Starting phenix.real_space_refine on Tue Jun 24 12:34:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_37656_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_37656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_37656.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_37656_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmm_37656/06_2025/8wmm_37656_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 25.78, per 1000 atoms: 0.90 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: 7.16 Conformation dependent library (CDL) restraints added in 4.9 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: 11.44 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: 16.84 Time building geometry restraints manager: 8.47 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: 41032 2.00 - 4.00: 462 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: 3523 0.036 - 0.071: 835 0.071 - 0.107: 268 0.107 - 0.143: 82 0.143 - 0.179: 12 Chirality restraints: 4720 Sorted by residual: 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' G O 15 " pdb=" C4' G O 15 " pdb=" O3' G O 15 " pdb=" C2' G O 15 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" C3' G D 106 " pdb=" C4' G D 106 " pdb=" O3' G D 106 " pdb=" C2' G D 106 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.02e-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: 0.00 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 88.350 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.180 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:14.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 : 0.003 0.100 29818 Z= 0.180 Angle : 0.556 9.998 41536 Z= 0.337 Chirality : 0.038 0.179 4720 Planarity : 0.003 0.066 4216 Dihedral : 17.959 120.247 12914 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (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 TRP 0.028 0.001 TRP B 487 HIS 0.005 0.001 HIS B 651 PHE 0.022 0.001 PHE A1441 TYR 0.039 0.001 TYR A 645 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.13238 ( 1250) hydrogen bonds : angle 5.32880 ( 3239) covalent geometry : bond 0.00330 (29818) covalent geometry : angle 0.55605 (41536) *********************** 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 : 3.534 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: 0.8184 (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: 0.7620 (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: 0.6581 (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: 0.7592 (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: 0.7434 (p90) REVERT: A 1255 GLU cc_start: 0.7233 (tt0) cc_final: 0.6445 (tm-30) REVERT: A 1269 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7316 (pttp) REVERT: A 1298 ILE cc_start: 0.8271 (mm) cc_final: 0.8056 (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: 0.7110 (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: 0.6845 (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: 0.8124 (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: 0.5623 (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: 0.6814 (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: 0.8167 (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: 0.6539 (tp30) 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: 0.7227 (mm) REVERT: B 1383 LYS cc_start: 0.7873 (tttm) cc_final: 0.7575 (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: 0.7396 (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: 1.4572 time to fit residues: 837.9594 Evaluate side-chains 390 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 388 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 248 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 464 ASN 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 B 617 ASN B1010 GLN B1108 HIS B1152 ASN B1397 GLN B1425 ASN G 84 ASN H 84 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.194075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149173 restraints weight = 89113.200| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.69 r_work: 0.3653 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 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 = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29818 Z= 0.190 Angle : 0.603 8.920 41536 Z= 0.328 Chirality : 0.041 0.248 4720 Planarity : 0.004 0.041 4216 Dihedral : 18.591 139.610 7067 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.57 % Allowed : 8.96 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2682 helix: 1.14 (0.15), residues: 1110 sheet: -0.23 (0.31), residues: 288 loop : -0.81 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 487 HIS 0.007 0.001 HIS A1031 PHE 0.037 0.002 PHE A 489 TYR 0.034 0.002 TYR A 645 ARG 0.007 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 1250) hydrogen bonds : angle 4.22055 ( 3239) covalent geometry : bond 0.00422 (29818) covalent geometry : angle 0.60345 (41536) *********************** 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 464 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 425 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8294 (mp) cc_final: 0.8060 (tt) REVERT: A 107 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7327 (mttt) REVERT: A 149 ILE cc_start: 0.7387 (pt) cc_final: 0.7142 (mt) REVERT: A 164 SER cc_start: 0.8684 (p) cc_final: 0.8465 (m) REVERT: A 248 GLU cc_start: 0.7175 (pm20) cc_final: 0.6649 (pm20) REVERT: A 265 PHE cc_start: 0.6807 (m-80) cc_final: 0.6307 (m-80) REVERT: A 545 LYS cc_start: 0.8028 (mttm) cc_final: 0.7748 (mttm) REVERT: A 593 TRP cc_start: 0.6927 (t60) cc_final: 0.6721 (t60) REVERT: A 604 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7779 (pt0) REVERT: A 686 VAL cc_start: 0.7824 (t) cc_final: 0.7624 (t) REVERT: A 697 ILE cc_start: 0.8655 (mt) cc_final: 0.8427 (mt) REVERT: A 957 ASN cc_start: 0.7442 (p0) cc_final: 0.7235 (p0) REVERT: A 973 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7517 (mtmm) REVERT: A 990 PHE cc_start: 0.7677 (m-80) cc_final: 0.7470 (m-80) REVERT: A 1071 MET cc_start: 0.6643 (mtp) cc_final: 0.6273 (mtp) REVERT: A 1105 ASP cc_start: 0.7578 (m-30) cc_final: 0.7308 (m-30) REVERT: A 1250 LYS cc_start: 0.7908 (mttt) cc_final: 0.7399 (mttm) REVERT: A 1254 PHE cc_start: 0.8074 (p90) cc_final: 0.7869 (p90) REVERT: A 1255 GLU cc_start: 0.7756 (tt0) cc_final: 0.7242 (tm-30) REVERT: A 1269 LYS cc_start: 0.7983 (ptpp) cc_final: 0.7768 (pttp) REVERT: A 1298 ILE cc_start: 0.8591 (mm) cc_final: 0.8311 (mm) REVERT: A 1378 ILE cc_start: 0.8087 (mt) cc_final: 0.7756 (mp) REVERT: B 15 ILE cc_start: 0.8348 (mp) cc_final: 0.7992 (tt) REVERT: B 119 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6873 (ptpp) REVERT: B 136 MET cc_start: 0.7432 (ttm) cc_final: 0.7162 (ttp) REVERT: B 200 THR cc_start: 0.6871 (m) cc_final: 0.6540 (t) REVERT: B 250 ILE cc_start: 0.7194 (mt) cc_final: 0.6951 (tp) REVERT: B 280 LYS cc_start: 0.8385 (tttt) cc_final: 0.7944 (ttpt) REVERT: B 317 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7118 (mm-30) REVERT: B 495 TYR cc_start: 0.7446 (m-10) cc_final: 0.6906 (m-10) REVERT: B 499 GLU cc_start: 0.6336 (pt0) cc_final: 0.6118 (mt-10) REVERT: B 597 GLU cc_start: 0.3909 (OUTLIER) cc_final: 0.3680 (mp0) REVERT: B 667 GLU cc_start: 0.7629 (pp20) cc_final: 0.7236 (pp20) REVERT: B 1003 THR cc_start: 0.7195 (p) cc_final: 0.6914 (t) REVERT: B 1020 PHE cc_start: 0.7865 (m-80) cc_final: 0.7442 (m-80) REVERT: B 1096 LEU cc_start: 0.7860 (mp) cc_final: 0.7647 (mp) REVERT: B 1235 ASN cc_start: 0.7044 (m110) cc_final: 0.6793 (m110) REVERT: B 1250 LYS cc_start: 0.8200 (mttt) cc_final: 0.7569 (mttp) REVERT: B 1255 GLU cc_start: 0.7798 (tt0) cc_final: 0.7531 (mm-30) REVERT: B 1298 ILE cc_start: 0.8688 (mm) cc_final: 0.8452 (mm) REVERT: B 1323 ARG cc_start: 0.7150 (ptm-80) cc_final: 0.6943 (ptt-90) REVERT: B 1369 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7397 (p) REVERT: B 1413 ASP cc_start: 0.7673 (p0) cc_final: 0.6851 (m-30) REVERT: B 1414 THR cc_start: 0.7834 (p) cc_final: 0.6843 (t) REVERT: B 1429 ILE cc_start: 0.8054 (tp) cc_final: 0.7715 (mt) REVERT: G 34 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7939 (mtmm) REVERT: G 35 LYS cc_start: 0.8684 (mptt) cc_final: 0.8477 (mmtm) REVERT: H 35 LYS cc_start: 0.8622 (mptt) cc_final: 0.8262 (mmtm) REVERT: H 51 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: H 128 LYS cc_start: 0.8385 (mttp) cc_final: 0.7974 (mtmm) outliers start: 39 outliers final: 12 residues processed: 443 average time/residue: 1.7469 time to fit residues: 907.3649 Evaluate side-chains 397 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 380 time to evaluate : 2.838 ------------------------------------------------------------------------------- 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 1194 LEU Chi-restraints excluded: chain A residue 1281 LEU 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 597 GLU 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 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 H residue 51 GLU 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 5 optimal weight: 0.5980 chunk 80 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 237 optimal weight: 0.4980 chunk 201 optimal weight: 0.0060 chunk 151 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B1152 ASN B1425 ASN B1436 GLN H 19 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.194990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150803 restraints weight = 81568.071| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.54 r_work: 0.3680 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29818 Z= 0.140 Angle : 0.559 8.027 41536 Z= 0.305 Chirality : 0.039 0.251 4720 Planarity : 0.004 0.043 4216 Dihedral : 18.404 117.721 7064 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.69 % Allowed : 12.09 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2682 helix: 1.25 (0.16), residues: 1108 sheet: -0.09 (0.30), residues: 288 loop : -0.80 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 660 HIS 0.023 0.001 HIS B1108 PHE 0.032 0.002 PHE B 101 TYR 0.030 0.002 TYR A 645 ARG 0.011 0.001 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 1250) hydrogen bonds : angle 3.99365 ( 3239) covalent geometry : bond 0.00306 (29818) covalent geometry : angle 0.55901 (41536) *********************** 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 449 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 407 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7350 (mttt) REVERT: A 119 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6831 (ptpp) REVERT: A 149 ILE cc_start: 0.7418 (pt) cc_final: 0.7216 (mt) REVERT: A 164 SER cc_start: 0.8614 (p) cc_final: 0.8367 (m) REVERT: A 248 GLU cc_start: 0.7113 (pm20) cc_final: 0.6607 (pm20) REVERT: A 265 PHE cc_start: 0.6906 (m-80) cc_final: 0.6391 (m-80) REVERT: A 467 LYS cc_start: 0.7226 (ptpt) cc_final: 0.6594 (tmmt) REVERT: A 545 LYS cc_start: 0.7940 (mttm) cc_final: 0.7654 (mttm) REVERT: A 587 MET cc_start: 0.4963 (mtm) cc_final: 0.4539 (mtm) REVERT: A 597 GLU cc_start: 0.3957 (OUTLIER) cc_final: 0.3695 (mp0) REVERT: A 598 ILE cc_start: 0.7134 (mp) cc_final: 0.6828 (mm) REVERT: A 686 VAL cc_start: 0.7759 (t) cc_final: 0.7554 (t) REVERT: A 697 ILE cc_start: 0.8583 (mt) cc_final: 0.8345 (mt) REVERT: A 973 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7435 (mtmm) REVERT: A 991 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 1071 MET cc_start: 0.6561 (mtp) cc_final: 0.6121 (mtp) REVERT: A 1250 LYS cc_start: 0.7891 (mttt) cc_final: 0.7384 (mttm) REVERT: A 1254 PHE cc_start: 0.8105 (p90) cc_final: 0.7878 (p90) REVERT: A 1255 GLU cc_start: 0.7802 (tt0) cc_final: 0.7234 (tp30) REVERT: A 1269 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7732 (pttp) REVERT: A 1298 ILE cc_start: 0.8546 (mm) cc_final: 0.8284 (mm) REVERT: A 1378 ILE cc_start: 0.8033 (mt) cc_final: 0.7789 (mp) REVERT: B 119 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6840 (ptpp) REVERT: B 128 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 136 MET cc_start: 0.7471 (ttm) cc_final: 0.7230 (ttp) REVERT: B 200 THR cc_start: 0.6877 (m) cc_final: 0.6559 (t) REVERT: B 232 TYR cc_start: 0.8350 (t80) cc_final: 0.7301 (t80) REVERT: B 495 TYR cc_start: 0.7080 (m-10) cc_final: 0.6765 (m-10) REVERT: B 499 GLU cc_start: 0.6466 (pt0) cc_final: 0.6086 (mt-10) REVERT: B 593 TRP cc_start: 0.6950 (t60) cc_final: 0.6679 (t60) REVERT: B 959 LYS cc_start: 0.7963 (ptmm) cc_final: 0.7743 (ptmm) REVERT: B 973 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7549 (mtmm) REVERT: B 1003 THR cc_start: 0.7195 (p) cc_final: 0.6911 (t) REVERT: B 1020 PHE cc_start: 0.7786 (m-80) cc_final: 0.7379 (m-80) REVERT: B 1039 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7650 (tt) REVERT: B 1096 LEU cc_start: 0.7816 (mp) cc_final: 0.7589 (mp) REVERT: B 1132 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: B 1235 ASN cc_start: 0.6924 (m110) cc_final: 0.6614 (m110) REVERT: B 1250 LYS cc_start: 0.8176 (mttt) cc_final: 0.7651 (mttp) REVERT: B 1255 GLU cc_start: 0.7800 (tt0) cc_final: 0.7329 (tm-30) REVERT: B 1298 ILE cc_start: 0.8583 (mm) cc_final: 0.8372 (mm) REVERT: B 1323 ARG cc_start: 0.7158 (ptm-80) cc_final: 0.6912 (ptt-90) REVERT: B 1369 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7183 (p) REVERT: B 1414 THR cc_start: 0.7792 (p) cc_final: 0.7321 (t) REVERT: B 1429 ILE cc_start: 0.8060 (tp) cc_final: 0.7704 (mt) REVERT: G 35 LYS cc_start: 0.8700 (mptt) cc_final: 0.8477 (mmtm) REVERT: H 35 LYS cc_start: 0.8629 (mptt) cc_final: 0.8281 (mmtm) REVERT: H 51 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: H 128 LYS cc_start: 0.8307 (mttp) cc_final: 0.7870 (mtmm) REVERT: H 130 LYS cc_start: 0.8318 (ttpm) cc_final: 0.8090 (ptmm) outliers start: 42 outliers final: 10 residues processed: 428 average time/residue: 1.8014 time to fit residues: 899.6471 Evaluate side-chains 405 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 386 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 522 ASP Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1132 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 67 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 235 GLN A1152 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B1152 ASN ** B1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.192891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148442 restraints weight = 79375.248| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.50 r_work: 0.3643 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 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 = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29818 Z= 0.190 Angle : 0.591 8.788 41536 Z= 0.321 Chirality : 0.041 0.217 4720 Planarity : 0.004 0.052 4216 Dihedral : 18.400 116.356 7064 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.65 % Allowed : 14.86 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 2682 helix: 1.05 (0.15), residues: 1110 sheet: -0.22 (0.30), residues: 286 loop : -0.94 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 593 HIS 0.005 0.001 HIS A1031 PHE 0.033 0.002 PHE A1020 TYR 0.024 0.002 TYR A 645 ARG 0.013 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 1250) hydrogen bonds : angle 4.07601 ( 3239) covalent geometry : bond 0.00419 (29818) covalent geometry : angle 0.59093 (41536) *********************** 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 450 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 409 time to evaluate : 2.693 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 1 MET cc_start: 0.6533 (tpp) cc_final: 0.6102 (tpp) REVERT: A 164 SER cc_start: 0.8634 (p) cc_final: 0.8429 (m) REVERT: A 248 GLU cc_start: 0.7150 (pm20) cc_final: 0.6627 (pm20) REVERT: A 265 PHE cc_start: 0.7017 (m-80) cc_final: 0.6448 (m-80) REVERT: A 467 LYS cc_start: 0.7300 (ptpt) cc_final: 0.6672 (tmmt) REVERT: A 535 ASN cc_start: 0.7211 (p0) cc_final: 0.7009 (p0) REVERT: A 545 LYS cc_start: 0.7942 (mttm) cc_final: 0.7659 (mttm) REVERT: A 597 GLU cc_start: 0.3890 (OUTLIER) cc_final: 0.3539 (mp0) REVERT: A 598 ILE cc_start: 0.7045 (mp) cc_final: 0.6789 (mm) REVERT: A 697 ILE cc_start: 0.8624 (mt) cc_final: 0.8422 (mt) REVERT: A 973 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7589 (mtmt) REVERT: A 1071 MET cc_start: 0.6516 (mtp) cc_final: 0.6064 (mtp) REVERT: A 1250 LYS cc_start: 0.7873 (mttt) cc_final: 0.7480 (mttm) REVERT: A 1254 PHE cc_start: 0.8129 (p90) cc_final: 0.7877 (p90) REVERT: A 1255 GLU cc_start: 0.7832 (tt0) cc_final: 0.7334 (tm-30) REVERT: A 1269 LYS cc_start: 0.7997 (ptpp) cc_final: 0.7776 (pttp) REVERT: A 1298 ILE cc_start: 0.8504 (mm) cc_final: 0.8278 (mm) REVERT: A 1323 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6781 (ttt-90) REVERT: B 31 ILE cc_start: 0.7546 (mm) cc_final: 0.7338 (mt) REVERT: B 128 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7614 (tt) REVERT: B 200 THR cc_start: 0.6987 (m) cc_final: 0.6738 (t) REVERT: B 232 TYR cc_start: 0.8347 (t80) cc_final: 0.7128 (t80) REVERT: B 499 GLU cc_start: 0.6587 (pt0) cc_final: 0.6225 (mt-10) REVERT: B 593 TRP cc_start: 0.6925 (t60) cc_final: 0.6715 (t60) REVERT: B 598 ILE cc_start: 0.7509 (mm) cc_final: 0.7260 (mp) REVERT: B 667 GLU cc_start: 0.7657 (pp20) cc_final: 0.7416 (pp20) REVERT: B 973 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7692 (mtmt) REVERT: B 1003 THR cc_start: 0.7225 (p) cc_final: 0.6880 (t) REVERT: B 1020 PHE cc_start: 0.7888 (m-80) cc_final: 0.7525 (m-80) REVERT: B 1039 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7755 (tt) REVERT: B 1096 LEU cc_start: 0.7791 (mp) cc_final: 0.7551 (mp) REVERT: B 1250 LYS cc_start: 0.8194 (mttt) cc_final: 0.7751 (mttm) REVERT: B 1255 GLU cc_start: 0.7833 (tt0) cc_final: 0.7321 (tm-30) REVERT: B 1305 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: B 1323 ARG cc_start: 0.7297 (ptm-80) cc_final: 0.7035 (ptt-90) REVERT: B 1414 THR cc_start: 0.7811 (p) cc_final: 0.7321 (t) REVERT: B 1429 ILE cc_start: 0.8066 (tp) cc_final: 0.7668 (mt) REVERT: G 35 LYS cc_start: 0.8723 (mptt) cc_final: 0.8497 (mmtm) REVERT: H 35 LYS cc_start: 0.8621 (mptt) cc_final: 0.8311 (mmtm) REVERT: H 51 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: H 108 LEU cc_start: 0.8208 (mt) cc_final: 0.7999 (mp) REVERT: H 126 ASP cc_start: 0.8013 (t70) cc_final: 0.7775 (t70) REVERT: H 128 LYS cc_start: 0.8356 (mttp) cc_final: 0.7880 (mtmm) REVERT: H 130 LYS cc_start: 0.8435 (ttpm) cc_final: 0.8201 (ptmm) outliers start: 41 outliers final: 15 residues processed: 430 average time/residue: 1.4189 time to fit residues: 711.9602 Evaluate side-chains 408 