Starting phenix.real_space_refine on Sat Aug 8 13:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmm_37656/08_2026/8wmm_37656.map" } resolution = 2.98 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 17186 2.51 5 N 4972 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28632 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10106 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 bond proxies already assigned to first conformer: 10300 Chain: "B" Number of atoms: 10106 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1212, 10098 Classifications: {'peptide': 1212} Link IDs: {'PTRANS': 30, 'TRANS': 1181} Chain breaks: 2 bond proxies already assigned to first conformer: 10300 Chain: "C" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2332 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 43} Link IDs: {'rna2p': 6, 'rna3p': 102} Chain breaks: 1 Chain: "F" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1108 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1108 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "O" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2332 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 43} Link IDs: {'rna2p': 6, 'rna3p': 102} Chain breaks: 1 Chain: "S" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "Y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP A 672 " occ=0.44 ... (14 atoms not shown) pdb=" OD2BASP A 672 " occ=0.56 residue: pdb=" N AASP B 672 " occ=0.44 ... (14 atoms not shown) pdb=" OD2BASP B 672 " occ=0.56 Time building chain proxies: 9.49, per 1000 atoms: 0.33 Number of scatterers: 28632 At special positions: 0 Unit cell: (206.757, 172.118, 107.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 294 15.00 Mg 2 11.99 O 6130 8.00 N 4972 7.00 C 17186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 35 sheets defined 47.0% alpha, 12.3% beta 124 base pairs and 174 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.041A pdb=" N GLY A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 89 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.717A pdb=" N HIS A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.544A pdb=" N LYS A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 317 through 334 removed outlier: 4.214A pdb=" N TYR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 6.290A pdb=" N GLU A 338 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.631A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.691A pdb=" N PHE A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.717A pdb=" N VAL A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 576 through 588 Proline residue: A 585 - end of helix Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.692A pdb=" N TYR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.714A pdb=" N ARG A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.896A pdb=" N LEU A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 932 through 943 removed outlier: 4.175A pdb=" N LYS A 936 " --> pdb=" O ARG A 932 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 976 Processing helix chain 'A' and resid 977 through 998 Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1031 through 1044 removed outlier: 4.432A pdb=" N ALA A1035 " --> pdb=" O HIS A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1059 through 1070 removed outlier: 3.852A pdb=" N ARG A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A1065 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A1066 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1111 Processing helix chain 'A' and resid 1193 through 1198 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1225 through 1235 Processing helix chain 'A' and resid 1265 through 1270 removed outlier: 4.162A pdb=" N LYS A1269 " --> pdb=" O GLY A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1309 Processing helix chain 'A' and resid 1353 through 1358 Processing helix chain 'A' and resid 1410 through 1415 removed outlier: 3.923A pdb=" N THR A1414 " --> pdb=" O ARG A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1440 removed outlier: 3.822A pdb=" N PHE A1438 " --> pdb=" O ILE A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.537A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 89 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 129 through 144 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.697A pdb=" N HIS B 157 " --> pdb=" O TRP B 153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.527A pdb=" N LYS B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 3.502A pdb=" N HIS B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 317 through 333 removed outlier: 4.185A pdb=" N TYR B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 335 No H-bonds generated for 'chain 'B' and resid 334 through 335' Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 356 through 365 removed outlier: 3.914A pdb=" N LYS B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.579A pdb=" N PHE B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 498 through 511 removed outlier: 3.522A pdb=" N THR B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 534 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 556 through 562 removed outlier: 3.559A pdb=" N GLU B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 588 Proline residue: B 585 - end of helix Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 599 through 612 Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.520A pdb=" N ARG B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 639 through 649 Processing helix chain 'B' and resid 662 through 672 removed outlier: 3.801A pdb=" N LEU B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 703 Processing helix chain 'B' and resid 932 through 943 removed outlier: 4.151A pdb=" N LYS B 936 " --> pdb=" O ARG B 932 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 937 " --> pdb=" O TYR B 933 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 939 " --> pdb=" O SER B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 976 removed outlier: 3.527A pdb=" N THR B 969 " --> pdb=" O ASN B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 998 Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 1017 through 1021 Processing helix chain 'B' and resid 1031 through 1044 removed outlier: 4.272A pdb=" N ALA B1035 " --> pdb=" O HIS B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1054 Processing helix chain 'B' and resid 1059 through 1070 removed outlier: 3.911A pdb=" N ARG B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B1065 " --> pdb=" O THR B1061 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B1066 " --> pdb=" O LYS B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1111 Processing helix chain 'B' and resid 1193 through 1198 Processing helix chain 'B' and resid 1202 through 1216 Processing helix chain 'B' and resid 1219 through 1224 Processing helix chain 'B' and resid 1225 through 1235 Processing helix chain 'B' and resid 1265 through 1270 removed outlier: 4.241A pdb=" N LYS B1269 " --> pdb=" O GLY B1266 " (cutoff:3.500A) Processing helix chain 'B' and resid 1299 through 1309 Processing helix chain 'B' and resid 1353 through 1358 Processing helix chain 'B' and resid 1410 through 1415 removed outlier: 4.137A pdb=" N THR B1414 " --> pdb=" O ARG B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1440 removed outlier: 4.055A pdb=" N PHE B1438 " --> pdb=" O ILE B1434 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.925A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 40 through 53 Processing helix chain 'G' and resid 57 through 72 Processing helix chain 'G' and resid 81 through 93 removed outlier: 3.774A pdb=" N GLN G 91 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG G 92 " --> pdb=" O PHE G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.925A pdb=" N LEU H 13 " --> pdb=" O ASP H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 57 through 72 Processing helix chain 'H' and resid 81 through 93 removed outlier: 3.774A pdb=" N GLN H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing sheet with id=AA1, first strand: chain 'A' and resid 961 through 963 removed outlier: 7.569A pdb=" N ILE A 712 " --> pdb=" O VAL A 962 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN A 4 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N HIS A 713 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 6 " --> pdb=" O HIS A 713 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU A 715 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 8 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 21 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE A 31 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP A 23 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY A 29 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 205 Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 