Starting phenix.real_space_refine on Mon Apr 6 22:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865.map" model { file = "/net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u57_63865/04_2026/9u57_63865_neut.cif" } resolution = 3.42 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= 0.003 sd= 0.032 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 104 5.16 5 C 14438 2.51 5 N 3678 2.21 5 O 3922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10915 Classifications: {'peptide': 1379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1320} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 10915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1379, 10915 Classifications: {'peptide': 1379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1320} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 172 Unusual residues: {'CLR': 5, 'R16': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.05, per 1000 atoms: 0.23 Number of scatterers: 22142 At special positions: 0 Unit cell: (179.25, 110.25, 147.75, 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 104 16.00 O 3922 8.00 N 3678 7.00 C 14438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 14 sheets defined 68.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.539A pdb=" N TRP A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 59 Processing helix chain 'A' and resid 71 through 94 removed outlier: 3.985A pdb=" N TYR A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.920A pdb=" N MET A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 131 Processing helix chain 'A' and resid 140 through 164 removed outlier: 3.773A pdb=" N VAL A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 192 removed outlier: 3.653A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 267 through 285 removed outlier: 3.740A pdb=" N LEU A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.554A pdb=" N ALA A 293 " --> pdb=" O TRP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.517A pdb=" N GLY A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.615A pdb=" N LEU A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 385 removed outlier: 4.019A pdb=" N ILE A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.755A pdb=" N LEU A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.673A pdb=" N GLN A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 Proline residue: A 424 - end of helix Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.797A pdb=" N LEU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.704A pdb=" N LEU A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 484 removed outlier: 3.582A pdb=" N LEU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 497 through 547 Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 552 through 595 removed outlier: 4.338A pdb=" N PHE A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Proline residue: A 569 - end of helix Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 653 through 663 removed outlier: 3.564A pdb=" N SER A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 699 Processing helix chain 'A' and resid 705 through 716 Processing helix chain 'A' and resid 717 through 725 removed outlier: 4.110A pdb=" N ASP A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 Processing helix chain 'A' and resid 741 through 757 Processing helix chain 'A' and resid 771 through 782 Processing helix chain 'A' and resid 801 through 805 Processing helix chain 'A' and resid 821 through 829 Processing helix chain 'A' and resid 829 through 836 Processing helix chain 'A' and resid 904 through 916 Processing helix chain 'A' and resid 917 through 946 removed outlier: 3.856A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 1002 removed outlier: 3.935A pdb=" N TYR A 959 " --> pdb=" O GLY A 955 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A1002 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1011 Processing helix chain 'A' and resid 1012 through 1030 removed outlier: 4.293A pdb=" N ILE A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1056 Processing helix chain 'A' and resid 1056 through 1092 removed outlier: 3.851A pdb=" N LEU A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Proline residue: A1065 - end of helix removed outlier: 3.535A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A1077 " --> pdb=" O ALA A1073 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1110 removed outlier: 4.374A pdb=" N TYR A1096 " --> pdb=" O ARG A1092 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A1099 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY A1100 " --> pdb=" O TYR A1096 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N THR A1108 " --> pdb=" O ASN A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1166 removed outlier: 4.236A pdb=" N ASN A1166 " --> pdb=" O ALA A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1187 removed outlier: 3.768A pdb=" N LEU A1181 " --> pdb=" O SER A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1218 removed outlier: 4.082A pdb=" N LEU A1192 " --> pdb=" O ASN A1188 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A1201 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1202 " --> pdb=" O ARG A1198 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1285 through 1290 removed outlier: 3.580A pdb=" N LEU A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1338 Processing helix chain 'A' and resid 1344 through 1355 Processing helix chain 'A' and resid 1357 through 1363 removed outlier: 3.506A pdb=" N ARG A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1369 removed outlier: 3.566A pdb=" N ASP A1369 " --> pdb=" O LEU A1366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1366 through 1369' Processing helix chain 'A' and resid 1373 through 1377 Processing helix chain 'A' and resid 1381 through 1396 removed outlier: 3.985A pdb=" N GLN A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1386 " --> pdb=" O GLY A1382 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1425 removed outlier: 3.933A pdb=" N THR A1420 " --> pdb=" O LEU A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1440 removed outlier: 3.661A pdb=" N THR A1439 " --> pdb=" O ARG A1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.563A pdb=" N LYS B 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 60 Processing helix chain 'B' and resid 75 through 95 Proline residue: B 88 - end of helix removed outlier: 4.013A pdb=" N ARG B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.511A pdb=" N VAL B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 removed outlier: 3.578A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 192 removed outlier: 3.967A pdb=" N TYR B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 267 through 285 removed outlier: 4.074A pdb=" N LEU B 271 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.826A pdb=" N ALA B 293 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.583A pdb=" N LEU B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 385 removed outlier: 4.030A pdb=" N ILE B 341 " --> pdb=" O TRP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 416 removed outlier: 4.193A pdb=" N THR B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.874A pdb=" N LEU B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 492 removed outlier: 3.762A pdb=" N LEU B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 547 removed outlier: 3.736A pdb=" N PHE