Starting phenix.real_space_refine on Mon May 26 20:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmn_37657/05_2025/8wmn_37657_neut.cif" } resolution = 2.82 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= 0.019 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 306 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 17302 2.51 5 N 5018 2.21 5 O 6202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28878 Number of models: 1 Model: "" Number of chains: 10 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: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 892 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "F" 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: "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: "N" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 892 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} 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: "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: 24.52, per 1000 atoms: 0.85 Number of scatterers: 28878 At special positions: 0 Unit cell: (184.025, 191.602, 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 306 15.00 Mg 2 11.99 O 6202 8.00 N 5018 7.00 C 17302 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: 6.92 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 34 sheets defined 47.1% alpha, 12.0% beta 125 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 11.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.589A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 88 removed outlier: 3.570A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) 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 165 removed outlier: 3.867A pdb=" N HIS A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 273 through 289 removed outlier: 3.523A pdb=" N SER A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 Processing helix chain 'A' and resid 317 through 334 removed outlier: 4.168A pdb=" N TYR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 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 373 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: 3.589A pdb=" N PHE A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.875A pdb=" N PHE A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 4.167A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 534 removed outlier: 3.556A pdb=" N VAL A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 557 through 562 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: 3.873A 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: 3.630A 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: 3.722A 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 947 removed outlier: 4.102A pdb=" N LYS A 936 " --> pdb=" O ARG A 932 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 937 " --> pdb=" O TYR A 933 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 976 Processing helix chain 'A' and resid 977 through 997 Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1045 through 1054 Processing helix chain 'A' and resid 1059 through 1070 removed outlier: 3.948A pdb=" N ARG A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP A1065 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 5.368A 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 1236 through 1240 Processing helix chain 'A' and resid 1267 through 1270 Processing helix chain 'A' and resid 1299 through 1309 Processing helix chain 'A' and resid 1353 through 1359 removed outlier: 3.603A pdb=" N ARG A1359 " --> pdb=" O GLU A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1414 removed outlier: 3.533A pdb=" N ASP A1413 " --> pdb=" O ARG A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1438 removed outlier: 4.073A pdb=" N PHE A1438 " --> pdb=" O ILE A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.648A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 88 removed outlier: 3.509A pdb=" N GLU B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) 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 162 removed outlier: 3.897A pdb=" N HIS B 157 " --> pdb=" O TRP B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 273 through 289 Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 317 through 334 removed outlier: 4.031A pdb=" N TYR B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) 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 364 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 466 removed outlier: 3.631A pdb=" N PHE B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.843A pdb=" N PHE