216 removed outlier: 4.377A pdb=" N GLU A 214 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA6, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.688A pdb=" N GLU A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 401 removed outlier: 5.544A pdb=" N LEU A 412 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N LEU A 395 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLN A 410 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N PHE A 397 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 11.309A pdb=" N HIS A 408 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB1, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AB2, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.831A pdb=" N GLN A1094 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1124 through 1126 Processing sheet with id=AB4, first strand: chain 'A' and resid 1130 through 1137 Processing sheet with id=AB5, first strand: chain 'A' and resid 1166 through 1168 removed outlier: 4.431A pdb=" N LEU A1181 " --> pdb=" O VAL A1168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AB7, first strand: chain 'A' and resid 1293 through 1297 removed outlier: 6.075A pdb=" N PHE A1283 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A1327 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A1285 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1370 through 1375 removed outlier: 3.853A pdb=" N LYS A1365 " --> pdb=" O TYR A1372 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A1374 " --> pdb=" O VAL A1363 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL A1363 " --> pdb=" O VAL A1374 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A1333 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A1419 " --> pdb=" O ASN A1427 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 961 through 963 removed outlier: 7.219A pdb=" N ILE B 712 " --> pdb=" O VAL B 962 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS B 21 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 31 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP B 23 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY B 29 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AC2, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 200 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 211 through 216 removed outlier: 3.943A pdb=" N GLU B 214 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 392 through 400 removed outlier: 5.536A pdb=" N LEU B 412 " --> pdb=" O CYS B 393 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N LEU B 395 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N GLN B 410 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N PHE B 397 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N HIS B 408 " --> pdb=" O PHE B 397 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 437 through 438 Processing sheet with id=AC7, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AC8, first strand: chain 'B' and resid 1003 through 1006 Processing sheet with id=AC9, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 3.769A pdb=" N GLN B1094 " --> pdb=" O LYS B1072 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1124 through 1126 Processing sheet with id=AD2, first strand: chain 'B' and resid 1130 through 1137 Processing sheet with id=AD3, first strand: chain 'B' and resid 1166 through 1167 Processing sheet with id=AD4, first strand: chain 'B' and resid 1260 through 1261 Processing sheet with id=AD5, first strand: chain 'B' and resid 1293 through 1297 removed outlier: 6.026A pdb=" N PHE B1283 " --> pdb=" O ASP B1327 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP B1327 " --> pdb=" O PHE B1283 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B1285 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1370 through 1375 removed outlier: 3.830A pdb=" N LYS B1365 " --> pdb=" O TYR B1372 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL B1374 " --> pdb=" O VAL B1363 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL B1363 " --> pdb=" O VAL B1374 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU B1333 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN B1419 " --> pdb=" O ASN B1427 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 74 through 76 removed outlier: 6.530A pdb=" N ILE G 6 " --> pdb=" O PHE G 37 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR G 39 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE G 8 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU G 114 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 129 " --> pdb=" O VAL G 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.530A pdb=" N ILE H 6 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR H 39 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE H 8 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU H 114 " --> pdb=" O VAL H 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) 946 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 584 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 174 stacking parallelities Total time for adding SS restraints: 8.86 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4387 1.32 - 1.44: 9365 1.44 - 1.57: 15408 1.57 - 1.69: 580 1.69 - 1.81: 78 Bond restraints: 29818 Sorted by residual: bond pdb=" ND1 HIS A 477 " pdb=" CE1 HIS A 477 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.82e+01 bond pdb=" CD GLN B1397 " pdb=" OE1 GLN B1397 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.45e+01 bond pdb=" CD GLN H 87 " pdb=" OE1 GLN H 87 " ideal model delta sigma weight residual 1.231 1.324 -0.093 1.90e-02 2.77e+03 2.38e+01 bond pdb=" CD GLN G 87 " pdb=" OE1 GLN G 87 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" CD2 HIS A 477 " pdb=" NE2 HIS A 477 " ideal model delta sigma weight residual 1.374 1.321 0.053 1.10e-02 8.26e+03 2.31e+01 ... (remaining 29813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 40688 2.00 - 4.00: 806 4.00 - 6.00: 38 6.00 - 8.00: 1 8.00 - 10.00: 3 Bond angle restraints: 41536 Sorted by residual: angle pdb=" N GLN B 410 " pdb=" CA GLN B 410 " pdb=" C GLN B 410 " ideal model delta sigma weight residual 110.52 100.52 10.00 1.48e+00 4.57e-01 4.56e+01 angle pdb=" CB HIS A 477 " pdb=" CG HIS A 477 " pdb=" CD2 HIS A 477 " ideal model delta sigma weight residual 131.20 122.57 8.63 1.30e+00 5.92e-01 4.41e+01 angle pdb=" N ILE A1343 " pdb=" CA ILE A1343 " pdb=" C ILE A1343 " ideal model delta sigma weight residual 106.21 112.56 -6.35 1.07e+00 8.73e-01 3.53e+01 angle pdb=" CB HIS A 477 " pdb=" CG HIS A 477 " pdb=" ND1 HIS A 477 " ideal model delta sigma weight residual 122.70 131.30 -8.60 1.50e+00 4.44e-01 3.29e+01 angle pdb=" N ASP B1344 " pdb=" CA ASP B1344 " pdb=" C ASP B1344 " ideal model delta sigma weight residual 112.68 106.70 5.98 1.33e+00 5.65e-01 2.02e+01 ... (remaining 41531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 16356 24.05 - 48.10: 1180 48.10 - 72.15: 456 72.15 - 96.20: 66 96.20 - 120.25: 4 Dihedral angle restraints: 18062 sinusoidal: 10120 harmonic: 7942 Sorted by residual: dihedral pdb=" O4' A O 95 " pdb=" C1' A O 95 " pdb=" N9 A O 95 " pdb=" C4 A O 95 " ideal model delta sinusoidal sigma weight residual -106.00 -164.39 58.39 1 1.70e+01 3.46e-03 1.58e+01 dihedral pdb=" O4' A D 95 " pdb=" C1' A D 95 " pdb=" N9 A D 95 " pdb=" C4 A D 95 " ideal model delta sinusoidal sigma weight residual -106.00 -163.69 57.69 1 1.70e+01 3.46e-03 1.55e+01 dihedral pdb=" CA PHE A1438 " pdb=" C PHE A1438 " pdb=" N ASN A1439 " pdb=" CA ASN A1439 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 18059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3364 0.036 - 0.072: 746 0.072 - 0.109: 442 0.109 - 0.145: 133 0.145 - 0.181: 35 Chirality restraints: 4720 Sorted by residual: chirality pdb=" C3' DA Y 16 " pdb=" C4' DA Y 16 " pdb=" O3' DA Y 16 " pdb=" C2' DA Y 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA VAL A 210 " pdb=" N VAL A 210 " pdb=" C VAL A 210 " pdb=" CB VAL A 210 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" C3' DA S 16 " pdb=" C4' DA S 16 " pdb=" O3' DA S 16 " pdb=" C2' DA S 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 4717 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1243 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO A1244 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1244 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1244 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1243 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C LYS A1243 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS A1243 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO A1244 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 645 " -0.023 2.00e-02 2.50e+03 1.66e-02 5.53e+00 pdb=" CG TYR A 645 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 645 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 645 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 