) REVERT: D 1357 GLU cc_start: 0.8731 (tp30) cc_final: 0.8187 (tm-30) REVERT: D 1379 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: E 26 ASN cc_start: 0.9314 (t0) cc_final: 0.8975 (t0) REVERT: E 46 LYS cc_start: 0.9182 (pptt) cc_final: 0.8878 (pptt) REVERT: E 78 TYR cc_start: 0.9071 (t80) cc_final: 0.8734 (t80) REVERT: E 79 TYR cc_start: 0.8014 (m-80) cc_final: 0.7292 (m-80) REVERT: E 84 LYS cc_start: 0.9005 (mttt) cc_final: 0.8349 (mttp) outliers start: 88 outliers final: 60 residues processed: 271 average time/residue: 0.1389 time to fit residues: 59.1035 Evaluate side-chains 269 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 892 LYS Chi-restraints excluded: chain D residue 899 CYS Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1262 LEU Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 216 optimal weight: 0.0980 chunk 68 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 HIS C 590 ASN ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1094 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.129737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096183 restraints weight = 93426.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.099155 restraints weight = 46500.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.101059 restraints weight = 30484.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.102239 restraints weight = 23555.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.102889 restraints weight = 20164.747| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23679 Z= 0.144 Angle : 0.811 17.064 31991 Z= 0.405 Chirality : 0.049 0.356 3638 Planarity : 0.005 0.090 4161 Dihedral : 6.115 52.985 3213 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.91 % Favored : 90.05 % Rotamer: Outliers : 2.85 % Allowed : 20.73 % Favored : 76.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.15), residues: 2936 helix: -0.09 (0.16), residues: 1000 sheet: -0.81 (0.30), residues: 293 loop : -2.25 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 651 TYR 0.035 0.002 TYR C1001 PHE 0.057 0.002 PHE C1210 TRP 0.012 0.001 TRP D 111 HIS 0.006 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00318 (23675) covalent geometry : angle 0.80831 (31985) SS BOND : bond 0.00835 ( 3) SS BOND : angle 4.60213 ( 6) hydrogen bonds : bond 0.04421 ( 898) hydrogen bonds : angle 5.86704 ( 2514) Misc. bond : bond 0.00155 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9119 (t70) cc_final: 0.8896 (t70) REVERT: A 33 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: A 106 ASN cc_start: 0.9025 (t0) cc_final: 0.8424 (t0) REVERT: B 49 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5876 (mm) REVERT: B 66 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5601 (m-80) REVERT: B 96 ASP cc_start: 0.9173 (p0) cc_final: 0.8675 (p0) REVERT: B 142 MET cc_start: 0.7354 (pmm) cc_final: 0.6891 (pmm) REVERT: B 187 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6068 (p90) REVERT: C 330 GLN cc_start: 0.3456 (OUTLIER) cc_final: 0.2700 (mp-120) REVERT: C 364 TYR cc_start: 0.9269 (m-10) cc_final: 0.8907 (m-80) REVERT: C 409 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7242 (mm) REVERT: C 642 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8106 (mmm160) REVERT: C 645 MET cc_start: 0.7322 (ptp) cc_final: 0.6968 (mtm) REVERT: C 789 MET cc_start: 0.8453 (mmm) cc_final: 0.8161 (mmm) REVERT: C 1041 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6251 (ttm170) REVERT: C 1056 LYS cc_start: 0.9026 (tppp) cc_final: 0.8805 (tppp) REVERT: C 1092 LEU cc_start: 0.4778 (OUTLIER) cc_final: 0.4548 (pt) REVERT: D 111 TRP cc_start: 0.8286 (m100) cc_final: 0.7718 (m100) REVERT: D 191 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5772 (pt) REVERT: D 215 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7321 (ppt90) REVERT: D 250 MET cc_start: 0.2073 (mmm) cc_final: 0.1543 (mmm) REVERT: D 467 CYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7123 (p) REVERT: D 479 MET cc_start: 0.8693 (mmm) cc_final: 0.8269 (mmm) REVERT: D 497 MET cc_start: 0.9100 (mtp) cc_final: 0.8615 (mtp) REVERT: D 519 MET cc_start: 0.7541 (mpp) cc_final: 0.7224 (mpp) REVERT: D 577 MET cc_start: 0.7733 (mmm) cc_final: 0.7495 (mmp) REVERT: D 637 MET cc_start: 0.8082 (tpp) cc_final: 0.7825 (tpp) REVERT: D 721 MET cc_start: 0.8249 (tmm) cc_final: 0.7717 (tmm) REVERT: D 735 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5733 (mp) REVERT: D 1250 MET cc_start: 0.3327 (mtm) cc_final: 0.2898 (mtm) REVERT: D 1357 GLU cc_start: 0.8729 (tp30) cc_final: 0.7965 (tm-30) REVERT: D 1379 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7992 (pp20) REVERT: E 26 ASN cc_start: 0.9291 (t0) cc_final: 0.8984 (t0) REVERT: E 46 LYS cc_start: 0.9161 (pptt) cc_final: 0.8844 (pptt) REVERT: E 78 TYR cc_start: 0.9018 (t80) cc_final: 0.8707 (t80) REVERT: E 79 TYR cc_start: 0.7885 (m-80) cc_final: 0.7386 (m-80) REVERT: E 84 LYS cc_start: 0.8946 (mttt) cc_final: 0.8319 (mttp) outliers start: 73 outliers final: 50 residues processed: 266 average time/residue: 0.1297 time to fit residues: 55.1145 Evaluate side-chains 266 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 443 HIS Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 892 LYS Chi-restraints excluded: chain D residue 899 CYS Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 256 optimal weight: 0.0870 chunk 56 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 0.4980 chunk 188 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 276 optimal weight: 7.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 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 = 0.4463 r_free = 0.4463 target = 0.130224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.096698 restraints weight = 92903.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.099686 restraints weight = 46356.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.101595 restraints weight = 30447.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.102640 restraints weight = 23501.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.103381 restraints weight = 20223.202| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 23679 Z= 0.171 Angle : 0.973 69.284 31991 Z= 0.454 Chirality : 0.065 2.590 3638 Planarity : 0.005 0.077 4161 Dihedral : 6.085 53.139 3213 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.95 % Favored : 90.02 % Rotamer: Outliers : 2.62 % Allowed : 21.04 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.15), residues: 2936 helix: -0.07 (0.16), residues: 997 sheet: -0.73 (0.31), residues: 293 loop : -2.21 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 651 TYR 0.033 0.002 TYR C1001 PHE 0.051 0.002 PHE C 794 TRP 0.011 0.001 TRP D 692 HIS 0.006 0.001 HIS C 932 Details of bonding type rmsd covalent geometry : bond 0.00389 (23675) covalent geometry : angle 0.97138 (31985) SS BOND : bond 0.00842 ( 3) SS BOND : angle 4.64294 ( 6) hydrogen bonds : bond 0.04397 ( 898) hydrogen bonds : angle 5.86802 ( 2514) Misc. bond : bond 0.01143 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6298.96 seconds wall clock time: 108 minutes 33.32 seconds (6513.32 seconds total)