B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 552 through 566 Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.922A pdb=" N LEU B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) Proline residue: B 574 - end of helix removed outlier: 3.871A pdb=" N GLU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.881A pdb=" N ASN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 Processing helix chain 'B' and resid 717 through 725 removed outlier: 4.317A pdb=" N ASP B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 757 removed outlier: 3.516A pdb=" N ASN B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 783 Processing helix chain 'B' and resid 801 through 805 Processing helix chain 'B' and resid 821 through 829 Processing helix chain 'B' and resid 829 through 836 Processing helix chain 'B' and resid 904 through 916 Processing helix chain 'B' and resid 917 through 946 removed outlier: 3.968A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 1000 removed outlier: 3.870A pdb=" N TYR B 959 " --> pdb=" O GLY B 955 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 974 " --> pdb=" O GLN B 970 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N MET B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 999 " --> pdb=" O ASN B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1011 Processing helix chain 'B' and resid 1012 through 1030 removed outlier: 4.369A pdb=" N ILE B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B1024 " --> pdb=" O PHE B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1056 Processing helix chain 'B' and resid 1056 through 1092 removed outlier: 3.870A pdb=" N LEU B1060 " --> pdb=" O SER B1056 " (cutoff:3.500A) Proline residue: B1065 - end of helix removed outlier: 4.181A pdb=" N THR B1080 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU B1083 " --> pdb=" O ASN B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1110 removed outlier: 4.479A pdb=" N TYR B1096 " --> pdb=" O ARG B1092 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE B1099 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B1100 " --> pdb=" O TYR B1096 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER B1107 " --> pdb=" O LEU B1103 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR B1108 " --> pdb=" O ASN B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1166 removed outlier: 3.606A pdb=" N PHE B1132 " --> pdb=" O ASN B1128 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN B1166 " --> pdb=" O ALA B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1187 Processing helix chain 'B' and resid 1188 through 1218 removed outlier: 3.932A pdb=" N SER B1201 " --> pdb=" O LEU B1197 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA B1209 " --> pdb=" O ASN B1205 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B1210 " --> pdb=" O SER B1206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1211 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B1216 " --> pdb=" O ARG B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1290 removed outlier: 3.724A pdb=" N ALA B1288 " --> pdb=" O SER B1284 " (cutoff:3.500A) Processing helix chain 'B' and resid 1333 through 1338 removed outlier: 3.526A pdb=" N LEU B1337 " --> pdb=" O VAL B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1344 through 1355 Processing helix chain 'B' and resid 1357 through 1363 removed outlier: 3.761A pdb=" N ARG B1363 " --> pdb=" O ASP B1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 1373 through 1377 Processing helix chain 'B' and resid 1380 through 1396 removed outlier: 3.859A pdb=" N ARG B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B1385 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B1386 " --> pdb=" O GLY B1382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B1391 " --> pdb=" O LEU B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1425 removed outlier: 3.539A pdb=" N ALA B1415 " --> pdb=" O VAL B1411 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1416 " --> pdb=" O ARG B1412 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B1420 " --> pdb=" O LEU B1416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B1425 " --> pdb=" O ILE B1421 " (cutoff:3.500A) Processing helix chain 'B' and resid 1436 through 1440 removed outlier: 3.627A pdb=" N THR B1439 " --> pdb=" O ARG B1436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.680A pdb=" N ASP A 198 " --> pdb=" O CYS A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 632 through 639 removed outlier: 5.374A pdb=" N GLY A 619 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN A 636 " --> pdb=" O ARG A 617 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG A 617 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP A 638 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER A 615 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 615 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 648 removed outlier: 6.251A pdb=" N ALA A 646 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 811 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 648 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 820 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS A 812 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL A 816 " --> pdb=" O HIS A 812 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 683 removed outlier: 3.812A pdb=" N VAL A 683 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP A 764 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 761 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL A 795 " --> pdb=" O TYR A 761 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 763 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1242 through 1248 removed outlier: 4.750A pdb=" N VAL A1247 " --> pdb=" O LYS A1297 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS A1297 " --> pdb=" O VAL A1247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1399 through 1401 removed outlier: 6.922A pdb=" N VAL A1272 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A1273 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A1449 " --> pdb=" O GLY A1273 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A1275 " --> pdb=" O LEU A1449 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A1456 " --> pdb=" O VAL A1448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1331 through 1332 removed outlier: 4.250A pdb=" N GLY A1331 " --> pdb=" O VAL A1372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A1372 " --> pdb=" O GLY A1331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 632 through 639 removed outlier: 5.367A pdb=" N GLY B 619 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN B 636 " --> pdb=" O ARG B 617 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B 617 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP B 638 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER B 615 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 615 " --> pdb=" O THR B 675 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 645 through 648 removed outlier: 6.252A pdb=" N ALA B 646 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 811 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 648 " --> pdb=" O VAL B 811 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 820 " --> pdb=" O ILE B 808 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS B 812 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 816 " --> pdb=" O HIS B 812 