645 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 645 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 645 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 645 " -0.004 2.00e-02 2.50e+03 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4368 2.76 - 3.29: 28840 3.29 - 3.83: 51266 3.83 - 4.36: 62637 4.36 - 4.90: 97935 Nonbonded interactions: 245046 Sorted by model distance: nonbonded pdb=" O ASN A1301 " pdb=" OE1 GLU A1305 " model vdw 2.219 3.040 nonbonded pdb=" O LYS A 109 " pdb=" OG1 THR A 112 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP B 953 " pdb=" OG SER B 958 " model vdw 2.244 3.040 nonbonded pdb=" O ARG B 466 " pdb=" OG1 THR B 502 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A1297 " pdb=" O GLY A1368 " model vdw 2.261 3.040 ... (remaining 245041 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 671 or resid 673 through 1442)) selection = (chain 'B' and (resid 1 through 671 or resid 673 through 1442)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'S' selection = chain 'Y' } 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=0.44 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: 2.930 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.820 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.004 0.100 29818 Z= 0.248 Angle : 0.615 9.998 41536 Z= 0.448 Chirality : 0.045 0.181 4720 Planarity : 0.003 0.066 4216 Dihedral : 17.959 120.247 12914 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.52 % Allowed : 0.88 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.16), residues: 2682 helix: 1.24 (0.16), residues: 1106 sheet: -0.48 (0.30), residues: 296 loop : -0.98 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.039 0.001 TYR A 645 PHE 0.022 0.001 PHE A1441 TRP 0.028 0.001 TRP B 487 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.25 (29818) covalent geometry : angle 0.61455 / 0.45 (41536) hydrogen bonds : bond 0.13238 / 8.96 ( 1250) hydrogen bonds : angle 5.32880 / 3.84 ( 3239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 481 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8184 (mp) cc_final: 0.7764 (tt) REVERT: A 34 MET cc_start: 0.7265 (mtp) cc_final: 0.6758 (mtt) REVERT: A 63 LYS cc_start: 0.7841 (ttpp) cc_final: 0.7621 (mtpt) REVERT: A 164 SER cc_start: 0.8491 (p) cc_final: 0.8205 (t) REVERT: A 171 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6163 (mt-10) REVERT: A 242 TRP cc_start: 0.7427 (m100) cc_final: 0.6945 (m100) REVERT: A 282 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6060 (mt-10) REVERT: A 317 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 319 LYS cc_start: 0.7553 (ptmm) cc_final: 0.7332 (pttt) REVERT: A 467 LYS cc_start: 0.6201 (ptpt) cc_final: 0.5834 (pptt) REVERT: A 571 GLU cc_start: 0.6968 (pt0) cc_final: 0.6670 (mt-10) REVERT: A 587 MET cc_start: 0.6936 (mtp) cc_final: 0.6635 (ptp) REVERT: A 604 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7721 (pt0) REVERT: A 697 ILE cc_start: 0.8087 (mt) cc_final: 0.7876 (mt) REVERT: A 938 ILE cc_start: 0.6912 (tp) cc_final: 0.6594 (tt) REVERT: A 973 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7384 (mtmm) REVERT: A 1037 ASP cc_start: 0.6777 (m-30) cc_final: 0.6433 (m-30) REVERT: A 1105 ASP cc_start: 0.7418 (m-30) cc_final: 0.7106 (m-30) REVERT: A 1179 LYS cc_start: 0.7895 (mttm) cc_final: 0.7591 (mmmm) REVERT: A 1207 LYS cc_start: 0.7662 (tttt) cc_final: 0.7435 (tttt) REVERT: A 1254 PHE cc_start: 0.7682 (p90) cc_final: 0.7435 (p90) REVERT: A 1255 GLU cc_start: 0.7233 (tt0) cc_final: 0.6446 (tm-30) REVERT: A 1269 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7317 (pttp) REVERT: A 1298 ILE cc_start: 0.8271 (mm) cc_final: 0.8055 (mm) REVERT: A 1378 ILE cc_start: 0.7589 (mt) cc_final: 0.7240 (mm) REVERT: A 1404 MET cc_start: 0.6914 (ptp) cc_final: 0.6562 (ptt) REVERT: A 1437 ILE cc_start: 0.7392 (mm) cc_final: 0.7183 (tp) REVERT: B 34 MET cc_start: 0.7115 (mtp) cc_final: 0.6578 (mtt) REVERT: B 56 SER cc_start: 0.7280 (t) cc_final: 0.7045 (p) REVERT: B 60 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7111 (mm-30) REVERT: B 104 ARG cc_start: 0.6988 (mtp-110) cc_final: 0.6783 (mtm-85) REVERT: B 145 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6921 (tp40) REVERT: B 182 LYS cc_start: 0.7748 (tptm) cc_final: 0.7457 (tttm) REVERT: B 200 THR cc_start: 0.6929 (m) cc_final: 0.6727 (t) REVERT: B 232 TYR cc_start: 0.8127 (t80) cc_final: 0.7139 (t80) REVERT: B 250 ILE cc_start: 0.7323 (mt) cc_final: 0.6844 (tp) REVERT: B 282 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5914 (mp0) REVERT: B 311 LYS cc_start: 0.8438 (tppt) cc_final: 0.8123 (tppt) REVERT: B 317 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 331 LYS cc_start: 0.7582 (tppt) cc_final: 0.7333 (tptt) REVERT: B 397 PHE cc_start: 0.6120 (m-10) cc_final: 0.5622 (m-10) REVERT: B 420 PRO cc_start: 0.7775 (Cg_exo) cc_final: 0.7554 (Cg_endo) REVERT: B 467 LYS cc_start: 0.6397 (ptpt) cc_final: 0.5987 (pptt) REVERT: B 499 GLU cc_start: 0.6052 (pt0) cc_final: 0.5501 (mt-10) REVERT: B 604 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 660 TRP cc_start: 0.7942 (m-10) cc_final: 0.7657 (m-10) REVERT: B 692 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6802 (mtt-85) REVERT: B 706 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7793 (tttm) REVERT: B 973 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7422 (mtmm) REVERT: B 990 PHE cc_start: 0.7659 (m-80) cc_final: 0.7241 (m-80) REVERT: B 1029 ILE cc_start: 0.7806 (pt) cc_final: 0.7598 (pt) REVERT: B 1037 ASP cc_start: 0.7067 (m-30) cc_final: 0.6794 (m-30) REVERT: B 1096 LEU cc_start: 0.6971 (mp) cc_final: 0.6767 (mp) REVERT: B 1105 ASP cc_start: 0.7663 (m-30) cc_final: 0.7368 (p0) REVERT: B 1130 TYR cc_start: 0.7829 (m-80) cc_final: 0.7619 (m-10) REVERT: B 1132 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6998 (mp0) REVERT: B 1186 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8166 (mmtm) REVERT: B 1250 LYS cc_start: 0.7971 (mttt) cc_final: 0.7166 (mtpt) REVERT: B 1255 GLU cc_start: 0.7256 (tt0) cc_final: 0.6472 (tm-30) REVERT: B 1298 ILE cc_start: 0.8462 (mm) cc_final: 0.8190 (mm) REVERT: B 1323 ARG cc_start: 0.6364 (ptm-80) cc_final: 0.6147 (ptt-90) REVERT: B 1378 ILE cc_start: 0.7508 (mt) cc_final: 0.7228 (mm) REVERT: B 1383 LYS cc_start: 0.7873 (tttm) cc_final: 0.7574 (tmmm) REVERT: B 1419 ASN cc_start: 0.7125 (m110) cc_final: 0.6903 (m-40) REVERT: B 1429 ILE cc_start: 0.7689 (tp) cc_final: 0.7397 (mt) REVERT: B 1431 LYS cc_start: 0.8060 (tptt) cc_final: 0.7832 (tptt) REVERT: B 1436 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7449 (mm-40) REVERT: G 34 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7519 (mtmm) REVERT: G 35 LYS cc_start: 0.8323 (mptt) cc_final: 0.8122 (mmtm) REVERT: G 87 GLN cc_start: 0.6422 (tp40) cc_final: 0.5925 (tp-100) REVERT: G 130 LYS cc_start: 0.7981 (ptmt) cc_final: 0.7743 (ptmm) REVERT: H 34 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7549 (mtmm) REVERT: H 35 LYS cc_start: 0.8383 (mptt) cc_final: 0.7858 (mmtm) REVERT: H 39 THR cc_start: 0.7482 (m) cc_final: 0.7220 (p) REVERT: H 110 ASN cc_start: 0.8271 (m-40) cc_final: 0.8069 (m-40) REVERT: H 123 MET cc_start: 0.7658 (ttt) cc_final: 0.7420 (ttm) REVERT: H 130 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7802 (ttpm) outliers start: 13 outliers final: 2 residues processed: 494 average time/residue: 0.7105 time to fit residues: 409.6639 Evaluate side-chains 389 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 387 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain B residue 1346 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A1152 ASN A1425 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B1108 HIS B1152 ASN B1397 GLN B1425 ASN G 84 ASN H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.193331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149224 restraints weight = 71471.247| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.31 r_work: 0.3663 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29818 Z= 0.225 Angle : 0.642 8.313 41536 Z= 0.360 Chirality : 0.044 0.291 4720 Planarity : 0.004 0.045 4216 Dihedral : 18.644 140.616 7067 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.81 % Allowed : 9.28 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.16), residues: 2682 helix: 0.97 (0.15), residues: 1110 sheet: -0.31 (0.30), residues: 290 loop : -0.88 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1122 TYR 0.035 0.002 TYR A 645 PHE 0.038 0.002 PHE A 489 TRP 0.028 0.002 TRP A 487 HIS 0.009 0.002 HIS B1031 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (29818) covalent geometry : angle 0.64163 / 0.36 (41536) hydrogen bonds : bond 0.05718 / 3.90 ( 1250) hydrogen bonds : angle 4.39053 / 3.15 ( 3239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8258 (mp) cc_final: 0.8037 (tt) REVERT: A 107 