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 388 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 1039 LEU 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 Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 123 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1152 ASN A1280 ASN ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 ASN B 145 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1152 ASN ** B1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1401 GLN B1436 GLN H 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.190991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148017 restraints weight = 68135.611| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.17 r_work: 0.3648 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 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 = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29818 Z= 0.222 Angle : 0.620 8.864 41536 Z= 0.336 Chirality : 0.042 0.221 4720 Planarity : 0.004 0.058 4216 Dihedral : 18.456 116.243 7064 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.85 % Allowed : 16.59 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2682 helix: 0.88 (0.15), residues: 1114 sheet: -0.31 (0.30), residues: 286 loop : -1.06 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 593 HIS 0.006 0.001 HIS A1031 PHE 0.034 0.002 PHE B 101 TYR 0.021 0.002 TYR A 645 ARG 0.016 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 1250) hydrogen bonds : angle 4.12180 ( 3239) covalent geometry : bond 0.00490 (29818) covalent geometry : angle 0.62016 (41536) *********************** 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 450 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 404 time to evaluate : 2.506 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 1 MET cc_start: 0.6540 (tpp) cc_final: 0.6092 (tpp) REVERT: A 21 LYS cc_start: 0.7314 (ttpp) cc_final: 0.7081 (ttmm) REVERT: A 164 SER cc_start: 0.8605 (p) cc_final: 0.8404 (m) REVERT: A 248 GLU cc_start: 0.7104 (pm20) cc_final: 0.6578 (pm20) REVERT: A 265 PHE cc_start: 0.7112 (m-80) cc_final: 0.6543 (m-80) REVERT: A 460 PHE cc_start: 0.7438 (t80) cc_final: 0.7206 (t80) REVERT: A 467 LYS cc_start: 0.7417 (ptpt) cc_final: 0.6771 (tmmt) REVERT: A 526 LYS cc_start: 0.7295 (mmtp) cc_final: 0.6808 (tptt) REVERT: A 545 LYS cc_start: 0.7970 (mttm) cc_final: 0.7680 (mttm) REVERT: A 597 GLU cc_start: 0.3864 (OUTLIER) cc_final: 0.3596 (mp0) REVERT: A 598 ILE cc_start: 0.7137 (mp) cc_final: 0.6883 (mm) REVERT: A 973 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7616 (mtmt) REVERT: A 1071 MET cc_start: 0.6447 (mtp) cc_final: 0.6029 (mtp) REVERT: A 1250 LYS cc_start: 0.7867 (mttt) cc_final: 0.7421 (mttm) REVERT: A 1254 PHE cc_start: 0.8126 (p90) cc_final: 0.7871 (p90) REVERT: A 1255 GLU cc_start: 0.7797 (tt0) cc_final: 0.7396 (tm-30) REVERT: A 1269 LYS cc_start: 0.8002 (ptpp) cc_final: 0.7788 (pttp) REVERT: A 1295 TYR cc_start: 0.7664 (m-80) cc_final: 0.7241 (m-80) REVERT: A 1298 ILE cc_start: 0.8479 (mm) cc_final: 0.8272 (mp) REVERT: A 1383 LYS cc_start: 0.8364 (tmmt) cc_final: 0.7823 (tttp) REVERT: B 101 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: B 119 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.7049 (ptpp) REVERT: B 141 LYS cc_start: 0.7807 (tmmm) cc_final: 0.7533 (tmmm) REVERT: B 200 THR cc_start: 0.6994 (m) cc_final: 0.6776 (t) REVERT: B 232 TYR cc_start: 0.8378 (t80) cc_final: 0.7144 (t80) REVERT: B 265 PHE cc_start: 0.7369 (m-80) cc_final: 0.6591 (m-80) REVERT: B 350 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: B 468 GLU cc_start: 0.6795 (tp30) cc_final: 0.6559 (tp30) REVERT: B 499 GLU cc_start: 0.6536 (pt0) cc_final: 0.6280 (mt-10) REVERT: B 598 ILE cc_start: 0.7524 (mm) cc_final: 0.7278 (mp) REVERT: B 604 GLU cc_start: 0.8049 (pt0) cc_final: 0.7636 (pp20) REVERT: B 1003 THR cc_start: 0.7207 (p) cc_final: 0.6894 (t) REVERT: B 1020 PHE cc_start: 0.7917 (m-80) cc_final: 0.7525 (m-80) REVERT: B 1039 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 1230 ASP cc_start: 0.7855 (t70) cc_final: 0.7607 (m-30) REVERT: B 1250 LYS cc_start: 0.8199 (mttt) cc_final: 0.7779 (mttm) REVERT: B 1255 GLU cc_start: 0.7788 (tt0) cc_final: 0.7328 (tm-30) REVERT: B 1305 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: B 1378 ILE cc_start: 0.8518 (mp) cc_final: 0.8307 (mm) REVERT: B 1413 ASP cc_start: 0.7628 (p0) cc_final: 0.7179 (p0) REVERT: B 1414 THR cc_start: 0.7782 (p) cc_final: 0.7171 (t) REVERT: B 1429 ILE cc_start: 0.8088 (tp) cc_final: 0.7658 (mt) REVERT: G 130 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8083 (ptmm) REVERT: H 35 LYS cc_start: 0.8603 (mptt) cc_final: 0.8283 (mmtm) REVERT: H 51 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: H 130 LYS cc_start: 0.8436 (ttpm) cc_final: 0.8196 (ptmm) outliers start: 46 outliers final: 23 residues processed: 430 average time/residue: 1.4603 time to fit residues: 733.0036 Evaluate side-chains 419 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 389 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 597 GLU 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 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE 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 412 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1039 LEU 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 B residue 1400 LEU 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 4 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 213 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1425 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** 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 = 0.4337 r_free = 0.4337 target = 0.192118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149313 restraints weight = 71106.164| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.24 r_work: 0.3665 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29818 Z= 0.167 Angle : 0.593 9.195 41536 Z= 0.321 Chirality : 0.040 0.217 4720 Planarity : 0.004 0.057 4216 Dihedral : 18.410 117.480 7064 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.65 % Allowed : 18.15 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2682 helix: 1.01 (0.15), residues: 1114 sheet: -0.27 (0.30), residues: 290 loop : -1.05 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 593 HIS 0.004 0.001 HIS A1031 PHE 0.033 0.002 PHE B 101 TYR 0.019 0.002 TYR A 645 ARG 0.014 0.001 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1250) hydrogen bonds : angle 4.03006 ( 3239) covalent geometry : bond 0.00365 (29818) covalent geometry : angle 0.59307 (41536) *********************** 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 436 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6513 (tpp) cc_final: 0.6049 (tpp) REVERT: A 248 GLU cc_start: 0.7097 (pm20) cc_final: 0.6514 (pm20) REVERT: A 265 PHE cc_start: 0.7201 (m-80) cc_final: 0.6653 (m-80) REVERT: A 317 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6822 (mm-30) REVERT: A 460 PHE cc_start: 0.7428 (t80) cc_final: 0.7206 (t80) REVERT: A 467 LYS cc_start: 0.7372 (ptpt) cc_final: 0.6791 (tmmt) REVERT: A 526 LYS cc_start: 0.7268 (mmtp) cc_final: 0.6798 (tptt) REVERT: A 545 LYS cc_start: 0.7942 (mttm) cc_final: 0.7663 (mttm) REVERT: A 597 GLU cc_start: 0.3870 (OUTLIER) cc_final: 0.3521 (mp0) REVERT: A 598 ILE cc_start: 0.7079 (mp) cc_final: 0.6829 (mm) REVERT: A 604 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7745 (pp20) REVERT: A 973 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7606 (mtmt) REVERT: A 1071 MET cc_start: 0.6424 (mtp) cc_final: 0.6007 (mtp) REVERT: A 1250 LYS cc_start: 0.7836 (mttt) cc_final: 0.7454 (mttm) REVERT: A 1254 PHE cc_start: 0.8148 (p90) cc_final: 0.7881 (p90) REVERT: A 1255 GLU cc_start: 0.7827 (tt0) cc_final: 0.7394 (tm-30) REVERT: A 1269 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7765 (pttp) REVERT: A 1295 TYR cc_start: 0.7700 (m-80) cc_final: 0.7274 (m-80) REVERT: A 1298 ILE cc_start: 0.8462 (mm) cc_final: 0.8259 (mp) REVERT: A 1413 ASP cc_start: 0.7547 (p0) cc_final: 0.6925 (p0) REVERT: B 3 LYS cc_start: 0.7356 (mmtt) cc_final: 0.7113 (mmtm) REVERT: B 101 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: B 141 LYS cc_start: 0.7800 (tmmm) cc_final: 0.7551 (tmmm) REVERT: B 182 LYS cc_start: 0.7647 (tttp) cc_final: 0.7426 (tptt) REVERT: B 200 THR cc_start: 0.7002 (m) cc_final: 0.6739 (t) REVERT: B 241 ASP cc_start: 0.7645 (p0) cc_final: 0.7373 (p0) REVERT: B 265 PHE cc_start: 0.7415 (m-80) cc_final: 0.6636 (m-80) REVERT: B 317 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 499 GLU cc_start: 0.6604 (pt0) cc_final: 0.6333 (mt-10) REVERT: B 598 ILE cc_start: 0.7507 (mm) cc_final: 0.7201 (mp) REVERT: B 604 GLU cc_start: 0.8041 (pt0) cc_final: 0.7618 (pp20) REVERT: B 973 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7683 (mtmt) REVERT: B 1003 THR cc_start: 0.7250 (p) cc_final: 0.6938 (t) REVERT: B 1020 PHE cc_start: 0.7826 (m-80) cc_final: 0.7407 (m-80) REVERT: B 1039 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7722 (tt) REVERT: B 1250 LYS cc_start: 0.8156 (mttt) cc_final: 0.7432 (mttp) REVERT: B 1255 GLU cc_start: 0.7781 (tt0) cc_final: 0.7318 (tm-30) REVERT: B 1378 ILE cc_start: 0.8529 (mp) cc_final: 0.8316 (mm) REVERT: B 1413 ASP cc_start: 0.7623 (p0) cc_final: 0.7129 (p0) REVERT: B 1414 THR cc_start: 0.7791 (p) cc_final: 0.7134 (t) REVERT: B 1429 ILE cc_start: 0.8070 (tp) cc_final: 0.7622 (mt) REVERT: G 130 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8008 (ptmm) REVERT: H 35 LYS cc_start: 0.8605 (mptt) cc_final: 0.8284 (mmtm) REVERT: H 51 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: H 128 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8102 (mtmm) REVERT: H 130 LYS cc_start: 0.8434 (ttpm) cc_final: 0.8189 (ptmm) outliers start: 41 outliers final: 27 residues processed: 416 average time/residue: 1.7482 time to fit residues: 853.7508 Evaluate side-chains 412 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 101 PHE 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 968 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1191 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 B residue 1400 LEU 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 4 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 121 ASN 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 56 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 202 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A1152 ASN A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1031 HIS ** B1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.192658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149557 restraints weight = 74790.261| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.33 r_work: 0.3669 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 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 = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29818 Z= 0.152 Angle : 0.593 11.678 41536 Z= 0.319 Chirality : 0.039 0.305 4720 Planarity : 0.004 0.072 4216 Dihedral : 18.369 117.741 7064 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.63 % Rotamer: Outliers : 1.45 % Allowed : 18.47 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2682 helix: 1.07 (0.15), residues: 1114 sheet: -0.23 (0.30), residues: 286 loop : -1.03 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 593 HIS 0.004 0.001 HIS A 157 PHE 0.030 0.001 PHE B 101 TYR 0.019 0.001 TYR A 645 ARG 0.016 0.001 ARG H 80 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1250) hydrogen bonds : angle 4.01876 ( 3239) covalent geometry : bond 0.00332 (29818) covalent geometry : angle 0.59258 (41536) *********************** 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 429 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 393 time to evaluate : 2.598 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: 0.6469 (tpp) cc_final: 0.6185 (tpp) REVERT: A 248 GLU cc_start: 0.7163 (pm20) cc_final: 0.6564 (pm20) REVERT: A 265 PHE cc_start: 0.7245 (m-80) cc_final: 0.6696 (m-80) REVERT: A 317 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 460 PHE cc_start: 0.7418 (t80) cc_final: 0.7208 (t80) REVERT: A 467 LYS cc_start: 0.7360 (ptpt) cc_final: 0.6719 (tmmt) REVERT: A 526 LYS cc_start: 0.7249 (mmtp) cc_final: 0.6779 (tptt) REVERT: A 545 LYS cc_start: 0.7927 (mttm) cc_final: 0.7637 (mttm) REVERT: A 597 GLU