B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 512 removed outlier: 3.643A pdb=" N VAL B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU B 512 " --> pdb=" O LEU B 508 " (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 557 through 563 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 removed outlier: 3.658A pdb=" N GLU B 597 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 612 Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.754A 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: 3.802A 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 947 removed outlier: 4.274A pdb=" N LYS B 936 " --> pdb=" O ARG B 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 937 " --> pdb=" O TYR B 933 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER B 939 " --> pdb=" O SER B 935 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 944 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE B 945 " --> pdb=" O ILE B 941 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 976 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 1032 through 1044 Processing helix chain 'B' and resid 1045 through 1054 Processing helix chain 'B' and resid 1059 through 1070 removed outlier: 3.926A pdb=" N ARG B1063 " --> pdb=" O SER B1059 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP B1065 " --> pdb=" O THR B1061 " (cutoff:3.500A) removed outlier: 5.211A 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 1236 through 1240 removed outlier: 3.520A pdb=" N TYR B1239 " --> pdb=" O ILE B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1267 through 1270 Processing helix chain 'B' and resid 1299 through 1309 removed outlier: 3.564A pdb=" N VAL B1303 " --> pdb=" O PRO B1299 " (cutoff:3.500A) Processing helix chain 'B' and resid 1353 through 1358 Processing helix chain 'B' and resid 1410 through 1414 removed outlier: 3.552A pdb=" N ASP B1413 " --> pdb=" O ARG B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1440 removed outlier: 4.457A pdb=" N PHE B1438 " --> pdb=" O ILE B1434 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 18 removed outlier: 3.862A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 removed outlier: 4.012A pdb=" N LYS G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 53 removed outlier: 3.689A pdb=" N VAL G 43 " --> pdb=" O THR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 72 Processing helix chain 'G' and resid 81 through 93 removed outlier: 3.776A pdb=" N GLN G 91 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 4.277A 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: 3.882A 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: 3.718A pdb=" N GLN H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 4.301A 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 711 through 715 removed outlier: 6.180A pdb=" N ASN A 4 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HIS A 713 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 6 " --> pdb=" O HIS A 713 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU A 715 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 8 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 15 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 36 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP A 17 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 34 " --> pdb=" O TRP A 17 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 19 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A1116 " --> pdb=" O SER A 36 " (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: 4.338A pdb=" N GLU A 214 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 401 removed outlier: 5.313A pdb=" N LEU A 412 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N LEU A 395 " --> pdb=" O GLN A 410 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N GLN A 410 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N PHE A 397 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N HIS A 408 " --> pdb=" O PHE A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA7, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 1003 through 1006 Processing sheet with id=AA9, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.739A pdb=" N GLN A1094 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1124 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1130 through 1137 Processing sheet with id=AB3, first strand: chain 'A' and resid 1166 through 1167 Processing sheet with id=AB4, first strand: chain 'A' and resid 1260 through 1261 Processing sheet with id=AB5, first strand: chain 'A' and resid 1293 through 1298 removed outlier: 4.740A pdb=" N PHE A1282 " --> pdb=" O ILE A1298 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE A1283 " --> pdb=" O ASP A1327 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP A1327 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1285 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1370 through 1375 removed outlier: 3.809A pdb=" N LYS A1365 " --> pdb=" O TYR A1372 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL A1374 " --> pdb=" O VAL A1363 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL A1363 " --> pdb=" O VAL A1374 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A1333 " --> pdb=" O ILE A1418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 715 removed outlier: 6.415A pdb=" N ILE B 15 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 36 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP B 17 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 34 " --> pdb=" O TRP B 17 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 19 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB9, first strand: chain 'B' and resid 200 through 205 Processing sheet with id=AC1, first strand: chain 'B' and resid 211 through 215 removed outlier: 4.434A pdb=" N GLU B 214 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 392 through 401 removed outlier: 5.419A pdb=" N LEU B 412 " --> pdb=" O CYS B 393 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N LEU B 395 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 10.958A pdb=" N GLN B 410 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N PHE B 397 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N HIS B 408 " --> pdb=" O PHE B 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 437 through 438 Processing sheet with id=AC4, first strand: chain 'B' and resid 468 through 469 removed outlier: 3.759A pdb=" N VAL B 469 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 495 " --> pdb=" O VAL B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 1003 through 1006 Processing sheet with id=AC6, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 4.097A pdb=" N GLN B1094 " --> pdb=" O LYS B1072 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1124 through 1126 Processing sheet with id=AC8, first strand: chain 'B' and resid 1130 through 1137 Processing sheet with id=AC9, first strand: chain 'B' and resid 1166 through 1168 removed outlier: 4.343A pdb=" N LEU B1181 " --> pdb=" O VAL B1168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1260 through 1261 Processing sheet with id=AD2, first strand: chain 'B' and resid 1293 through 1298 removed outlier: 4.449A pdb=" N PHE B1282 " --> pdb=" O ILE B1298 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE B1283 " --> pdb=" O ASP B1327 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP B1327 " --> pdb=" O PHE B1283 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B1285 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1370 through 1375 removed outlier: 3.811A pdb=" N LYS B1365 " --> pdb=" O TYR B1372 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B1374 " --> pdb=" O VAL B1363 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL B1363 " --> pdb=" O VAL B1374 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU B1333 " --> pdb=" O ILE B1418 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 6 through 8 removed outlier: 6.122A pdb=" N LEU G 114 " --> pdb=" O VAL G 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD6, first strand: chain 'H' and resid 37 through 39 Processing sheet with id=AD7, first strand: chain 'H' and resid 113 through 115 removed outlier: 6.257A pdb=" N LEU H 114 " --> pdb=" O VAL H 132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 305 hydrogen bonds 586 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 15.84 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6380 1.33 - 1.45: 7980 1.45 - 1.57: 15052 1.57 - 1.69: 606 1.69 - 1.82: 78 Bond restraints: 30096 Sorted by residual: bond pdb=" CA THR A 502 " pdb=" C THR A 502 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.26e-02 6.30e+03 6.92e+00 bond pdb=" CA LYS B 311 " pdb=" C LYS B 311 " ideal model delta sigma weight residual 1.522 1.500 0.023 9.30e-03 1.16e+04 5.96e+00 bond pdb=" CA PHE A 565 " pdb=" C PHE A 565 " ideal model delta sigma weight residual 1.519 1.495 0.023 1.15e-02 7.56e+03 4.15e+00 bond pdb=" C ARG A1145 " pdb=" N VAL A1146 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.40e-02 5.10e+03 3.68e+00 bond pdb=" CA LYS B 542 " pdb=" C