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7364 (mttt) REVERT: A 119 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6727 (ptpp) REVERT: A 149 ILE cc_start: 0.7428 (pt) cc_final: 0.7162 (mt) REVERT: A 248 GLU cc_start: 0.7152 (pm20) cc_final: 0.6631 (pm20) REVERT: A 265 PHE cc_start: 0.6805 (m-80) cc_final: 0.6304 (m-80) REVERT: A 503 MET cc_start: 0.6164 (OUTLIER) cc_final: 0.5914 (mmp) REVERT: A 545 LYS cc_start: 0.8050 (mttm) cc_final: 0.7735 (mttm) REVERT: A 604 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7802 (pt0) REVERT: A 697 ILE cc_start: 0.8665 (mt) cc_final: 0.8436 (mt) REVERT: A 973 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7502 (mtmm) REVERT: A 990 PHE cc_start: 0.7657 (m-80) cc_final: 0.7426 (m-80) REVERT: A 1071 MET cc_start: 0.6636 (mtp) cc_final: 0.6295 (mtp) REVERT: A 1105 ASP cc_start: 0.7516 (m-30) cc_final: 0.7228 (m-30) REVERT: A 1250 LYS cc_start: 0.7962 (mttt) cc_final: 0.7526 (mttm) REVERT: A 1254 PHE cc_start: 0.8034 (p90) cc_final: 0.7823 (p90) REVERT: A 1255 GLU cc_start: 0.7745 (tt0) cc_final: 0.7240 (tm-30) REVERT: A 1264 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7537 (mm-40) REVERT: A 1269 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7747 (pttp) REVERT: A 1298 ILE cc_start: 0.8603 (mm) cc_final: 0.8305 (mm) REVERT: A 1369 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7290 (p) REVERT: A 1378 ILE cc_start: 0.8124 (mt) cc_final: 0.7777 (mp) REVERT: A 1437 ILE cc_start: 0.7737 (mm) cc_final: 0.7439 (tp) REVERT: B 15 ILE cc_start: 0.8321 (mp) cc_final: 0.7987 (tt) REVERT: B 119 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6830 (ptpp) REVERT: B 200 THR cc_start: 0.6834 (m) cc_final: 0.6548 (t) REVERT: B 250 ILE cc_start: 0.7211 (mt) cc_final: 0.6950 (tp) REVERT: B 286 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6656 (mm-30) REVERT: B 317 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7167 (mm-30) REVERT: B 360 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6427 (tm-30) REVERT: B 418 SER cc_start: 0.7848 (p) cc_final: 0.7573 (p) REVERT: B 597 GLU cc_start: 0.3914 (OUTLIER) cc_final: 0.3665 (mp0) REVERT: B 667 GLU cc_start: 0.7610 (pp20) cc_final: 0.7198 (pp20) REVERT: B 984 ASP cc_start: 0.8212 (m-30) cc_final: 0.7937 (m-30) REVERT: B 1003 THR cc_start: 0.7182 (p) cc_final: 0.6913 (t) REVERT: B 1020 PHE cc_start: 0.7900 (m-80) cc_final: 0.7440 (m-80) REVERT: B 1096 LEU cc_start: 0.7887 (mp) cc_final: 0.7686 (mp) REVERT: B 1132 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7302 (mp0) REVERT: B 1250 LYS cc_start: 0.8214 (mttt) cc_final: 0.7663 (mttp) REVERT: B 1255 GLU cc_start: 0.7795 (tt0) cc_final: 0.7257 (tm-30) REVERT: B 1298 ILE cc_start: 0.8716 (mm) cc_final: 0.8488 (mm) REVERT: B 1305 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 1323 ARG cc_start: 0.7178 (ptm-80) cc_final: 0.6935 (ptt-90) REVERT: B 1413 ASP cc_start: 0.7663 (p0) cc_final: 0.6875 (m-30) REVERT: B 1414 THR cc_start: 0.7851 (p) cc_final: 0.6897 (t) REVERT: B 1429 ILE cc_start: 0.8082 (tp) cc_final: 0.7746 (mt) REVERT: G 34 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7911 (mtmm) REVERT: G 35 LYS cc_start: 0.8643 (mptt) cc_final: 0.8442 (mmtm) REVERT: H 35 LYS cc_start: 0.8604 (mptt) cc_final: 0.8236 (mmtm) REVERT: H 128 LYS cc_start: 0.8386 (mttp) cc_final: 0.7914 (mtmm) outliers start: 45 outliers final: 18 residues processed: 445 average time/residue: 0.7087 time to fit residues: 368.0988 Evaluate side-chains 413 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 388 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1383 LYS Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1108 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1237 GLU Chi-restraints excluded: chain B residue 1305 GLU Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain H residue 124 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 18 optimal weight: 0.5980 chunk 245 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 225 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A1152 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 617 ASN B1010 GLN B1108 HIS B1142 ASN B1152 ASN B1401 GLN B1436 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.193166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148848 restraints weight = 77717.585| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.43 r_work: 0.3653 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29818 Z= 0.184 Angle : 0.597 7.993 41536 Z= 0.336 Chirality : 0.043 0.275 4720 Planarity : 0.004 0.049 4216 Dihedral : 18.535 120.010 7064 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.77 % Allowed : 12.61 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.16), residues: 2682 helix: 0.92 (0.15), residues: 1112 sheet: -0.22 (0.30), residues: 290 loop : -0.96 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 364 TYR 0.031 0.002 TYR A 645 PHE 0.033 0.002 PHE B 101 TRP 0.038 0.002 TRP B 660 HIS 0.007 0.001 HIS B1031 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (29818) covalent geometry : angle 0.59725 / 0.34 (41536) hydrogen bonds : bond 0.05144 / 3.54 ( 1250) hydrogen bonds : angle 4.23411 / 3.03 ( 3239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 412 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7407 (mttt) REVERT: A 149 ILE cc_start: 0.7522 (pt) cc_final: 0.7310 (mt) REVERT: A 248 GLU cc_start: 0.7202 (pm20) cc_final: 0.6691 (pm20) REVERT: A 265 PHE cc_start: 0.6897 (m-80) cc_final: 0.6339 (m-80) REVERT: A 467 LYS cc_start: 0.7310 (ptpt) cc_final: 0.6697 (tmmt) REVERT: A 545 LYS cc_start: 0.7974 (mttm) cc_final: 0.7690 (mttm) REVERT: A 973 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7488 (mtmm) REVERT: A 1071 MET cc_start: 0.6592 (mtp) cc_final: 0.6121 (mtp) REVERT: A 1250 LYS cc_start: 0.7923 (mttt) cc_final: 0.7510 (mttm) REVERT: A 1254 PHE cc_start: 0.8096 (p90) cc_final: 0.7857 (p90) REVERT: A 1255 GLU cc_start: 0.7775 (tt0) cc_final: 0.7289 (tm-30) REVERT: A 1269 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7734 (pttp) REVERT: A 1298 ILE cc_start: 0.8569 (mm) cc_final: 0.8316 (mm) REVERT: A 1323 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6886 (ttt180) REVERT: A 1369 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7162 (p) REVERT: A 1378 ILE cc_start: 0.8132 (mt) cc_final: 0.7858 (mp) REVERT: A 1440 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: B 31 ILE cc_start: 0.7583 (mm) cc_final: 0.7167 (mt) REVERT: B 119 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6804 (ptpp) REVERT: B 128 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7871 (tt) REVERT: B 136 MET cc_start: 0.7470 (ttm) cc_final: 0.7236 (ttp) REVERT: B 200 THR cc_start: 0.6897 (m) cc_final: 0.6599 (t) REVERT: B 317 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 360 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 597 GLU cc_start: 0.3936 (OUTLIER) cc_final: 0.3713 (mp0) REVERT: B 598 ILE cc_start: 0.7603 (mp) cc_final: 0.7367 (mm) REVERT: B 604 GLU cc_start: 0.7873 (pt0) cc_final: 0.7374 (pp20) REVERT: B 973 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7545 (mtmm) REVERT: B 984 ASP cc_start: 0.8312 (m-30) cc_final: 0.7987 (m-30) REVERT: B 1003 THR cc_start: 0.7196 (p) cc_final: 0.6917 (t) REVERT: B 1020 PHE cc_start: 0.7885 (m-80) cc_final: 0.7422 (m-80) REVERT: B 1039 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7738 (tt) REVERT: B 1096 LEU cc_start: 0.7855 (mp) cc_final: 0.7638 (mp) REVERT: B 1132 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6436 (mp0) REVERT: B 1145 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7028 (mtp85) REVERT: B 1188 LEU cc_start: 0.7544 (mt) cc_final: 0.7336 (mp) REVERT: B 1235 ASN cc_start: 0.6973 (m110) cc_final: 0.6622 (m110) REVERT: B 1250 LYS cc_start: 0.8209 (mttt) cc_final: 0.7539 (mttp) REVERT: B 1255 GLU cc_start: 0.7834 (tt0) cc_final: 0.7322 (tm-30) REVERT: B 1298 ILE cc_start: 0.8673 (mm) cc_final: 0.8456 (mm) REVERT: B 1323 ARG cc_start: 0.7225 (ptm-80) cc_final: 0.7014 (ptt-90) REVERT: B 1369 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7349 (p) REVERT: B 1404 MET cc_start: 0.7892 (ptp) cc_final: 0.7456 (ptp) REVERT: B 1414 THR cc_start: 0.7867 (p) cc_final: 0.7425 (t) REVERT: B 1429 ILE cc_start: 0.8075 (tp) cc_final: 0.7696 (mt) REVERT: G 34 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7981 (mtmm) REVERT: G 35 LYS cc_start: 0.8683 (mptt) cc_final: 0.8451 (mmtm) REVERT: H 35 LYS cc_start: 0.8600 (mptt) cc_final: 0.8240 (mmtm) REVERT: H 126 ASP cc_start: 0.7973 (t70) cc_final: 0.7725 (t70) REVERT: H 128 LYS cc_start: 0.8437 (mttp) cc_final: 0.7939 (mtmm) outliers start: 44 outliers final: 13 residues processed: 432 average time/residue: 0.7116 time to fit residues: 358.7240 Evaluate side-chains 411 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 390 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1108 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1305 GLU Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 81 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 224 optimal weight: 0.1980 chunk 198 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 249 optimal weight: 5.9990 chunk 9 optimal weight: 0.0170 chunk 247 optimal weight: 9.