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.314A pdb=" N TYR B 761 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL B 795 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE B 763 " --> pdb=" O VAL B 795 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1243 through 1248 removed outlier: 3.505A pdb=" N ARG B1299 " --> pdb=" O GLU B1245 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL B1247 " --> pdb=" O LYS B1297 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LYS B1297 " --> pdb=" O VAL B1247 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B1302 " --> pdb=" O CYS B1305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1399 through 1403 removed outlier: 6.426A pdb=" N GLY B1273 " --> pdb=" O LEU B1447 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B1449 " --> pdb=" O GLY B1273 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B1275 " --> pdb=" O LEU B1449 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B1458 " --> pdb=" O ILE B1446 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B1456 " --> pdb=" O VAL B1448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1331 through 1332 removed outlier: 4.142A pdb=" N GLY B1331 " --> pdb=" O VAL B1372 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B1372 " --> pdb=" O GLY B1331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 1348 hydrogen bonds defined for protein. 3972 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: 4.30 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3482 1.30 - 1.43: 6007 1.43 - 1.57: 12991 1.57 - 1.70: 0 1.70 - 1.83: 180 Bond restraints: 22660 Sorted by residual: bond pdb=" C THR A1190 " pdb=" O THR A1190 " ideal model delta sigma weight residual 1.236 1.316 -0.080 1.15e-02 7.56e+03 4.81e+01 bond pdb=" C THR B1190 " pdb=" O THR B1190 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.15e-02 7.56e+03 4.35e+01 bond pdb=" C LEU B1193 " pdb=" O LEU B1193 " ideal model delta sigma weight residual 1.236 1.311 -0.075 1.16e-02 7.43e+03 4.16e+01 bond pdb=" C ASP A 489 " pdb=" O ASP A 489 " ideal model delta sigma weight residual 1.237 1.308 -0.071 1.16e-02 7.43e+03 3.79e+01 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.235 1.308 -0.073 1.23e-02 6.61e+03 3.52e+01 ... (remaining 22655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 30486 3.24 - 6.49: 292 6.49 - 9.73: 37 9.73 - 12.98: 8 12.98 - 16.22: 3 Bond angle restraints: 30826 Sorted by residual: angle pdb=" CA PRO A1221 " pdb=" C PRO A1221 " pdb=" O PRO A1221 " ideal model delta sigma weight residual 122.08 110.18 11.90 1.28e+00 6.10e-01 8.64e+01 angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 111.03 100.73 10.30 1.11e+00 8.12e-01 8.61e+01 angle pdb=" N MET A 488 " pdb=" CA MET A 488 " pdb=" C MET A 488 " ideal model delta sigma weight residual 112.89 102.16 10.73 1.24e+00 6.50e-01 7.49e+01 angle pdb=" N ASP A 489 " pdb=" CA ASP A 489 " pdb=" C ASP A 489 " ideal model delta sigma weight residual 111.14 103.37 7.77 1.08e+00 8.57e-01 5.17e+01 angle pdb=" C VAL A 180 " pdb=" N GLY A 181 " pdb=" CA GLY A 181 " ideal model delta sigma weight residual 119.98 127.08 -7.10 1.11e+00 8.12e-01 4.09e+01 ... (remaining 30821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11764 17.90 - 35.80: 1550 35.80 - 53.69: 502 53.69 - 71.59: 101 71.59 - 89.49: 35 Dihedral angle restraints: 13952 sinusoidal: 5968 harmonic: 7984 Sorted by residual: dihedral pdb=" CD ARG B1002 " pdb=" NE ARG B1002 " pdb=" CZ ARG B1002 " pdb=" NH1 ARG B1002 " ideal model delta sinusoidal sigma weight residual 0.00 84.09 -84.09 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CD ARG A 91 " pdb=" NE ARG A 91 " pdb=" CZ ARG A 91 " pdb=" NH1 ARG A 91 " ideal model delta sinusoidal sigma weight residual 0.00 -62.64 62.64 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CD ARG A1354 " pdb=" NE ARG A1354 " pdb=" CZ ARG A1354 " pdb=" NH1 ARG A1354 " ideal model delta sinusoidal sigma weight residual 0.00 51.43 -51.43 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 13949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3137 0.071 - 0.141: 376 0.141 - 0.212: 41 0.212 - 0.283: 8 0.283 - 0.354: 2 Chirality restraints: 3564 Sorted by residual: chirality pdb=" CB VAL A 491 " pdb=" CA VAL A 491 " pdb=" CG1 VAL A 491 " pdb=" CG2 VAL A 491 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB VAL B 38 " pdb=" CA VAL B 38 " pdb=" CG1 VAL B 38 " pdb=" CG2 VAL B 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA VAL A1196 " pdb=" N VAL A1196 " pdb=" C VAL A1196 " pdb=" CB VAL A1196 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3561 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1002 " -1.105 9.50e-02 1.11e+02 4.95e-01 1.48e+02 pdb=" NE ARG B1002 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B1002 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B1002 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B1002 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 91 " -0.995 9.50e-02 1.11e+02 4.46e-01 1.20e+02 pdb=" NE ARG A 91 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 91 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 91 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1354 " 0.858 9.50e-02 1.11e+02 3.85e-01 8.99e+01 pdb=" NE ARG A1354 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG A1354 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1354 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1354 " 0.024 2.00e-02 2.50e+03 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1162 2.72 - 3.27: 23502 3.27 - 3.81: 36727 3.81 - 4.36: 41979 4.36 - 4.90: 69806 Nonbonded interactions: 173176 Sorted by model distance: nonbonded pdb=" O ASN A 691 " pdb=" ND2 ASN A 691 " model vdw 2.180 3.120 nonbonded pdb=" OH TYR B 73 " pdb=" O MET B 192 " model vdw 2.204 3.040 nonbonded pdb=" O LEU B 129 " pdb=" OG1 THR B 132 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A1056 " pdb=" OG SER A1059 " model vdw 2.213 3.040 nonbonded pdb=" N ASP B1314 " pdb=" OD1 ASP B1314 " model vdw 2.216 3.120 ... (remaining 173171 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' and (resid 4 through 1467 or resid 1503 through 1505)) selection = (chain 'B' and (resid 4 through 1467 or resid 1503 through 1505)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.610 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22662 Z= 0.314 Angle : 0.823 16.220 30830 Z= 0.483 Chirality : 0.048 0.354 3564 Planarity : 0.013 0.495 3820 Dihedral : 18.118 89.490 8802 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.32 % Allowed : 29.88 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2746 helix: 0.94 (0.13), residues: 1724 sheet: 0.87 (0.49), residues: 116 loop : -0.95 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1396 TYR 0.031 0.002 TYR B 73 PHE 0.025 0.001 PHE A 191 TRP 0.023 0.001 TRP B1349 HIS 0.002 0.001 HIS B 998 Details of bonding type rmsd covalent geometry : bond 0.00461 (22660) covalent geometry : angle 0.82339 (30826) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.43861 ( 4) hydrogen bonds : bond 0.17302 ( 1348) hydrogen bonds : angle 6.37291 ( 3972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 272 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 55 TRP cc_start: 0.7130 (m-10) cc_final: 0.6567 (m100) REVERT: A 56 LEU cc_start: 0.7513 (tt) cc_final: 0.6992 (mt) REVERT: A 80 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 142 TYR cc_start: 0.7521 (m-80) cc_final: 0.7253 (m-80) REVERT: A 257 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8364 (tptt) REVERT: A 259 VAL cc_start: 0.6621 (m) cc_final: 0.6411 (p) REVERT: A 357 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: A 1008 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: A 1022 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6497 (tmmm) REVERT: A 1396 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7925 (mpp80) REVERT: B 94 MET cc_start: 0.7437 (tmm) cc_final: 0.6989 (ptm) REVERT: B 102 ASP cc_start: 0.4343 (OUTLIER) cc_final: 0.3365 (p0) REVERT: B 127 MET cc_start: 0.7190 (ppp) cc_final: 0.6883 (ppp) REVERT: B 141 TRP cc_start: 0.7077 (m-10) cc_final: 0.6404 (m-10) REVERT: B 142 TYR cc_start: 0.6262 (m-80) cc_final: 0.5851 (m-80) REVERT: B 162 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8709 (mm) REVERT: B 169 SER cc_start: 0.7099 (OUTLIER) cc_final: 0.6779 (p) REVERT: B 192 MET cc_start: 0.7750 (mpp) cc_final: 0.7511 (mpp) REVERT: B 494 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5109 (m-10) REVERT: B 700 PHE cc_start: 0.5668 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: B 750 MET cc_start: 0.7596 (ptp) cc_final: 0.6591 (tpt) REVERT: B 1088 ASP cc_start: 0.7713 (m-30) cc_final: 0.7458 (m-30) REVERT: B 1148 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 1371 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: B 1431 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7863 (mt) outliers start: 127 outliers final: 77 residues processed: 364 average time/residue: 0.1357 time to fit residues: 80.5286 Evaluate side-chains 335 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 246 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1349 TRP Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1015 ARG Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1258 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1342 GLU Chi-restraints excluded: chain B residue 1371 GLU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1388 SER Chi-restraints excluded: chain B residue 1431 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 411 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1128 ASN B1230 ASN B1287 ASN B1336 ASN B1356 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.173964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121597 restraints weight = 48689.778| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.68 r_work: 0.3473 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22662 Z= 0.142 Angle : 0.655 13.522 30830 Z= 0.323 Chirality : 0.042 0.295 3564 Planarity : 0.005 0.131 3820 Dihedral : 9.820 59.890 3844 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.53 % Allowed : 26.78 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2746 helix: 1.22 (0.12), residues: 1790 sheet: 0.42 (0.44), residues: 138 loop : -0.85 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1002 TYR 0.029 0.001 TYR A 75 PHE 0.022 0.001 PHE A 90 TRP 0.018 0.001 TRP B1349 HIS 0.004 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00277 (22660) covalent geometry : angle 0.65505 (30826) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.35293 ( 4) hydrogen bonds : bond 0.06018 ( 1348) hydrogen bonds : angle 4.87094 ( 3972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 265 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7273 (mm) REVERT: A 55 TRP cc_start: 0.7190 (m-10) cc_final: 0.6818 (m100) REVERT: A 142 TYR cc_start: 0.7378 (m-80) cc_final: 0.6789 (m-80) REVERT: A 257 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8352 (tptt) REVERT: A 488 MET cc_start: 0.5217 (mmm) cc_final: 0.4996 (mmm) REVERT: A 584 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.6962 (p0) REVERT: A 733 ILE cc_start: 0.4431 (OUTLIER) cc_final: 0.4226 (mp) REVERT: A 750 MET cc_start: 0.6915 (ptt) cc_final: 0.5843 (ttp) REVERT: A 761 TYR cc_start: 0.3666 (t80) cc_final: 0.2624 (t80) REVERT: A 813 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5949 (tm-30) REVERT: A 919 TRP cc_start: 0.5346 (OUTLIER) cc_final: 0.4677 (m-90) REVERT: A 1008 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: A 1022 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6525 (tmmm) REVERT: A 1396 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8220 (mpp80) REVERT: B 121 TRP cc_start: 0.7674 (m100) cc_final: 0.7403 (m100) REVERT: B 127 MET cc_start: 0.7190 (ppp) cc_final: 0.6941 (ppp) REVERT: B 141 TRP cc_start: 0.7058 (m-10) cc_final: 0.6386 (m-10) REVERT: B 142 TYR cc_start: 0.6326 (m-80) cc_final: 0.5917 (m-80) REVERT: B 162 LEU cc_start: 0.8870 (mm) cc_final: 0.8630 (mm) REVERT: B 186 PHE cc_start: 0.8421 (t80) cc_final: 0.8162 (t80) REVERT: B 191 PHE cc_start: 0.8226 (t80) cc_final: 0.7898 (t80) REVERT: B 194 LEU cc_start: 0.3770 (OUTLIER) cc_final: 0.3548 (tp) REVERT: B 494 TYR cc_start: 0.5861 (OUTLIER) cc_final: 0.5321 (m-10) REVERT: B 750 MET cc_start: 0.7607 (ptp) cc_final: 0.6834 (tpt) REVERT: B 762 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6425 (tp) REVERT: B 813 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6041 (tm-30) REVERT: B 1070 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (t80) REVERT: B 1088 ASP cc_start: 0.7754 (m-30) cc_final: 0.7442 (m-30) REVERT: B 1110 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7014 (tpm170) REVERT: B 1118 MET cc_start: 0.8495 (tpp) cc_final: 0.8041 (pmm) REVERT: B 1216 TYR cc_start: 0.6899 (m-80) cc_final: 0.6685 (m-80) REVERT: B 1242 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7990 (tp) outliers start: 132 outliers final: 75 residues processed: 379 average time/residue: 0.1347 time to fit residues: 83.8081 Evaluate side-chains 322 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 234 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 934 PHE Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1349 TRP Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1242 ILE Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1307 VAL Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1372 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 228 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 195 optimal weight: 30.0000 chunk 264 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.172255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119790 restraints weight = 49216.075| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.74 r_work: 0.3424 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22662 Z= 0.154 Angle : 0.649 14.005 30830 Z= 0.317 Chirality : 0.042 0.201 3564 Planarity : 0.004 0.041 3820 Dihedral : 9.038 59.573 3768 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.66 % Allowed : 26.45 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 2746 helix: 1.32 (0.12), residues: 1784 sheet: 0.46 (0.45), residues: 138 loop : -0.89 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1396 TYR 0.022 0.001 TYR A 75 PHE 0.022 0.001 PHE A 90 TRP 0.017 0.001 TRP B1349 HIS 0.003 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00335 (22660) covalent geometry : angle 0.64895 (30826) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.35699 ( 4) hydrogen bonds : bond 0.05741 ( 1348) hydrogen bonds : angle 4.77091 ( 3972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 248 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 142 TYR cc_start: 0.7449 (m-80) cc_final: 0.6804 (m-80) REVERT: A 257 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8386 (tptt) REVERT: A 357 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: A 462 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7238 (tmtt) REVERT: A 584 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7463 (p0) REVERT: A 761 TYR cc_start: 0.3818 (t80) cc_final: 0.3015 (t80) REVERT: A 767 LEU cc_start: -0.3917 (OUTLIER) cc_final: -0.4127 (mm) REVERT: A 813 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5942 (tm-30) REVERT: A 919 TRP cc_start: 0.5558 (OUTLIER) cc_final: 0.4812 (m-90) REVERT: A 1008 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5400 (m-80) REVERT: A 1022 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6563 (tmmm) REVERT: B 127 MET cc_start: 0.7314 (ppp) cc_final: 0.7048 (ppp) REVERT: B 141 TRP cc_start: 0.7112 (m-10) cc_final: 0.6424 (m-10) REVERT: B 142 TYR cc_start: 0.6421 (m-80) cc_final: 0.5729 (m-80) REVERT: B 162 LEU cc_start: 0.8892 (mm) cc_final: 0.8690 (mm) REVERT: B 186 PHE cc_start: 0.8391 (t80) cc_final: 0.8185 (t80) REVERT: B 494 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.5197 (m-10) REVERT: B 750 MET cc_start: 0.7663 (ptp) cc_final: 0.6793 (tpt) REVERT: B 762 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6478 (tp) REVERT: B 813 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6092 (tm-30) REVERT: B 1070 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8459 (t80) REVERT: B 1118 MET cc_start: 0.8365 (tpp) cc_final: 0.8110 (pmm) REVERT: B 1216 TYR cc_start: 0.6958 (m-80) cc_final: 0.6724 (m-80) outliers start: 135 outliers final: 84 residues processed: 360 average time/residue: 0.1270 time to fit residues: 75.8274 Evaluate side-chains 333 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 236 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1349 TRP Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1070 PHE Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1108 THR Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 10 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1336 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.171682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119892 restraints weight = 49050.159| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.67 r_work: 0.3417 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22662 Z= 0.156 Angle : 0.646 15.818 30830 Z= 0.316 Chirality : 0.042 0.218 3564 Planarity : 0.004 0.040 3820 Dihedral : 8.863 59.686 3762 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 6.16 % Allowed : 26.66 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2746 helix: 1.30 (0.12), residues: 1786 sheet: 0.48 (0.45), residues: 138 loop : -0.90 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1396 TYR 0.053 0.002 TYR A 75 PHE 0.035 0.001 PHE B 700 TRP 0.021 0.001 TRP B1349 HIS 0.003 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00343 (22660) covalent geometry : angle 0.64637 (30826) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.37691 ( 4) hydrogen bonds : bond 0.05601 ( 1348) hydrogen bonds : angle 4.70900 ( 3972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 245 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 142 TYR cc_start: 0.7344 (m-80) cc_final: 0.6897 (m-80) REVERT: A 186 PHE cc_start: 0.8254 (t80) cc_final: 0.7990 (t80) REVERT: A 257 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8446 (tptt) REVERT: A 357 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: A 462 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7187 (tmtt) REVERT: A 584 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7435 (p0) REVERT: A 733 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3992 (mp) REVERT: A 750 MET cc_start: 0.6966 (ptt) cc_final: 0.6716 (ppp) REVERT: A 761 TYR cc_start: 0.4025 (t80) cc_final: 0.3116 (t80) REVERT: A 767 LEU cc_start: -0.3904 (OUTLIER) cc_final: -0.4125 (mm) REVERT: A 813 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: A 919 TRP cc_start: 0.5626 (OUTLIER) cc_final: 0.4915 (m-90) REVERT: A 1008 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5303 (m-80) REVERT: A 1022 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6673 (tmmm) REVERT: A 1157 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 127 MET cc_start: 0.7331 (ppp) cc_final: 0.7068 (ppp) REVERT: B 141 TRP cc_start: 0.7135 (m-10) cc_final: 0.6425 (m-10) REVERT: B 142 TYR cc_start: 0.6517 (m-80) cc_final: 0.5840 (m-80) REVERT: B 162 LEU cc_start: 0.8869 (mm) cc_final: 0.8624 (mm) REVERT: B 186 PHE cc_start: 0.8301 (t80) cc_final: 0.8022 (t80) REVERT: B 188 ILE cc_start: 0.8527 (pt) cc_final: 0.8048 (pp) REVERT: B 494 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.5083 (m-10) REVERT: B 750 MET cc_start: 0.7775 (ptp) cc_final: 0.6804 (tpt) REVERT: B 813 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: B 1110 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7502 (mtp180) REVERT: B 1118 MET cc_start: 0.8348 (tpp) cc_final: 0.8140 (pmm) REVERT: B 1154 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (ttp) REVERT: B 1431 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (mt) outliers start: 147 outliers final: 89 residues processed: 367 average time/residue: 0.1256 time to fit residues: 76.9634 Evaluate side-chains 331 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 227 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1015 ARG Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1154 MET Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1315 LEU Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 211 optimal weight: 0.0040 chunk 70 optimal weight: 30.0000 chunk 188 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** B 697 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 = 0.4478 r_free = 0.4478 target = 0.172616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121411 restraints weight = 48747.954| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.80 r_work: 0.3430 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22662 Z= 0.131 Angle : 0.631 15.166 30830 Z= 0.305 Chirality : 0.041 0.203 3564 Planarity : 0.004 0.041 3820 Dihedral : 8.494 59.935 3753 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.57 % Allowed : 27.24 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 2746 helix: 1.43 (0.12), residues: 1788 sheet: 0.50 (0.45), residues: 138 loop : -0.90 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.039 0.001 TYR A 75 PHE 0.023 0.001 PHE B 700 TRP 0.013 0.001 TRP B1349 HIS 0.002 0.000 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00272 (22660) covalent geometry : angle 0.63064 (30826) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.34239 ( 4) hydrogen bonds : bond 0.05258 ( 1348) hydrogen bonds : angle 4.60201 ( 3972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 249 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7273 (mm) REVERT: A 56 LEU cc_start: 0.7495 (tt) cc_final: 0.6867 (mt) REVERT: A 142 TYR cc_start: 0.7320 (m-80) cc_final: 0.6898 (m-80) REVERT: A 186 PHE cc_start: 0.8234 (t80) cc_final: 0.7964 (t80) REVERT: A 192 MET cc_start: 0.7337 (mpp) cc_final: 0.7102 (mpp) REVERT: A 257 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8463 (tptt) REVERT: A 357 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 462 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7136 (tmtt) REVERT: A 733 ILE cc_start: 0.4213 (OUTLIER) cc_final: 0.3990 (mp) REVERT: A 750 MET cc_start: 0.6967 (ptt) cc_final: 0.5892 (ttp) REVERT: A 