LYS B 542 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.27e-02 6.20e+03 3.48e+00 ... (remaining 30091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 41369 2.31 - 4.62: 546 4.62 - 6.92: 45 6.92 - 9.23: 9 9.23 - 11.54: 1 Bond angle restraints: 41970 Sorted by residual: angle pdb=" C PHE A 565 " pdb=" N PRO A 566 " pdb=" CA PRO A 566 " ideal model delta sigma weight residual 120.38 111.38 9.00 1.03e+00 9.43e-01 7.64e+01 angle pdb=" C PHE A 565 " pdb=" CA PHE A 565 " pdb=" CB PHE A 565 " ideal model delta sigma weight residual 109.85 101.51 8.34 1.14e+00 7.69e-01 5.35e+01 angle pdb=" N TRP A 428 " pdb=" CA TRP A 428 " pdb=" C TRP A 428 " ideal model delta sigma weight residual 111.69 104.35 7.34 1.23e+00 6.61e-01 3.56e+01 angle pdb=" N ILE H 31 " pdb=" CA ILE H 31 " pdb=" C ILE H 31 " ideal model delta sigma weight residual 112.50 105.61 6.89 1.39e+00 5.18e-01 2.45e+01 angle pdb=" N GLN B 410 " pdb=" CA GLN B 410 " pdb=" C GLN B 410 " ideal model delta sigma weight residual 110.36 103.37 6.99 1.55e+00 4.16e-01 2.03e+01 ... (remaining 41965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 16404 24.77 - 49.53: 1237 49.53 - 74.30: 517 74.30 - 99.06: 33 99.06 - 123.83: 5 Dihedral angle restraints: 18196 sinusoidal: 10254 harmonic: 7942 Sorted by residual: dihedral pdb=" CA ASN A 228 " pdb=" C ASN A 228 " pdb=" N GLY A 229 " pdb=" CA GLY A 229 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C PHE A 565 " pdb=" N PHE A 565 " pdb=" CA PHE A 565 " pdb=" CB PHE A 565 " ideal model delta harmonic sigma weight residual -122.60 -110.99 -11.61 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA PHE B1024 " pdb=" C PHE B1024 " pdb=" N SER B1025 " pdb=" CA SER B1025 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 18193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3693 0.045 - 0.090: 819 0.090 - 0.134: 215 0.134 - 0.179: 36 0.179 - 0.224: 5 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CB ILE B1298 " pdb=" CA ILE B1298 " pdb=" CG1 ILE B1298 " pdb=" CG2 ILE B1298 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA PHE A 565 " pdb=" N PHE A 565 " pdb=" C PHE A 565 " pdb=" CB PHE A 565 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A1437 " pdb=" N ILE A1437 " pdb=" C ILE A1437 " pdb=" CB ILE A1437 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 4765 not shown) Planarity restraints: 4228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 427 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU A 427 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU A 427 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP A 428 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 303 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO B 304 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 459 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C LEU A 459 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 459 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 460 " -0.013 2.00e-02 2.50e+03 ... (remaining 4225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 375 2.63 - 3.20: 26409 3.20 - 3.77: 49972 3.77 - 4.33: 67843 4.33 - 4.90: 101647 Nonbonded interactions: 246246 Sorted by model distance: nonbonded pdb=" OD1 ASP G 99 " pdb="MG MG G 201 " model vdw 2.068 2.170 nonbonded pdb=" OD1 ASP H 99 " pdb="MG MG H 201 " model vdw 2.081 2.170 nonbonded pdb=" OD2 ASP B1202 " pdb=" O2' A F 67 " model vdw 2.231 3.040 nonbonded pdb=" O LYS B 109 " pdb=" OG1 THR B 112 " model vdw 2.239 3.040 nonbonded pdb=" OE2 GLU A 396 " pdb=" OH TYR A 648 " model vdw 2.250 3.040 ... (remaining 246241 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: 0.01 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 'N' } ncs_group { reference = chain 'F' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 84.630 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.160 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 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 0.047 30096 Z= 0.177 Angle : 0.665 11.538 41970 Z= 0.397 Chirality : 0.041 0.224 4768 Planarity : 0.004 0.056 4228 Dihedral : 18.451 123.829 13048 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.84 % Allowed : 1.33 % Favored : 97.83 % Cbeta Deviations : 0.04 % 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: -0.57 (0.16), residues: 2682 helix: 0.26 (0.15), residues: 1080 sheet: -0.01 (0.32), residues: 258 loop : -0.94 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 230 HIS 0.005 0.001 HIS B 408 PHE 0.032 0.002 PHE A 565 TYR 0.022 0.002 TYR A 645 