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1152 ASN A1280 ASN A1439 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B1108 HIS B1152 ASN B1401 GLN B1425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.197328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153845 restraints weight = 85314.091| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.56 r_work: 0.3671 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29818 Z= 0.135 Angle : 0.561 9.061 41536 Z= 0.318 Chirality : 0.040 0.267 4720 Planarity : 0.004 0.049 4216 Dihedral : 18.476 121.477 7064 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.57 % Allowed : 14.38 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.16), residues: 2682 helix: 1.05 (0.15), residues: 1112 sheet: -0.11 (0.30), residues: 288 loop : -0.91 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 364 TYR 0.028 0.002 TYR A 645 PHE 0.040 0.002 PHE B 101 TRP 0.032 0.002 TRP A 593 HIS 0.025 0.001 HIS B1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (29818) covalent geometry : angle 0.56055 / 0.32 (41536) hydrogen bonds : bond 0.04557 / 3.14 ( 1250) hydrogen bonds : angle 4.09095 / 2.92 ( 3239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 404 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ILE cc_start: 0.7523 (pt) cc_final: 0.7315 (mt) REVERT: A 168 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6432 (mm-30) REVERT: A 248 GLU cc_start: 0.7137 (pm20) cc_final: 0.6632 (pm20) REVERT: A 265 PHE cc_start: 0.6935 (m-80) cc_final: 0.6390 (m-80) REVERT: A 467 LYS cc_start: 0.7336 (ptpt) cc_final: 0.6696 (tmmt) REVERT: A 545 LYS cc_start: 0.7957 (mttm) cc_final: 0.7690 (mttm) REVERT: A 581 LYS cc_start: 0.8249 (mtmt) cc_final: 0.8000 (mtmt) REVERT: A 671 LYS cc_start: 0.8348 (tmtp) cc_final: 0.8118 (tttm) REVERT: A 973 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7569 (mtmt) REVERT: A 1071 MET cc_start: 0.6552 (mtp) cc_final: 0.6107 (mtp) REVERT: A 1132 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6655 (OUTLIER) REVERT: A 1254 PHE cc_start: 0.8109 (p90) cc_final: 0.7888 (p90) REVERT: A 1255 GLU cc_start: 0.7823 (tt0) cc_final: 0.7314 (tm-30) REVERT: A 1269 LYS cc_start: 0.7982 (ptpp) cc_final: 0.7737 (pttp) REVERT: A 1298 ILE cc_start: 0.8546 (mm) cc_final: 0.8287 (mm) REVERT: A 1369 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7099 (p) REVERT: A 1378 ILE cc_start: 0.8052 (mt) cc_final: 0.7807 (mp) REVERT: A 1440 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: B 128 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 136 MET cc_start: 0.7487 (ttm) cc_final: 0.7253 (ttp) REVERT: B 232 TYR cc_start: 0.8368 (t80) cc_final: 0.7355 (t80) REVERT: B 317 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 360 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7567 (tm-30) REVERT: B 593 TRP cc_start: 0.6845 (t60) cc_final: 0.6595 (t60) REVERT: B 597 GLU cc_start: 0.3964 (OUTLIER) cc_final: 0.3757 (mp0) REVERT: B 604 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7495 (pp20) REVERT: B 973 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7630 (mtmt) REVERT: B 984 ASP cc_start: 0.8321 (m-30) cc_final: 0.7994 (m-30) REVERT: B 1003 THR cc_start: 0.7183 (p) cc_final: 0.6907 (t) REVERT: B 1020 PHE cc_start: 0.7896 (m-80) cc_final: 0.7490 (m-80) REVERT: B 1096 LEU cc_start: 0.7838 (mp) cc_final: 0.7602 (mp) REVERT: B 1132 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6353 (mp0) REVERT: B 1145 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7011 (mtp85) REVERT: B 1235 ASN cc_start: 0.6984 (m110) cc_final: 0.6598 (m110) REVERT: B 1250 LYS cc_start: 0.8180 (mttt) cc_final: 0.7634 (mttp) REVERT: B 1255 GLU cc_start: 0.7844 (tt0) cc_final: 0.7331 (tm-30) REVERT: B 1298 ILE cc_start: 0.8606 (mm) cc_final: 0.8398 (mm) REVERT: B 1323 ARG cc_start: 0.7227 (ptm-80) cc_final: 0.6966 (ptt-90) REVERT: B 1369 THR cc_start: 0.7462 (OUTLIER) cc_final: 0.7132 (p) REVERT: B 1383 LYS cc_start: 0.8616 (tmmm) cc_final: 0.8146 (ttpt) REVERT: B 1404 MET cc_start: 0.7910 (ptp) cc_final: 0.7560 (ptp) REVERT: B 1414 THR cc_start: 0.7828 (p) cc_final: 0.7362 (t) REVERT: B 1429 ILE cc_start: 0.8044 (tp) cc_final: 0.7679 (mt) REVERT: G 34 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7976 (mtmm) REVERT: G 59 LYS cc_start: 0.7286 (mmtp) cc_final: 0.7074 (mmtp) REVERT: H 35 LYS cc_start: 0.8621 (mptt) cc_final: 0.8270 (mmtm) REVERT: H 51 GLU cc_start: 0.7726 (tt0) cc_final: 0.7487 (mt-10) REVERT: H 126 ASP cc_start: 0.7973 (t70) cc_final: 0.7724 (t70) REVERT: H 128 LYS cc_start: 0.8362 (mttp) cc_final: 0.7842 (mtmm) REVERT: H 130 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8215 (ptmm) outliers start: 39 outliers final: 22 residues processed: 423 average time/residue: 0.6960 time to fit residues: 344.3051 Evaluate side-chains 414 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 386 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 597 GLU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 685 GLN Chi-restraints excluded: chain B residue 1108 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1305 GLU Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 10 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 258 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 233 optimal weight: 0.0270 chunk 229 optimal weight: 3.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B1108 HIS B1152 ASN B1401 GLN B1436 GLN H 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147210 restraints weight = 102087.078| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.93 r_work: 0.3620 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29818 Z= 0.191 Angle : 0.599 9.450 41536 Z= 0.335 Chirality : 0.043 0.408 4720 Planarity : 0.004 0.044 4216 Dihedral : 18.474 120.429 7064 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 1.89 % Allowed : 15.82 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.16), residues: 2682 helix: 0.92 (0.15), residues: 1112 sheet: -0.28 (0.30), residues: 286 loop : -1.05 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 364 TYR 0.027 0.002 TYR B 648 PHE 0.039 0.002 PHE B 101 TRP 0.035 0.002 TRP A 593 HIS 0.039 0.002 HIS B1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (29818) covalent geometry : angle 0.59874 / 0.33 (41536) hydrogen bonds : bond 0.04933 / 3.41 ( 1250) hydrogen bonds : angle 4.15409 / 2.96 ( 3239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 401 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7259 (ttpp) cc_final: 0.7040 (ttmm) REVERT: A 34 MET cc_start: 0.7963 (mpt) cc_final: 0.7729 (mpt) REVERT: A 102 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6920 (mp0) REVERT: A 248 GLU cc_start: 0.7203 (pm20) cc_final: 0.6654 (pm20) REVERT: A 265 PHE cc_start: 0.6997 (m-80) cc_final: 0.6414 (m-80) REVERT: A 467 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6793 (tmmt) REVERT: A 545 LYS cc_start: 0.7926 (mttm) cc_final: 0.7663 (mttm) REVERT: A 973 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7531 (mtmm) REVERT: A 1071 MET cc_start: 0.6613 (mtp) cc_final: 0.6172 (mtp) REVERT: A 1250 LYS cc_start: 0.7889 (mttt) cc_final: 0.7495 (mttm) REVERT: A 1254 PHE cc_start: 0.8126 (p90) cc_final: 0.7874 (p90) REVERT: A 1255 GLU cc_start: 0.7893 (tt0) cc_final: 0.7363 (tm-30) REVERT: A 1269 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7755 (pttp) REVERT: A 1298 ILE cc_start: 0.8540 (mm) cc_final: 0.8294 (mm) REVERT: A 1369 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 1378 ILE cc_start: 0.8228 (mt) cc_final: 0.8027 (mm) REVERT: A 1440 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: B 31 ILE cc_start: 0.7386 (mm) cc_final: 0.7103 (mm) REVERT: B 119 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6941 (ptpp) REVERT: B 136 MET cc_start: 0.7529 (ttm) cc_final: 0.7329 (ttp) REVERT: B 200 THR cc_start: 0.6907 (m) cc_final: 0.6654 (t) REVERT: B 232 TYR cc_start: 0.8368 (t80) cc_final: 0.7217 (t80) REVERT: B 317 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 360 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 593 TRP cc_start: 0.6983 (t60) cc_final: 0.6764 (t60) REVERT: B 598 ILE cc_start: 0.7484 (mm) cc_final: 0.7224 (mp) REVERT: B 604 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: B 638 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4472 (pp) REVERT: B 667 GLU cc_start: 0.7679 (pp20) cc_final: 0.7224 (pp20) REVERT: B 973 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7652 (mtmt) REVERT: B 984 ASP cc_start: 0.8344 (m-30) cc_final: 