761 TYR cc_start: 0.4023 (t80) cc_final: 0.2811 (t80) REVERT: A 813 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6140 (tm-30) REVERT: A 919 TRP cc_start: 0.5598 (OUTLIER) cc_final: 0.4906 (m-90) REVERT: A 1008 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: A 1022 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6639 (tmmm) REVERT: A 1343 HIS cc_start: 0.7173 (m-70) cc_final: 0.6897 (m170) REVERT: A 1394 LEU cc_start: 0.8937 (tp) cc_final: 0.8611 (tp) REVERT: B 94 MET cc_start: 0.7202 (tmm) cc_final: 0.6730 (ptm) REVERT: B 127 MET cc_start: 0.7275 (ppp) cc_final: 0.7014 (ppp) REVERT: B 141 TRP cc_start: 0.7056 (m-10) cc_final: 0.6367 (m-10) REVERT: B 142 TYR cc_start: 0.6480 (m-80) cc_final: 0.5826 (m-80) REVERT: B 162 LEU cc_start: 0.8858 (mm) cc_final: 0.8589 (mm) REVERT: B 494 TYR cc_start: 0.5504 (OUTLIER) cc_final: 0.5068 (m-10) REVERT: B 750 MET cc_start: 0.7754 (ptp) cc_final: 0.6850 (tpt) REVERT: B 761 TYR cc_start: 0.4101 (t80) cc_final: 0.3026 (t80) REVERT: B 813 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: B 1088 ASP cc_start: 0.7857 (m-30) cc_final: 0.7578 (m-30) REVERT: B 1110 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7460 (mtp180) REVERT: B 1118 MET cc_start: 0.8413 (tpp) cc_final: 0.8164 (pmm) outliers start: 133 outliers final: 88 residues processed: 359 average time/residue: 0.1232 time to fit residues: 73.5101 Evaluate side-chains 335 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 237 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 836 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1015 ARG Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1227 ILE Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 24 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 273 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** B 697 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 = 0.4455 r_free = 0.4455 target = 0.170721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118418 restraints weight = 49912.263| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.95 r_work: 0.3387 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22662 Z= 0.163 Angle : 0.653 15.845 30830 Z= 0.318 Chirality : 0.043 0.201 3564 Planarity : 0.004 0.040 3820 Dihedral : 8.455 59.841 3748 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.83 % Allowed : 27.24 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 2746 helix: 1.33 (0.12), residues: 1790 sheet: 0.52 (0.46), residues: 138 loop : -0.93 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1019 TYR 0.035 0.002 TYR A 75 PHE 0.020 0.002 PHE B 700 TRP 0.017 0.001 TRP B1349 HIS 0.003 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00368 (22660) covalent geometry : angle 0.65352 (30826) SS BOND : bond 0.00049 ( 2) SS BOND : angle 0.38632 ( 4) hydrogen bonds : bond 0.05556 ( 1348) hydrogen bonds : angle 4.65475 ( 3972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 244 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7254 (mm) REVERT: A 127 MET cc_start: 0.7918 (tmm) cc_final: 0.7689 (ppp) REVERT: A 142 TYR cc_start: 0.7331 (m-80) cc_final: 0.6880 (m-80) REVERT: A 186 PHE cc_start: 0.8237 (t80) cc_final: 0.7990 (t80) REVERT: A 257 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8573 (tptt) REVERT: A 357 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 462 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7155 (tmtt) REVERT: A 584 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7289 (p0) REVERT: A 750 MET cc_start: 0.6972 (ptt) cc_final: 0.6732 (ptt) REVERT: A 761 TYR cc_start: 0.3985 (t80) cc_final: 0.2917 (t80) REVERT: A 767 LEU cc_start: -0.3988 (OUTLIER) cc_final: -0.4198 (mm) REVERT: A 813 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.6068 (tm-30) REVERT: A 919 TRP cc_start: 0.5699 (OUTLIER) cc_final: 0.4895 (m-90) REVERT: A 1008 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5652 (m-80) REVERT: A 1022 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6697 (tmmm) REVERT: A 1157 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 127 MET cc_start: 0.7383 (ppp) cc_final: 0.7126 (ppp) REVERT: B 141 TRP cc_start: 0.7156 (m-10) cc_final: 0.6451 (m-10) REVERT: B 142 TYR cc_start: 0.6589 (m-80) cc_final: 0.5953 (m-80) REVERT: B 162 LEU cc_start: 0.8852 (mm) cc_final: 0.8604 (mm) REVERT: B 186 PHE cc_start: 0.8327 (t80) cc_final: 0.8115 (t80) REVERT: B 494 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.5104 (m-10) REVERT: B 750 MET cc_start: 0.7778 (ptp) cc_final: 0.6827 (tpt) REVERT: B 761 TYR cc_start: 0.4361 (t80) cc_final: 0.3450 (t80) REVERT: B 813 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6040 (tm-30) REVERT: B 1110 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7399 (mtp180) REVERT: B 1154 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8543 (ttp) outliers start: 139 outliers final: 94 residues processed: 352 average time/residue: 0.1296 time to fit residues: 74.7920 Evaluate side-chains 346 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 239 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1154 MET Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1390 SER Chi-restraints excluded: chain B residue 1430 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 106 optimal weight: 0.8980 chunk 223 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** B 697 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 = 0.4470 r_free = 0.4470 target = 0.172076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.118090 restraints weight = 49447.950| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.85 r_work: 0.3434 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22662 Z= 0.129 Angle : 0.632 16.441 30830 Z= 0.306 Chirality : 0.042 0.234 3564 Planarity : 0.004 0.045 3820 Dihedral : 8.085 59.200 3738 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.90 % Allowed : 27.91 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2746 helix: 1.47 (0.12), residues: 1786 sheet: 0.54 (0.45), residues: 138 loop : -0.91 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1117 TYR 0.030 0.001 TYR A 75 PHE 0.021 0.001 PHE A1264 TRP 0.018 0.001 TRP B1349 HIS 0.002 0.000 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00264 (22660) covalent geometry : angle 0.63204 (30826) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.35471 ( 4) hydrogen bonds : bond 0.05147 ( 1348) hydrogen bonds : angle 4.52783 ( 3972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 243 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7271 (mm) REVERT: A 56 LEU cc_start: 0.7520 (tt) cc_final: 0.6900 (mt) REVERT: A 127 MET cc_start: 0.7889 (tmm) cc_final: 0.7662 (ppp) REVERT: A 142 TYR cc_start: 0.7320 (m-80) cc_final: 0.6881 (m-80) REVERT: A 186 PHE cc_start: 0.8243 (t80) cc_final: 0.7952 (t80) REVERT: A 257 LYS cc_start: 0.8813 (mmtp) cc_final: 0.8569 (tptt) REVERT: A 357 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: A 462 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7152 (tmtt) REVERT: A 584 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7406 (p0) REVERT: A 733 ILE cc_start: 0.4204 (OUTLIER) cc_final: 0.3880 (mp) REVERT: A 750 MET cc_start: 0.6954 (ptt) cc_final: 0.6713 (ptt) REVERT: A 761 TYR cc_start: 0.4030 (t80) cc_final: 0.2954 (t80) REVERT: A 767 LEU cc_start: -0.3954 (OUTLIER) cc_final: -0.4203 (mm) REVERT: A 813 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6183 (tm-30) REVERT: A 919 TRP cc_start: 0.5607 (OUTLIER) cc_final: 0.4924 (m-90) REVERT: A 1008 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: A 1022 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6641 (tmmm) REVERT: A 1157 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 1377 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: B 94 MET cc_start: 0.7102 (tmm) cc_final: 0.6668 (ptm) REVERT: B 141 TRP cc_start: 0.7144 (m-10) cc_final: 0.6456 (m-10) REVERT: B 142 TYR cc_start: 0.6584 (m-80) cc_final: 0.5923 (m-80) REVERT: B 162 LEU cc_start: 0.8828 (mm) cc_final: 0.8576 (mm) REVERT: B 494 TYR cc_start: 0.5443 (OUTLIER) cc_final: 0.5121 (m-10) REVERT: B 750 MET cc_start: 0.7750 (ptp) cc_final: 0.6825 (tpt) REVERT: B 761 TYR cc_start: 0.4434 (t80) cc_final: 0.3602 (t80) REVERT: B 813 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.6039 (tm-30) REVERT: B 1051 LEU cc_start: 0.8592 (tt) cc_final: 0.8341 (tt) REVERT: B 1110 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7312 (mtp180) outliers start: 117 outliers final: 84 residues processed: 337 average time/residue: 0.1270 time to fit residues: 71.3458 Evaluate side-chains 332 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 234 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1377 GLU Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1390 SER Chi-restraints excluded: chain B residue 1430 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 182 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 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 = 0.4468 r_free = 0.4468 target = 0.171735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120493 restraints weight = 49576.862| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.84 r_work: 0.3412 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22662 Z= 0.140 Angle : 0.655 16.809 30830 Z= 0.314 Chirality : 0.042 0.201 3564 Planarity : 0.004 0.047 3820 Dihedral : 8.077 59.465 3738 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.03 % Allowed : 27.95 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2746 helix: 1.46 (0.12), residues: 1790 sheet: 0.47 (0.45), residues: 138 loop : -0.95 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 910 TYR 0.030 0.001 TYR A 75 PHE 0.019 0.001 PHE B 186 TRP 0.018 0.001 TRP B1349 HIS 0.002 0.001 HIS B1435 Details of bonding type rmsd covalent geometry : bond 0.00304 (22660) covalent geometry : angle 0.65483 (30826) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.37697 ( 4) hydrogen bonds : bond 0.05182 ( 1348) hydrogen bonds : angle 4.53702 ( 3972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 243 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7281 (mm) REVERT: A 56 LEU cc_start: 0.7489 (tt) cc_final: 0.6891 (mt) REVERT: A 142 TYR cc_start: 0.7330 (m-80) cc_final: 0.6890 (m-80) REVERT: A 186 PHE cc_start: 0.8223 (t80) cc_final: 0.7881 (t80) REVERT: A 257 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8591 (tptt) REVERT: A 357 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: A 462 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7169 (tmtt) REVERT: A 584 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7192 (p0) REVERT: A 733 ILE cc_start: 0.4253 (OUTLIER) cc_final: 0.3954 (mp) REVERT: A 761 TYR cc_start: 0.3980 (t80) cc_final: 0.2927 (t80) REVERT: A 767 LEU cc_start: -0.3953 (OUTLIER) cc_final: -0.4190 (mm) REVERT: A 813 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6187 (tm-30) REVERT: A 919 TRP cc_start: 0.5689 (OUTLIER) cc_final: 0.4947 (m-90) REVERT: A 1008 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5667 (m-80) REVERT: A 1022 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6672 (tmmm) REVERT: A 1157 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 1377 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: B 94 MET cc_start: 0.7127 (tmm) cc_final: 0.6676 (ptm) REVERT: B 127 MET cc_start: 0.7405 (ppp) cc_final: 0.7156 (ppp) REVERT: B 141 TRP cc_start: 0.7271 (m-10) cc_final: 0.6566 (m-10) REVERT: B 142 TYR cc_start: 0.6628 (m-80) cc_final: 0.5973 (m-80) REVERT: B 162 LEU cc_start: 0.8843 (mm) cc_final: 0.8599 (mm) REVERT: B 186 PHE cc_start: 0.8310 (t80) cc_final: 0.8094 (t80) REVERT: B 494 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.5122 (m-10) REVERT: B 750 MET cc_start: 0.7760 (ptp) cc_final: 0.6819 (tpt) REVERT: B 761 TYR cc_start: 0.4508 (t80) cc_final: 0.3785 (t80) REVERT: B 813 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: B 1110 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7338 (mtp180) REVERT: B 1230 ASN cc_start: 0.7376 (m110) cc_final: 0.7017 (m110) outliers start: 120 outliers final: 90 residues processed: 338 average time/residue: 0.1233 time to fit residues: 70.0986 Evaluate side-chains 337 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 233 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1266 ILE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 ASP Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1377 GLU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1390 SER Chi-restraints excluded: chain B residue 1430 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 83 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 184 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 212 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116178 restraints weight = 49571.371| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.90 r_work: 0.3387 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22662 Z= 0.175 Angle : 0.686 16.690 30830 Z= 0.332 Chirality : 0.044 0.513 3564 Planarity : 0.004 0.047 3820 Dihedral : 8.205 59.878 3738 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.90 % Allowed : 28.16 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2746 helix: 1.31 (0.12), residues: 1790 sheet: 0.38 (0.45), residues: 138 loop : -0.98 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.029 0.002 TYR A 75 PHE 0.046 0.002 PHE B 109 TRP 0.017 0.001 TRP B1349 HIS 0.003 0.001 HIS A1343 Details of bonding type rmsd covalent geometry : bond 0.00397 (22660) covalent geometry : angle 0.68625 (30826) SS BOND : bond 0.00096 ( 2) SS BOND : angle 1.04952 ( 4) hydrogen bonds : bond 0.05539 ( 1348) hydrogen bonds : angle 4.67820 ( 3972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 237 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7261 (mm) REVERT: A 127 MET cc_start: 0.7881 (tmm) cc_final: 0.7656 (ppp) REVERT: A 142 TYR cc_start: 0.7367 (m-80) cc_final: 0.6910 (m-80) REVERT: A 186 PHE cc_start: 0.8241 (t80) cc_final: 0.7935 (t80) REVERT: A 357 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: A 462 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7177 (tmtt) REVERT: A 584 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 750 MET cc_start: 0.6989 (ptt) cc_final: 0.5823 (ttp) REVERT: A 761 TYR cc_start: 0.3942 (t80) cc_final: 0.2456 (t80) REVERT: A 767 LEU cc_start: -0.3994 (OUTLIER) cc_final: -0.4224 (mm) REVERT: A 813 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6287 (tm-30) REVERT: A 919 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.4928 (m-90) REVERT: A 1008 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5642 (m-80) REVERT: A 1022 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6708 (tmmm) REVERT: A 1157 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 1431 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8284 (mm) REVERT: B 94 MET cc_start: 