cc_start: 0.3916 (OUTLIER) cc_final: 0.3640 (mp0) REVERT: A 598 ILE cc_start: 0.7058 (mp) cc_final: 0.6815 (mm) REVERT: A 973 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7569 (mtmt) REVERT: A 993 MET cc_start: 0.5984 (tpp) cc_final: 0.5611 (tpp) REVERT: A 1071 MET cc_start: 0.6404 (mtp) cc_final: 0.5985 (mtp) REVERT: A 1250 LYS cc_start: 0.7819 (mttt) cc_final: 0.7099 (mtpt) REVERT: A 1254 PHE cc_start: 0.8143 (p90) cc_final: 0.7923 (p90) REVERT: A 1255 GLU cc_start: 0.7859 (tt0) cc_final: 0.7415 (tm-30) REVERT: A 1269 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7760 (pttp) REVERT: A 1295 TYR cc_start: 0.7710 (m-80) cc_final: 0.7263 (m-80) REVERT: A 1383 LYS cc_start: 0.8414 (tmmt) cc_final: 0.7991 (tttm) REVERT: A 1413 ASP cc_start: 0.7520 (p0) cc_final: 0.6925 (p0) REVERT: B 3 LYS cc_start: 0.7370 (mmtt) cc_final: 0.7099 (mmtm) REVERT: B 101 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5395 (m-80) REVERT: B 141 LYS cc_start: 0.7799 (tmmm) cc_final: 0.7556 (tmmm) REVERT: B 200 THR cc_start: 0.7037 (m) cc_final: 0.6773 (t) REVERT: B 241 ASP cc_start: 0.7657 (p0) cc_final: 0.7360 (p0) REVERT: B 265 PHE cc_start: 0.7458 (m-80) cc_final: 0.6665 (m-80) REVERT: B 317 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 349 ILE cc_start: 0.8027 (tp) cc_final: 0.7414 (pp) REVERT: B 499 GLU cc_start: 0.6654 (pt0) cc_final: 0.6378 (mt-10) REVERT: B 598 ILE cc_start: 0.7481 (mm) cc_final: 0.7177 (mp) REVERT: B 604 GLU cc_start: 0.8047 (pt0) cc_final: 0.7616 (pp20) REVERT: B 667 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6919 (mm-30) REVERT: B 973 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7711 (mtmt) REVERT: B 1003 THR cc_start: 0.7260 (p) cc_final: 0.6955 (t) REVERT: B 1020 PHE cc_start: 0.7819 (m-80) cc_final: 0.7411 (m-80) REVERT: B 1039 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7743 (tt) REVERT: B 1250 LYS cc_start: 0.8138 (mttt) cc_final: 0.7418 (mttp) REVERT: B 1255 GLU cc_start: 0.7813 (tt0) cc_final: 0.7338 (tm-30) REVERT: B 1378 ILE cc_start: 0.8581 (mp) cc_final: 0.8367 (mm) REVERT: B 1413 ASP cc_start: 0.7634 (p0) cc_final: 0.7153 (p0) REVERT: B 1414 THR cc_start: 0.7752 (p) cc_final: 0.7076 (t) REVERT: B 1429 ILE cc_start: 0.8076 (tp) cc_final: 0.7623 (mt) REVERT: H 35 LYS cc_start: 0.8637 (mptt) cc_final: 0.8308 (mmtm) REVERT: H 51 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: H 130 LYS cc_start: 0.8440 (ttpm) cc_final: 0.8232 (ptmm) outliers start: 36 outliers final: 27 residues processed: 414 average time/residue: 1.4542 time to fit residues: 703.3298 Evaluate side-chains 410 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 379 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 149 ILE 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 958 SER Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1182 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 B residue 1400 LEU Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 4 ASP 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 69 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 205 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 chunk 54 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.193165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149535 restraints weight = 86319.417| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.60 r_work: 0.3652 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29818 Z= 0.150 Angle : 0.603 14.586 41536 Z= 0.322 Chirality : 0.041 0.562 4720 Planarity : 0.004 0.066 4216 Dihedral : 18.340 117.766 7064 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 1.77 % Allowed : 19.04 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2682 helix: 1.10 (0.15), residues: 1110 sheet: -0.26 (0.30), residues: 288 loop : -1.03 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 593 HIS 0.003 0.001 HIS A 157 PHE 0.030 0.001 PHE B 101 TYR 0.018 0.001 TYR A 645 ARG 0.013 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 1250) hydrogen bonds : angle 3.99996 ( 3239) covalent geometry : bond 0.00329 (29818) covalent geometry : angle 0.60307 (41536) *********************** 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 428 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 384 time to evaluate : 2.544 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 166 LYS cc_start: 0.7960 (tmmt) cc_final: 0.7730 (ttpp) REVERT: A 248 GLU cc_start: 0.7136 (pm20) cc_final: 0.6564 (pm20) REVERT: A 265 PHE cc_start: 0.7294 (m-80) cc_final: 0.6754 (m-80) REVERT: A 317 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 460 PHE cc_start: 0.7384 (t80) cc_final: 0.7164 (t80) REVERT: A 467 LYS cc_start: 0.7347 (ptpt) cc_final: 0.6807 (tmmt) REVERT: A 526 LYS cc_start: 0.7181 (mmtp) cc_final: 0.6780 (tptt) REVERT: A 545 LYS cc_start: 0.7936 (mttm) cc_final: 0.7633 (mttm) REVERT: A 598 ILE cc_start: 0.7100 (mp) cc_final: 0.6884 (mm) REVERT: A 973 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7568 (mtmt) REVERT: A 1071 MET cc_start: 0.6405 (mtp) cc_final: 0.5962 (mtp) REVERT: A 1250 LYS cc_start: 0.7806 (mttt) cc_final: 0.7285 (mtpm) REVERT: A 1255 GLU cc_start: 0.7914 (tt0) cc_final: 0.7471 (tm-30) REVERT: A 1269 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7758 (pttp) REVERT: A 1287 GLU cc_start: 0.6786 (pp20) cc_final: 0.6343 (pp20) REVERT: A 1295 TYR cc_start: 0.7734 (m-80) cc_final: 0.7278 (m-80) REVERT: A 1383 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8129 (tttm) REVERT: B 3 LYS cc_start: 0.7384 (mmtt) cc_final: 0.7158 (mmtm) REVERT: B 31 ILE cc_start: 0.7741 (mm) cc_final: 0.7449 (mt) REVERT: B 101 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5288 (m-80) REVERT: B 141 LYS cc_start: 0.7842 (tmmm) cc_final: 0.7635 (tmmm) REVERT: B 200 THR cc_start: 0.7186 (m) cc_final: 0.6915 (t) REVERT: B 241 ASP cc_start: 0.7673 (p0) cc_final: 0.7291 (p0) REVERT: B 265 PHE cc_start: 0.7471 (m-80) cc_final: 0.6706 (m-80) REVERT: B 349 ILE cc_start: 0.8022 (tp) cc_final: 0.7509 (pp) REVERT: B 350 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: B 499 GLU cc_start: 0.6708 (pt0) cc_final: 0.6461 (mt-10) REVERT: B 598 ILE cc_start: 0.7329 (mm) cc_final: 0.6961 (mp) REVERT: B 