0.7981 (m-30) REVERT: B 1003 THR cc_start: 0.7218 (p) cc_final: 0.6924 (t) REVERT: B 1020 PHE cc_start: 0.7916 (m-80) cc_final: 0.7518 (m-80) REVERT: B 1096 LEU cc_start: 0.7817 (mp) cc_final: 0.7557 (mp) REVERT: B 1250 LYS cc_start: 0.8201 (mttt) cc_final: 0.7647 (mttp) REVERT: B 1255 GLU cc_start: 0.7881 (tt0) cc_final: 0.7366 (tm-30) REVERT: B 1323 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.6918 (ptt180) REVERT: B 1404 MET cc_start: 0.7931 (ptp) cc_final: 0.7476 (ptp) REVERT: B 1414 THR cc_start: 0.7858 (p) cc_final: 0.7391 (t) REVERT: B 1429 ILE cc_start: 0.8071 (tp) cc_final: 0.7678 (mt) REVERT: G 34 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7982 (mtmm) REVERT: G 59 LYS cc_start: 0.7411 (mmtp) cc_final: 0.7176 (mmtp) REVERT: H 35 LYS cc_start: 0.8628 (mptt) cc_final: 0.8315 (mmtm) outliers start: 47 outliers final: 21 residues processed: 424 average time/residue: 0.6974 time to fit residues: 345.6328 Evaluate side-chains 411 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1229 ILE Chi-restraints excluded: chain B residue 1305 GLU Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 81 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN A1152 ASN A1280 ASN ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 HIS B1401 GLN H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.191058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146812 restraints weight = 83448.744| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.56 r_work: 0.3627 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29818 Z= 0.225 Angle : 0.632 9.577 41536 Z= 0.352 Chirality : 0.044 0.291 4720 Planarity : 0.005 0.051 4216 Dihedral : 18.529 120.222 7064 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 1.97 % Allowed : 16.79 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.15), residues: 2682 helix: 0.78 (0.15), residues: 1108 sheet: -0.28 (0.29), residues: 310 loop : -1.17 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1145 TYR 0.027 0.002 TYR B 648 PHE 0.035 0.002 PHE B 101 TRP 0.036 0.002 TRP A 593 HIS 0.015 0.001 HIS B1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (29818) covalent geometry : angle 0.63207 / 0.35 (41536) hydrogen bonds : bond 0.05094 / 3.53 ( 1250) hydrogen bonds : angle 4.20855 / 3.00 ( 3239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6598 (tpp) cc_final: 0.6137 (tpp) REVERT: A 34 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7637 (mpt) REVERT: A 101 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: A 102 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6906 (mp0) REVERT: A 248 GLU cc_start: 0.7164 (pm20) cc_final: 0.6688 (pm20) REVERT: A 265 PHE cc_start: 0.7061 (m-80) cc_final: 0.6455 (m-80) REVERT: A 330 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 467 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6845 (tmmt) REVERT: A 545 LYS cc_start: 0.7947 (mttm) cc_final: 0.7673 (mttm) REVERT: A 671 LYS cc_start: 0.8398 (tmtp) cc_final: 0.8178 (tttm) REVERT: A 973 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7624 (mtmt) REVERT: A 1071 MET cc_start: 0.6597 (mtp) cc_final: 0.6135 (mtp) REVERT: A 1250 LYS cc_start: 0.7880 (mttt) cc_final: 0.7534 (mttt) REVERT: A 1254 PHE cc_start: 0.8122 (p90) cc_final: 0.7870 (p90) REVERT: A 1255 GLU cc_start: 0.7867 (tt0) cc_final: 0.7386 (tm-30) REVERT: A 1269 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7809 (pttp) REVERT: A 1295 TYR cc_start: 0.7718 (m-80) cc_final: 0.7243 (m-80) REVERT: A 1298 ILE cc_start: 0.8511 (mm) cc_final: 0.8277 (mm) REVERT: A 1369 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 1378 ILE cc_start: 0.8288 (mt) cc_final: 0.8069 (mm) REVERT: A 1383 LYS cc_start: 0.8335 (tmmt) cc_final: 0.7795 (tttp) REVERT: A 1440 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: B 31 ILE cc_start: 0.7377 (mm) cc_final: 0.7125 (mm) REVERT: B 101 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5800 (m-10) REVERT: B 119 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6943 (ptpp) REVERT: B 200 THR cc_start: 0.6961 (m) cc_final: 0.6718 (t) REVERT: B 232 TYR cc_start: 0.8397 (t80) cc_final: 0.7224 (t80) REVERT: B 346 ASN cc_start: 0.7805 (m-40) cc_final: 0.7538 (m-40) REVERT: B 350 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.7123 (mtm-85) REVERT: B 360 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 598 ILE cc_start: 0.7503 (mm) cc_final: 0.7265 (mp) REVERT: B 604 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7572 (pp20) REVERT: B 638 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4459 (pp) REVERT: B 973 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7674 (mtmt) REVERT: B 984 ASP cc_start: 0.8303 (m-30) cc_final: 0.7921 (m-30) REVERT: B 1003 THR cc_start: 0.7257 (p) cc_final: 0.6922 (t) REVERT: B 1020 PHE cc_start: 0.7917 (m-80) cc_final: 0.7473 (m-80) REVERT: B 1096 LEU cc_start: 0.7843 (mp) cc_final: 0.7586 (mp) REVERT: B 1230 ASP cc_start: 0.7909 (t70) cc_final: 0.7623 (m-30) REVERT: B 1250 LYS cc_start: 0.8206 (mttt) cc_final: 0.7650 (mttp) REVERT: B 1255 GLU cc_start: 0.7835 (tt0) cc_final: 0.7361 (tm-30) REVERT: B 1404 MET cc_start: 0.7906 (ptp) cc_final: 0.7534 (ptp) REVERT: B 1414 THR cc_start: 0.7826 (p) cc_final: 0.7347 (t) REVERT: B 1429 ILE cc_start: 0.8088 (tp) cc_final: 0.7672 (mt) REVERT: G 34 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7921 (mtmm) REVERT: G 59 LYS cc_start: 0.7386 (mmtp) cc_final: 0.7141 (mmtp) REVERT: G 130 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8113 (ptmm) REVERT: H 35 LYS cc_start: 0.8630 (mptt) cc_final: 0.8314 (mmtm) REVERT: H 128 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8131 (mtmm) outliers start: 49 outliers final: 24 residues processed: 425 average time/residue: 0.7074 time to fit residues: 351.6026 Evaluate side-chains 420 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1108 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1305 GLU Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 234 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 286 optimal weight: 40.0000 chunk 289 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1152 ASN A1280 ASN ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.192857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149103 restraints weight = 76297.461| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.37 r_work: 0.3630 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29818 Z= 0.238 Angle : 0.654 15.572 41536 Z= 0.360 Chirality : 0.046 0.387 4720 Planarity : 0.005 0.064 4216 Dihedral : 18.556 119.989 7064 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.97 % Allowed : 17.75 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.15), residues: 2682 helix: 0.65 (0.15), residues: 1110 sheet: -0.31 (0.29), residues: 310 loop : -1.25 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 364 TYR 0.025 0.002 TYR B 648 PHE 0.036 0.002 PHE B 101 TRP 0.035 0.002 TRP A 976 HIS 0.042 0.002 HIS B1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (29818) covalent geometry : angle 0.65368 / 0.36 (41536) hydrogen bonds : bond 0.05256 / 3.65 ( 1250) hydrogen bonds : angle 4.27694 / 3.04 ( 3239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6588 (tpp) cc_final: 0.6158 (tpp) REVERT: A 119 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6831 (ptpp) REVERT: A 248 GLU cc_start: 0.7173 (pm20) cc_final: 0.6646 (pm20) REVERT: A 265 PHE cc_start: 0.7167 (m-80) cc_final: 0.6585 (m-80) REVERT: A 467 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6828 (tmmt) REVERT: A 545 LYS cc_start: 0.7969 (mttm) cc_final: 0.7696 (mttm) REVERT: A 671 LYS cc_start: 0.8419 (tmtp) cc_final: 0.8183 (tttm) REVERT: A 973 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7576 (mtmm) REVERT: A 1021 SER cc_start: 0.7903 (t) cc_final: 0.7695 (t) REVERT: A 1071 MET cc_start: 0.6577 (mtp) cc_final: 0.6122 (mtp) REVERT: A 1230 ASP cc_start: 0.7737 (t70) cc_final: 0.7481 (m-30) REVERT: A 1250 LYS cc_start: 0.7889 (mttt) cc_final: 0.7517 (mttm) REVERT: A 1254 PHE cc_start: 0.8116 (p90) cc_final: 0.7855 (p90) REVERT: A 1255 GLU cc_start: 0.7875 (tt0) cc_final: 0.7439 (tm-30) REVERT: A 1269 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7802 (pttp) REVERT: A 1295 TYR cc_start: 0.7757 (m-80) cc_final: 0.7218 (m-80) REVERT: A 1298 ILE cc_start: 0.8496 (mm) cc_final: 0.8263 (mm) REVERT: A 1378 ILE cc_start: 0.8349 (mt) cc_final: 0.8136 (mm) REVERT: A 1440 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 1 MET cc_start: 0.6768 (mpp) cc_final: 0.6558 (mpm) REVERT: B 31 ILE cc_start: 0.7518 (mm) cc_final: 0.7314 (mm) REVERT: B 101 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5917 (m-10) REVERT: B 119 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7009 (ptpp) REVERT: B 200 THR cc_start: 0.7039 (m) cc_final: 0.6806 (t) REVERT: B 232 TYR cc_start: 0.8389 (t80) cc_final: 0.7188 (t80) REVERT: B 265 PHE cc_start: 0.7380 (m-80) cc_final: 0.6593 (m-80) REVERT: B 350 ARG cc_start: 0.7494 (mtm-85) cc_final: 0.7081 (mtm-85) REVERT: B 360 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 598 ILE cc_start: 0.7537 (mm) cc_final: 0.7287 (mp) REVERT: B 604 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: B 638 LEU cc_start: 0.4733 (OUTLIER) cc_final: 0.4341 (pp) REVERT: B 667 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7173 (mm-30) REVERT: B 973 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7703 (mtmt) REVERT: B 1003 THR cc_start: 0.7254 (p) cc_final: 0.6917 (t) REVERT: B 1020 PHE cc_start: 0.7936 (m-80) cc_final: 0.7519 (m-80) REVERT: B 1096 LEU cc_start: 0.7848 (mp) cc_final: 0.7594 (mp) REVERT: B 1230 ASP cc_start: 0.7921 (t70) cc_final: 0.7640 (m-30) REVERT: B 1250 LYS cc_start: 0.8207 (mttt) cc_final: 0.7636 (mttp) REVERT: B 1255 GLU cc_start: 0.7816 (tt0) cc_final: 0.7359 (tm-30) REVERT: B 1383 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8382 (ttpt) REVERT: B 1414 THR cc_start: 0.7860 (p) cc_final: 0.7375 (t) REVERT: B 1429 ILE cc_start: 0.8105 (tp) cc_final: 0.7650 (mt) REVERT: G 34 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7890 (mtmm) REVERT: G 59 LYS cc_start: 0.7362 (mmtp) cc_final: 0.7117 (mmtp) REVERT: G 130 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8090 (ptmm) REVERT: H 35 LYS cc_start: 0.8617 (mptt) cc_final: 0.8287 (mmtm) outliers start: 49 outliers final: 26 residues processed: 418 average time/residue: 0.6965 time to fit residues: 340.8959 Evaluate side-chains 413 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 378 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1184 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1383 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 270 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 285 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 chunk 264 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1152 ASN A1425 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1401 GLN H 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.192784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148462 restraints weight = 94507.401| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.80 r_work: 0.3637 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29818 Z= 0.148 Angle : 0.609 17.230 41536 Z= 0.337 Chirality : 0.042 0.386 4720 Planarity : 0.004 0.055 4216 Dihedral : 18.490 121.873 7064 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.29 % Allowed : 19.24 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.15), residues: 2682 helix: 0.89 (0.15), residues: 1110 sheet: -0.32 (0.30), residues: 288 loop : -1.16 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 364 TYR 0.022 0.001 TYR B 648 PHE 0.033 0.002 PHE B 101 TRP 0.031 0.002 TRP B 593 HIS 0.007 0.001 HIS B1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (29818) covalent geometry : angle 0.60920 / 0.34 (41536) hydrogen bonds : bond 0.04572 / 3.19 ( 1250) hydrogen bonds : angle 4.16349 / 2.96 ( 3239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 388 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6587 (tpp) cc_final: 0.6121 (tpp) REVERT: A 119 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6796 (ptpp) REVERT: A 164 SER cc_start: 0.8609 (m) cc_final: 0.8376 (p) REVERT: A 248 GLU cc_start: 0.7164 (pm20) cc_final: 0.6661 (pm20) REVERT: A 265 PHE cc_start: 0.7193 (m-80) cc_final: 0.6630 (m-80) REVERT: A 317 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6911 (mm-30) REVERT: A 460 PHE cc_start: 0.7452 (t80) cc_final: 0.7196 (t80) REVERT: A 467 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6806 (tmmt) REVERT: A 545 LYS cc_start: 0.7949 (mttm) cc_final: 0.7672 (mttm) REVERT: A 671 LYS cc_start: 0.8445 (tmtp) cc_final: 0.8223 (tttm) REVERT: A 973 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7614 (mtmt) REVERT: A 1071 MET cc_start: 0.6591 (mtp) cc_final: 0.6123 (mtp) REVERT: A 1250 LYS cc_start: 0.7857 (mttt) cc_final: 0.7472 (mttm) REVERT: A 1254 PHE cc_start: 0.8131 (p90) cc_final: 0.7915 (p90) REVERT: A 1255 GLU cc_start: 0.7909 (tt0) cc_final: 0.7409 (tm-30) REVERT: A 1269 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7809 (pttp) REVERT: A 1295 TYR cc_start: 0.7767 (m-80) cc_final: 0.7230 (m-80) REVERT: A 1298 ILE cc_start: 0.8440 (mm) cc_final: 0.8230 (mp) REVERT: A 1378 ILE cc_start: 0.8314 (mt) cc_final: 0.8107 (mm) REVERT: A 1383 LYS cc_start: 0.8390 (tmmt) cc_final: 0.7821 (tttm) REVERT: A 1413 ASP cc_start: 0.7599 (p0) cc_final: 0.6912 (p0) REVERT: A 1440 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 101 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5633 (m-10) REVERT: B 141 LYS cc_start: 0.7832 (tmmm) cc_final: 0.7576 (tmmm) REVERT: B 164 SER cc_start: 0.8654 (m) cc_final: 0.8427 (p) REVERT: B 182 LYS cc_start: 0.7616 (tttm) cc_final: 0.7383 (tttt) REVERT: B 200 THR cc_start: 0.7028 (m) cc_final: 0.6769 (t) REVERT: B 241 ASP cc_start: 0.7683 (p0) cc_final: 0.7460 (p0) REVERT: B 265 PHE cc_start: 0.7409 (m-80) cc_final: 0.6638 (m-80) REVERT: B 350 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6963 (mtm-85) REVERT: B 360 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 598 ILE cc_start: 0.7522 (mm) cc_final: 0.7254 (mp) REVERT: B 604 GLU cc_start: 0.7989 (pt0) cc_final: 0.7559 (pp20) REVERT: B 973 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7710 (mtmt) REVERT: B 1003 THR cc_start: 0.7253 (p) cc_final: 0.6926 (t) REVERT: B 1020 PHE cc_start: 0.7846 (m-80) cc_final: 0.7445 (m-80) REVERT: B 1096 LEU cc_start: 0.7884 (mp) cc_final: 0.7615 (mp) REVERT: B 1250 LYS cc_start: 0.8170 (mttt) cc_final: 0.7464 (mttp) REVERT: B 1255 GLU cc_start: 0.7858 (tt0) cc_final: 0.7360 (tm-30) REVERT: B 1383 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8470 (ttpt) REVERT: B 1404 MET cc_start: 0.8221 (ptp) cc_final: 0.7990 (ptp) REVERT: B 1413 ASP cc_start: 0.7624 (p0) cc_final: 0.7153 (p0) REVERT: B 1414 THR cc_start: 0.7830 (p) cc_final: 0.7176 (t) REVERT: B 1429 ILE cc_start: 0.8091 (tp) cc_final: 0.7644 (mt) REVERT: G 34 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7872 (mtmm) REVERT: G 59 LYS cc_start: 0.7404 (mmtp) cc_final: 0.7152 (mmtp) REVERT: H 35 LYS cc_start: 0.8652 (mptt) cc_final: 0.8325 (mmtm) outliers start: 32 outliers final: 22 residues processed: 405 average time/residue: 0.6843 time to fit residues: 325.0102 Evaluate side-chains 410 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 383 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1184 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1383 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 222 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 279 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 28 optimal weight: 0.0000 chunk 169 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.193185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149666 restraints weight = 86274.828| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.59 r_work: 0.3660 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29818 Z= 0.140 Angle : 0.614 17.753 41536 Z= 0.337 Chirality : 0.041 0.392 4720 Planarity : 0.004 0.079 4216 Dihedral : 18.442 122.059 7064 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 1.29 % Allowed : 19.84 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.16), residues: 2682 helix: 0.97 (0.15), residues: 1110 sheet: -0.32 (0.30), residues: 288 loop : -1.10 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 364 TYR 0.020 0.001 TYR B 648 PHE 0.030 0.001 PHE B 101 TRP 0.047 0.002 TRP A 593 HIS 0.004 0.001 HIS A 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (29818) covalent geometry : angle 0.61446 / 0.34 (41536) hydrogen bonds : bond 0.04389 / 3.06 ( 1250) hydrogen bonds : angle 4.13191 / 2.94 ( 3239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 388 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6496 (tpp) cc_final: 0.6045 (tpp) REVERT: A 164 SER cc_start: 0.8604 (m) cc_final: 0.8323 (p) REVERT: A 248 GLU cc_start: 0.7142 (pm20) cc_final: 0.6579 (pm20) REVERT: A 265 PHE cc_start: 0.7219 (m-80) cc_final: 0.6641 (m-80) REVERT: A 317 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 460 PHE cc_start: 0.7443 (t80) cc_final: 0.7191 (t80) REVERT: A 467 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6760 (tmmt) REVERT: A 545 LYS cc_start: 0.7908 (mttm) cc_final: 0.7627 (mttm) REVERT: A 671 LYS cc_start: 0.8436 (tmtp) cc_final: 0.8207 (tttm) REVERT: A 973 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7492 (mtmm) REVERT: A 1071 MET cc_start: 0.6537 (mtp) cc_final: 0.6074 (mtp) REVERT: A 1250 LYS cc_start: 0.7863 (mttt) cc_final: 0.7476 (mttm) REVERT: A 1254 PHE cc_start: 0.8125 (p90) cc_final: 0.7887 (p90) REVERT: A 1255 GLU cc_start: 0.7867 (tt0) cc_final: 0.7372 (tm-30) REVERT: A 1269 