0.7154 (tmm) cc_final: 0.6716 (ptm) REVERT: B 127 MET cc_start: 0.7476 (ppp) cc_final: 0.7104 (ppp) REVERT: B 137 ARG cc_start: 0.4559 (OUTLIER) cc_final: 0.2482 (tpt90) REVERT: B 141 TRP cc_start: 0.7315 (m-10) cc_final: 0.6644 (m-10) REVERT: B 142 TYR cc_start: 0.6760 (m-80) cc_final: 0.6156 (m-80) REVERT: B 162 LEU cc_start: 0.8837 (mm) cc_final: 0.8614 (mm) REVERT: B 494 TYR cc_start: 0.5451 (OUTLIER) cc_final: 0.5116 (m-10) REVERT: B 750 MET cc_start: 0.7784 (ptp) cc_final: 0.6790 (tpt) REVERT: B 761 TYR cc_start: 0.4351 (OUTLIER) cc_final: 0.3796 (t80) REVERT: B 813 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5999 (tm-30) REVERT: B 1009 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7297 (m170) REVERT: B 1110 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7289 (mtp180) REVERT: B 1230 ASN cc_start: 0.7497 (m110) cc_final: 0.7073 (m110) REVERT: B 1369 ASP cc_start: 0.6849 (t0) cc_final: 0.6445 (t0) outliers start: 117 outliers final: 92 residues processed: 329 average time/residue: 0.1249 time to fit residues: 68.7115 Evaluate side-chains 341 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 233 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 482 ASN Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1390 SER Chi-restraints excluded: chain B residue 1430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 158 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 189 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 ASN ** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 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 = 0.4477 r_free = 0.4477 target = 0.172400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.121141 restraints weight = 49514.472| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.86 r_work: 0.3432 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22662 Z= 0.130 Angle : 0.665 16.980 30830 Z= 0.318 Chirality : 0.043 0.449 3564 Planarity : 0.004 0.047 3820 Dihedral : 8.006 59.476 3738 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.48 % Allowed : 28.37 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2746 helix: 1.46 (0.12), residues: 1792 sheet: 0.48 (0.45), residues: 136 loop : -0.97 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1117 TYR 0.027 0.001 TYR A 75 PHE 0.057 0.001 PHE B 186 TRP 0.019 0.001 TRP B1349 HIS 0.002 0.000 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00264 (22660) covalent geometry : angle 0.66451 (30826) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.09175 ( 4) hydrogen bonds : bond 0.05073 ( 1348) hydrogen bonds : angle 4.50881 ( 3972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 236 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7235 (mm) REVERT: A 56 LEU cc_start: 0.7490 (tt) cc_final: 0.6864 (mt) REVERT: A 127 MET cc_start: 0.7856 (tmm) cc_final: 0.7634 (ppp) REVERT: A 142 TYR cc_start: 0.7370 (m-80) cc_final: 0.6913 (m-80) REVERT: A 186 PHE cc_start: 0.8247 (t80) cc_final: 0.7951 (t80) REVERT: A 357 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: A 462 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7106 (tmtt) REVERT: A 584 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7142 (p0) REVERT: A 733 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3925 (mp) REVERT: A 750 MET cc_start: 0.6962 (ptt) cc_final: 0.5819 (ttp) REVERT: A 761 TYR cc_start: 0.3977 (t80) cc_final: 0.2549 (t80) REVERT: A 767 LEU cc_start: -0.3955 (OUTLIER) cc_final: -0.4183 (mm) REVERT: A 919 TRP cc_start: 0.5608 (OUTLIER) cc_final: 0.4913 (m-90) REVERT: A 1008 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5737 (m-80) REVERT: A 1022 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6567 (tmmm) REVERT: A 1157 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 1431 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8258 (mm) REVERT: A 1445 LYS cc_start: 0.6482 (pttt) cc_final: 0.5464 (mtpp) REVERT: B 94 MET cc_start: 0.7199 (tmm) cc_final: 0.6776 (ptm) REVERT: B 127 MET cc_start: 0.7495 (ppp) cc_final: 0.7108 (ppp) REVERT: B 137 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.2482 (tpt90) REVERT: B 141 TRP cc_start: 0.7306 (m-10) cc_final: 0.6613 (m-10) REVERT: B 142 TYR cc_start: 0.6708 (m-80) cc_final: 0.6086 (m-80) REVERT: B 162 LEU cc_start: 0.8807 (mm) cc_final: 0.8580 (mm) REVERT: B 494 TYR cc_start: 0.5402 (OUTLIER) cc_final: 0.5123 (m-10) REVERT: B 750 MET cc_start: 0.7786 (ptp) cc_final: 0.6807 (tpt) REVERT: B 761 TYR cc_start: 0.4417 (OUTLIER) cc_final: 0.3838 (t80) REVERT: B 813 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6044 (tm-30) REVERT: B 1008 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: B 1230 ASN cc_start: 0.7435 (m110) cc_final: 0.7030 (m110) REVERT: B 1369 ASP cc_start: 0.6910 (t0) cc_final: 0.6544 (t0) outliers start: 107 outliers final: 84 residues processed: 321 average time/residue: 0.1250 time to fit residues: 66.2392 Evaluate side-chains 330 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 230 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 919 TRP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1022 LYS Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1104 ASN Chi-restraints excluded: chain A residue 1112 TYR Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1390 SER Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1430 MET Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 720 HIS Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 813 GLU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1020 PHE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1104 ASN Chi-restraints excluded: chain B residue 1112 TYR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1194 THR Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1293 VAL Chi-restraints excluded: chain B residue 1295 VAL Chi-restraints excluded: chain B residue 1310 PHE Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1372 VAL Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1390 SER Chi-restraints excluded: chain B residue 1430 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 156 optimal weight: 0.0050 chunk 222 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 ASN A 691 ASN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 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 = 0.4471 r_free = 0.4471 target = 0.171879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120285 restraints weight = 49479.071| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.96 r_work: 0.3407 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22662 Z= 0.139 Angle : 0.670 15.651 30830 Z= 0.321 Chirality : 0.043 0.418 3564 Planarity : 0.004 0.046 3820 Dihedral : 7.912 59.643 3736 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.53 % Allowed : 28.54 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2746 helix: 1.47 (0.12), residues: 1792 sheet: 0.45 (0.45), residues: 136 loop : -0.97 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.027 0.001 TYR A 75 PHE 0.056 0.001 PHE B 186 TRP 0.030 0.001 TRP B1349 HIS 0.002 0.000 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00298 (22660) covalent geometry : angle 0.67038 (30826) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.04487 ( 4) hydrogen bonds : bond 0.05113 ( 1348) hydrogen bonds : angle 4.51419 ( 3972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6828.88 seconds wall clock time: 117 minutes 7.30 seconds (7027.30 seconds total)