604 GLU cc_start: 0.8060 (pt0) cc_final: 0.7618 (pp20) REVERT: B 638 LEU cc_start: 0.4454 (OUTLIER) cc_final: 0.4142 (pp) REVERT: B 667 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6962 (mm-30) REVERT: B 973 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7675 (mtmt) REVERT: B 1003 THR cc_start: 0.7227 (p) cc_final: 0.6916 (t) REVERT: B 1020 PHE cc_start: 0.7827 (m-80) cc_final: 0.7398 (m-80) REVERT: B 1039 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (tt) REVERT: B 1250 LYS cc_start: 0.8128 (mttt) cc_final: 0.7485 (mttp) REVERT: B 1255 GLU cc_start: 0.7871 (tt0) cc_final: 0.7420 (tm-30) REVERT: B 1413 ASP cc_start: 0.7633 (p0) cc_final: 0.7119 (p0) REVERT: B 1414 THR cc_start: 0.7730 (p) cc_final: 0.7038 (t) REVERT: B 1429 ILE cc_start: 0.8095 (tp) cc_final: 0.7618 (mt) REVERT: H 35 LYS cc_start: 0.8659 (mptt) cc_final: 0.8347 (mmtm) REVERT: H 51 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: H 130 LYS cc_start: 0.8441 (ttpm) cc_final: 0.8236 (ptmm) outliers start: 44 outliers final: 26 residues processed: 412 average time/residue: 1.3704 time to fit residues: 660.8726 Evaluate side-chains 407 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 377 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1191 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 B residue 1400 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 67 LYS Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 81 optimal weight: 0.0020 chunk 212 optimal weight: 1.9990 chunk 240 optimal weight: 0.0060 chunk 94 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1397 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 = 0.4350 r_free = 0.4350 target = 0.193389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149583 restraints weight = 86988.503| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.64 r_work: 0.3658 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29818 Z= 0.143 Angle : 0.600 14.329 41536 Z= 0.320 Chirality : 0.040 0.444 4720 Planarity : 0.004 0.050 4216 Dihedral : 18.322 117.923 7064 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 1.49 % Allowed : 19.60 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2682 helix: 1.08 (0.15), residues: 1110 sheet: -0.12 (0.31), residues: 272 loop : -0.96 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 593 HIS 0.004 0.001 HIS B1031 PHE 0.028 0.001 PHE B 101 TYR 0.017 0.001 TYR B 645 ARG 0.012 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1250) hydrogen bonds : angle 4.00298 ( 3239) covalent geometry : bond 0.00314 (29818) covalent geometry : angle 0.60022 (41536) *********************** 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 421 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 3.030 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 166 LYS cc_start: 0.7938 (tmmt) cc_final: 0.7703 (ttpp) REVERT: A 248 GLU cc_start: 0.7162 (pm20) cc_final: 0.6527 (pm20) REVERT: A 265 PHE cc_start: 0.7287 (m-80) cc_final: 0.6708 (m-80) REVERT: A 317 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 460 PHE cc_start: 0.7391 (t80) cc_final: 0.7174 (t80) REVERT: A 467 LYS cc_start: 0.7429 (ptpt) cc_final: 0.6782 (tmmt) REVERT: A 545 LYS cc_start: 0.7901 (mttm) cc_final: 0.7617 (mttm) REVERT: A 598 ILE cc_start: 0.7019 (mp) cc_final: 0.6804 (mm) REVERT: A 973 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7519 (mtmt) REVERT: A 1071 MET cc_start: 0.6425 (mtp) cc_final: 0.5974 (mtp) REVERT: A 1250 LYS cc_start: 0.7836 (mttt) cc_final: 0.7493 (mttm) REVERT: A 1255 GLU cc_start: 0.7859 (tt0) cc_final: 0.7406 (tm-30) REVERT: A 1269 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7769 (pttp) REVERT: A 1287 GLU cc_start: 0.6829 (pp20) cc_final: 0.6358 (pp20) REVERT: A 1295 TYR cc_start: 0.7744 (m-80) cc_final: 0.7272 (m-80) REVERT: A 1305 GLU cc_start: 0.7773 (mp0) cc_final: 0.7414 (mp0) REVERT: A 1309 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7244 (mt0) REVERT: A 1383 LYS cc_start: 0.8498 (tmmt) cc_final: 0.8252 (tttm) REVERT: B 3 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7133 (mmtm) REVERT: B 101 PHE cc_start: 0.5756 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: B 141 LYS cc_start: 0.7841 (tmmm) cc_final: 0.7629 (tmmm) REVERT: B 200 THR cc_start: 0.7143 (m) cc_final: 0.6897 (t) REVERT: B 241 ASP cc_start: 0.7736 (p0) cc_final: 0.7321 (p0) REVERT: B 265 PHE cc_start: 0.7513 (m-80) cc_final: 0.6699 (m-80) REVERT: B 286 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 349 ILE cc_start: 0.7964 (tp) cc_final: 0.7438 (pp) REVERT: B 350 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.6930 (mtm-85) REVERT: B 364 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7299 (mpp80) REVERT: B 499 GLU cc_start: 0.6654 (pt0) cc_final: 0.6371 (mt-10) REVERT: B 598 ILE cc_start: 0.7267 (mm) cc_final: 0.6863 (mp) REVERT: B 604 GLU cc_start: 0.8078 (pt0) cc_final: 0.7620 (pp20) REVERT: B 638 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.4222 (pp) REVERT: B 667 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 973 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7697 (mtmt) REVERT: B 976 TRP cc_start: 0.5778 (m-10) cc_final: 0.5571 (m-10) REVERT: B 1003 THR cc_start: 0.7243 (p) cc_final: 0.6935 (t) REVERT: B 1020 PHE cc_start: 0.7796 (m-80) cc_final: 0.7334 (m-80) REVERT: B 1039 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7801 (tt) REVERT: B 1250 LYS cc_start: 0.8128 (mttt) cc_final: 0.7422 (mttp) REVERT: B 1255 GLU cc_start: 0.7830 (tt0) cc_final: 0.7349 (tm-30) REVERT: B 1413 ASP cc_start: 0.7642 (p0) cc_final: 0.7138 (p0) REVERT: B 1414 THR cc_start: 0.7682 (p) cc_final: 0.6975 (t) REVERT: B 1429 ILE cc_start: 0.8040 (tp) cc_final: 0.7575 (mt) REVERT: H 51 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: H 130 LYS cc_start: 0.8441 (ttpm) cc_final: 0.8223 (ptmm) outliers start: 37 outliers final: 29 residues processed: 404 average time/residue: 1.5068 time to fit residues: 712.4304 Evaluate side-chains 412 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 378 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 364 ARG Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1197 ILE 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 