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7768 (pttp) REVERT: A 1295 TYR cc_start: 0.7733 (m-80) cc_final: 0.7267 (m-80) REVERT: A 1298 ILE cc_start: 0.8437 (mm) cc_final: 0.8222 (mp) REVERT: A 1309 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7264 (mt0) REVERT: A 1323 ARG cc_start: 0.7232 (ttp80) cc_final: 0.6741 (ttt-90) REVERT: A 1378 ILE cc_start: 0.8317 (mt) cc_final: 0.8093 (mm) REVERT: A 1383 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8039 (tttm) REVERT: A 1413 ASP cc_start: 0.7556 (p0) cc_final: 0.6912 (p0) REVERT: A 1440 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 101 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5401 (m-80) REVERT: B 141 LYS cc_start: 0.7816 (tmmm) cc_final: 0.7578 (tmmm) REVERT: B 200 THR cc_start: 0.6998 (m) cc_final: 0.6748 (t) REVERT: B 241 ASP cc_start: 0.7756 (p0) cc_final: 0.7504 (p0) REVERT: B 265 PHE cc_start: 0.7417 (m-80) cc_final: 0.6633 (m-80) REVERT: B 350 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.6992 (mtm-85) REVERT: B 360 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 598 ILE cc_start: 0.7483 (mm) cc_final: 0.7202 (mp) REVERT: B 604 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7556 (pp20) REVERT: B 973 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7717 (mtmt) REVERT: B 1003 THR cc_start: 0.7259 (p) cc_final: 0.6929 (t) REVERT: B 1020 PHE cc_start: 0.7811 (m-80) cc_final: 0.7379 (m-80) REVERT: B 1096 LEU cc_start: 0.7858 (mp) cc_final: 0.7587 (mp) REVERT: B 1250 LYS cc_start: 0.8158 (mttt) cc_final: 0.7442 (mttp) REVERT: B 1255 GLU cc_start: 0.7853 (tt0) cc_final: 0.7342 (tm-30) REVERT: B 1383 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8443 (ttpt) REVERT: B 1413 ASP cc_start: 0.7628 (p0) cc_final: 0.7132 (p0) REVERT: B 1414 THR cc_start: 0.7778 (p) cc_final: 0.7099 (t) REVERT: B 1429 ILE cc_start: 0.8088 (tp) cc_final: 0.7625 (mt) REVERT: G 34 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7894 (mtmm) REVERT: G 59 LYS cc_start: 0.7400 (mmtp) cc_final: 0.7143 (mmtp) REVERT: H 35 LYS cc_start: 0.8641 (mptt) cc_final: 0.8288 (mmtm) REVERT: H 123 MET cc_start: 0.8236 (ttm) cc_final: 0.7765 (ttt) outliers start: 32 outliers final: 18 residues processed: 407 average time/residue: 0.6578 time to fit residues: 314.3487 Evaluate side-chains 404 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1383 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 9 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 198 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 221 optimal weight: 0.6980 chunk 291 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1309 GLN H 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.192951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151299 restraints weight = 59921.831| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.95 r_work: 0.3699 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29818 Z= 0.152 Angle : 0.621 16.692 41536 Z= 0.340 Chirality : 0.042 0.383 4720 Planarity : 0.004 0.076 4216 Dihedral : 18.432 121.767 7064 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 1.08 % Allowed : 20.16 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.16), residues: 2682 helix: 0.97 (0.15), residues: 1110 sheet: -0.30 (0.30), residues: 288 loop : -1.08 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 364 TYR 0.021 0.001 TYR B 648 PHE 0.030 0.002 PHE B 226 TRP 0.052 0.002 TRP B 593 HIS 0.004 0.001 HIS A 529 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (29818) covalent geometry : angle 0.62117 / 0.34 (41536) hydrogen bonds : bond 0.04432 / 3.10 ( 1250) hydrogen bonds : angle 4.14047 / 2.95 ( 3239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5364 Ramachandran restraints generated. 2682 Oldfield, 0 Emsley, 2682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 385 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6461 (tpp) cc_final: 0.6028 (tpp) REVERT: A 164 SER cc_start: 0.8600 (m) cc_final: 0.8374 (p) REVERT: A 248 GLU cc_start: 0.7069 (pm20) cc_final: 0.6547 (pm20) REVERT: A 265 PHE cc_start: 0.7258 (m-80) cc_final: 0.6698 (m-80) REVERT: A 317 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6750 (mm-30) REVERT: A 460 PHE cc_start: 0.7409 (t80) cc_final: 0.7159 (t80) REVERT: A 467 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6832 (tmmt) REVERT: A 545 LYS cc_start: 0.7906 (mttm) cc_final: 0.7618 (mttm) REVERT: A 671 LYS cc_start: 0.8408 (tmtp) cc_final: 0.8176 (tttm) REVERT: A 973 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7540 (mtmt) REVERT: A 1071 MET cc_start: 0.6431 (mtp) cc_final: 0.5992 (mtp) REVERT: A 1250 LYS cc_start: 0.7848 (mttt) cc_final: 0.7385 (mttm) REVERT: A 1254 PHE cc_start: 0.8071 (p90) cc_final: 0.7835 (p90) REVERT: A 1255 GLU cc_start: 0.7797 (tt0) cc_final: 0.7370 (tm-30) REVERT: A 1269 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7744 (pttp) REVERT: A 1295 TYR cc_start: 0.7735 (m-80) cc_final: 0.7221 (m-80) REVERT: A 1298 ILE cc_start: 0.8432 (mm) cc_final: 0.8222 (mp) REVERT: A 1309 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7241 (mt0) REVERT: A 1378 ILE cc_start: 0.8306 (mt) cc_final: 0.8081 (mm) REVERT: A 1383 LYS cc_start: 0.8391 (tmmt) cc_final: 0.8065 (tttm) REVERT: A 1413 ASP cc_start: 0.7485 (p0) cc_final: 0.6865 (p0) REVERT: A 1440 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: B 101 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.5394 (m-10) REVERT: B 141 LYS cc_start: 0.7793 (tmmm) cc_final: 0.7575 (tmmm) REVERT: B 200 THR cc_start: 0.7017 (m) cc_final: 0.6791 (t) REVERT: B 226 PHE cc_start: 0.7468 (m-10) cc_final: 0.7072 (m-10) REVERT: B 241 ASP cc_start: 0.7697 (p0) cc_final: 0.7373 (p0) REVERT: B 265 PHE cc_start: 0.7419 (m-80) cc_final: 0.6632 (m-80) REVERT: B 349 ILE cc_start: 0.8085 (tp) cc_final: 0.7489 (pp) REVERT: B 425 PHE cc_start: 0.8139 (t80) cc_final: 0.7906 (t80) REVERT: B 598 ILE cc_start: 0.7494 (mm) cc_final: 0.7198 (mp) REVERT: B 604 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: B 973 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7715 (mtmt) REVERT: B 1003 THR cc_start: 0.7215 (p) cc_final: 0.6915 (t) REVERT: B 1020 PHE cc_start: 0.7840 (m-80) cc_final: 0.7387 (m-80) REVERT: B 1096 LEU cc_start: 0.7901 (mp) cc_final: 0.7650 (mp) REVERT: B 1230 ASP cc_start: 0.7753 (t70) cc_final: 0.7529 (m-30) REVERT: B 1250 LYS cc_start: 0.8148 (mttt) cc_final: 0.7414 (mttp) REVERT: B 1255 GLU cc_start: 0.7792 (tt0) cc_final: 0.7339 (tm-30) REVERT: B 1383 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: B 1413 ASP cc_start: 0.7579 (p0) cc_final: 0.7077 (p0) REVERT: B 1414 THR cc_start: 0.7755 (p) cc_final: 0.7067 (t) REVERT: B 1429 ILE cc_start: 0.8033 (tp) cc_final: 0.7593 (mt) REVERT: G 34 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7826 (mtmm) REVERT: G 59 LYS cc_start: 0.7302 (mmtp) cc_final: 0.7052 (mmtp) REVERT: H 35 LYS cc_start: 0.8613 (mptt) cc_final: 0.8268 (mmtm) REVERT: H 123 MET cc_start: 0.8187 (ttm) cc_final: 0.7754 (ttt) REVERT: H 130 LYS cc_start: 0.8274 (ttpm) cc_final: 0.8047 (ptmm) outliers start: 27 outliers final: 19 residues processed: 401 average time/residue: 0.6674 time to fit residues: 314.7836 Evaluate side-chains 403 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 379 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1369 THR Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain A residue 1440 GLU Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1346 ASN Chi-restraints excluded: chain B residue 1369 THR Chi-restraints excluded: chain B residue 1383 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 174 optimal weight: 0.0270 chunk 260 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 chunk 175 optimal weight: 0.2980 chunk 142 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1031 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151088 restraints weight = 70930.336| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.24 r_work: 0.3688 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29818 Z= 0.142 Angle : 0.613 16.338 41536 Z= 0.336 Chirality : 0.041 0.392 4720 Planarity : 0.004 0.072 4216 Dihedral : 18.408 122.187 7064 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 1.08 % Allowed : 20.48 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.16), residues: 2682 helix: 0.99 (0.15), residues: 1110 sheet: -0.29 (0.30), residues: 292 loop : -1.04 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 104 TYR 0.019 0.001 TYR B 648 PHE 0.027 0.001 PHE B 101 TRP 0.045 0.002 TRP B 593 HIS 0.006 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (29818) covalent geometry : angle 0.61307 / 0.34 (41536) hydrogen bonds : bond 0.04305 / 3.02 ( 1250) hydrogen bonds : angle 4.10753 / 2.93 ( 3239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11913.91 seconds wall clock time: 203 minutes 29.62 seconds (12209.62 seconds total)