4 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 116 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 202 optimal weight: 0.0970 chunk 175 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 HIS ** B1397 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 = 0.4345 r_free = 0.4345 target = 0.193038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149664 restraints weight = 77816.441| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.43 r_work: 0.3668 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 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 = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29818 Z= 0.159 Angle : 0.620 14.477 41536 Z= 0.329 Chirality : 0.041 0.433 4720 Planarity : 0.004 0.058 4216 Dihedral : 18.326 117.517 7064 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 1.37 % Allowed : 20.36 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2682 helix: 1.02 (0.15), residues: 1110 sheet: -0.00 (0.31), residues: 276 loop : -0.94 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 593 HIS 0.004 0.001 HIS A1031 PHE 0.044 0.002 PHE A 462 TYR 0.016 0.001 TYR A 645 ARG 0.013 0.001 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 1250) hydrogen bonds : angle 4.05954 ( 3239) covalent geometry : bond 0.00352 (29818) covalent geometry : angle 0.62021 (41536) ********************** 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 422 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 388 time to evaluate : 2.841 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 166 LYS cc_start: 0.7951 (tmmt) cc_final: 0.7726 (ttpp) REVERT: A 248 GLU cc_start: 0.7126 (pm20) cc_final: 0.6533 (pm20) REVERT: A 265 PHE cc_start: 0.7332 (m-80) cc_final: 0.6774 (m-80) REVERT: A 317 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 460 PHE cc_start: 0.7373 (t80) cc_final: 0.7151 (t80) REVERT: A 467 LYS cc_start: 0.7437 (ptpt) cc_final: 0.6812 (tmmt) REVERT: A 545 LYS cc_start: 0.7913 (mttm) cc_final: 0.7617 (mttm) REVERT: A 598 ILE cc_start: 0.7057 (mp) cc_final: 0.6806 (mm) REVERT: A 671 LYS cc_start: 0.8443 (tmtp) cc_final: 0.8198 (tttm) REVERT: A 973 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7533 (mtmt) REVERT: A 1039 LEU cc_start: 0.8099 (tp) cc_final: 0.7874 (tt) REVERT: A 1071 MET cc_start: 0.6416 (mtp) cc_final: 0.5969 (mtp) REVERT: A 1250 LYS cc_start: 0.7826 (mttt) cc_final: 0.7288 (mtpm) REVERT: A 1255 GLU cc_start: 0.7821 (tt0) cc_final: 0.7411 (tm-30) REVERT: A 1269 LYS cc_start: 0.7991 (ptpp) cc_final: 0.7757 (pttp) REVERT: A 1287 GLU cc_start: 0.6830 (pp20) cc_final: 0.6360 (pp20) REVERT: A 1295 TYR cc_start: 0.7741 (m-80) cc_final: 0.7273 (m-80) REVERT: A 1383 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8231 (tttm) REVERT: B 3 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7150 (mmtm) REVERT: B 101 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5270 (m-80) REVERT: B 200 THR cc_start: 0.7192 (m) cc_final: 0.6963 (t) REVERT: B 241 ASP cc_start: 0.7700 (p0) cc_final: 0.7287 (p0) REVERT: B 265 PHE cc_start: 0.7495 (m-80) cc_final: 0.6756 (m-80) REVERT: B 349 ILE cc_start: 0.8019 (tp) cc_final: 0.7501 (pp) REVERT: B 350 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.7006 (mtm-85) REVERT: B 499 GLU cc_start: 0.6630 (pt0) cc_final: 0.6349 (mt-10) REVERT: B 598 ILE cc_start: 0.7282 (mm) cc_final: 0.6869 (mp) REVERT: B 604 GLU cc_start: 0.8061 (pt0) cc_final: 0.7611 (pp20) REVERT: B 638 LEU cc_start: 0.4376 (OUTLIER) cc_final: 0.4044 (pp) REVERT: B 667 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6969 (mm-30) REVERT: B 973 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7663 (mtmm) REVERT: B 976 TRP cc_start: 0.5773 (m-10) cc_final: 0.5559 (m-10) REVERT: B 1020 PHE cc_start: 0.7839 (m-80) cc_final: 0.7376 (m-80) REVERT: B 1039 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 1250 LYS cc_start: 0.8128 (mttt) cc_final: 0.7419 (mttp) REVERT: B 1255 GLU cc_start: 0.7833 (tt0) cc_final: 0.7365 (tm-30) REVERT: B 1413 ASP cc_start: 0.7616 (p0) cc_final: 0.7097 (p0) REVERT: B 1414 THR cc_start: 0.7680 (p) cc_final: 0.6966 (t) REVERT: B 1429 ILE cc_start: 0.8039 (tp) cc_final: 0.7569 (mt) REVERT: H 51 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: H 130 LYS cc_start: 0.8454 (ttpm) cc_final: 0.8231 (ptmm) outliers start: 34 outliers final: 25 residues processed: 404 average time/residue: 1.4583 time to fit residues: 688.4666 Evaluate side-chains 406 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1426 ILE Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 284 GLU Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 958 SER Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1225 SER 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 4 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 121 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 32 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 252 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 HIS ** B1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1401 GLN H 110 ASN H 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.192886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150060 restraints weight = 71135.554| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.26 r_work: 0.3674 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 29818 Z= 0.238 Angle : 0.739 59.193 41536 Z= 0.416 Chirality : 0.043 0.594 4720 Planarity : 0.004 0.060 4216 Dihedral : 18.331 117.478 7062 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 1.45 % Allowed : 20.24 % Favored : 78.31 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2682 helix: 1.02 (0.15), residues: 1110 sheet: 0.01 (0.31), residues: 276 loop : -0.94 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 593 HIS 0.005 0.001 HIS A1031 PHE 0.038 0.002 PHE B 226 TYR 0.016 0.002 TYR B 645 ARG 0.035 0.001 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 1250) hydrogen bonds : angle 4.06619 ( 3239) covalent geometry : bond 0.00487 (29818) covalent geometry : angle 0.73925 (41536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26694.47 seconds wall clock time: 465 minutes 18.46 seconds (27918.46 seconds total)