ARG 0.016 0.001 ARG B 426 Details of bonding type rmsd hydrogen bonds : bond 0.14311 ( 1234) hydrogen bonds : angle 5.98164 ( 3193) covalent geometry : bond 0.00329 (30096) covalent geometry : angle 0.66479 (41970) *********************** 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 394 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 373 time to evaluate : 2.555 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 13 ASN cc_start: 0.8395 (p0) cc_final: 0.8099 (p0) REVERT: A 21 LYS cc_start: 0.7124 (tttp) cc_final: 0.6626 (ttmm) REVERT: A 63 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7672 (mtmm) REVERT: A 103 LYS cc_start: 0.5944 (mppt) cc_final: 0.5528 (mppt) REVERT: A 182 LYS cc_start: 0.7336 (tptm) cc_final: 0.7093 (mmtt) REVERT: A 323 GLU cc_start: 0.6928 (tp30) cc_final: 0.6001 (tp30) REVERT: A 327 GLN cc_start: 0.7428 (mt0) cc_final: 0.6808 (mt0) REVERT: A 357 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6188 (mm-30) REVERT: A 417 LYS cc_start: 0.4274 (mttt) cc_final: 0.3473 (ttmm) REVERT: A 460 PHE cc_start: 0.8258 (t80) cc_final: 0.7511 (t80) REVERT: A 695 LYS cc_start: 0.6069 (ttpp) cc_final: 0.5573 (ttpp) REVERT: A 941 ILE cc_start: 0.5041 (mm) cc_final: 0.4797 (tt) REVERT: A 995 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6831 (tm130) REVERT: A 1036 LEU cc_start: 0.7775 (tt) cc_final: 0.7516 (tm) REVERT: A 1037 ASP cc_start: 0.6984 (m-30) cc_final: 0.6617 (m-30) REVERT: A 1126 LYS cc_start: 0.6667 (ptmt) cc_final: 0.6397 (tttt) REVERT: A 1133 LYS cc_start: 0.6940 (tttt) cc_final: 0.5910 (ptpt) REVERT: A 1302 GLU cc_start: 0.6565 (mp0) cc_final: 0.6223 (mp0) REVERT: A 1365 LYS cc_start: 0.7752 (pttt) cc_final: 0.7358 (ptpt) REVERT: A 1366 THR cc_start: 0.7952 (t) cc_final: 0.7745 (m) REVERT: A 1395 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6635 (tt0) REVERT: B 13 ASN cc_start: 0.8291 (p0) cc_final: 0.8056 (p0) REVERT: B 21 LYS cc_start: 0.6747 (tptt) cc_final: 0.6277 (ttmm) REVERT: B 63 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7785 (mtmm) REVERT: B 151 TYR cc_start: 0.6350 (m-80) cc_final: 0.6082 (m-80) REVERT: B 317 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 323 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6622 (mt-10) REVERT: B 331 LYS cc_start: 0.6568 (mppt) cc_final: 0.6308 (mttp) REVERT: B 397 PHE cc_start: 0.7420 (m-80) cc_final: 0.7035 (m-80) REVERT: B 503 MET cc_start: 0.6304 (ttt) cc_final: 0.5973 (mtp) REVERT: B 587 MET cc_start: 0.6905 (mpp) cc_final: 0.6619 (mpp) REVERT: B 695 LYS cc_start: 0.6005 (ttpp) cc_final: 0.5728 (ttpp) REVERT: B 1037 ASP cc_start: 0.6629 (m-30) cc_final: 0.6289 (m-30) REVERT: B 1110 LEU cc_start: 0.8390 (mm) cc_final: 0.8088 (mp) REVERT: B 1118 LYS cc_start: 0.7316 (tttp) cc_final: 0.7098 (tttm) REVERT: B 1119 GLN cc_start: 0.7571 (mt0) cc_final: 0.7352 (tt0) REVERT: B 1133 LYS cc_start: 0.7220 (tttt) cc_final: 0.6219 (ttpt) REVERT: B 1167 LYS cc_start: 0.7190 (tmmt) cc_final: 0.6959 (ttpp) REVERT: B 1173 VAL cc_start: 0.7517 (t) cc_final: 0.7246 (p) REVERT: B 1181 LEU cc_start: 0.8190 (mt) cc_final: 0.7957 (mt) REVERT: B 1256 LEU cc_start: 0.7447 (tt) cc_final: 0.7197 (tm) REVERT: B 1274 GLU cc_start: 0.7352 (tt0) cc_final: 0.7137 (tt0) REVERT: B 1302 GLU cc_start: 0.5717 (pm20) cc_final: 0.5370 (pm20) REVERT: B 1323 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7183 (ptm-80) REVERT: G 48 LYS cc_start: 0.7040 (tptp) cc_final: 0.6564 (tttm) REVERT: G 57 ASP cc_start: 0.7328 (p0) cc_final: 0.7054 (p0) REVERT: G 63 LYS cc_start: 0.7696 (mtpp) cc_final: 0.7270 (mmpt) REVERT: H 56 MET cc_start: 0.5133 (mmt) cc_final: 0.4438 (ttp) outliers start: 21 outliers final: 8 residues processed: 388 average time/residue: 1.4476 time to fit residues: 654.6980 Evaluate side-chains 312 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 304 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1221 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.0980 chunk 268 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1309 GLN B 124 GLN B 429 GLN ** B1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1427 ASN G 109 ASN H 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.227725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181149 restraints weight = 88295.675| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.94 r_work: 0.4061 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4040 r_free = 0.4040 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30096 Z= 0.160 Angle : 0.625 14.993 41970 Z= 0.335 Chirality : 0.041 0.236 4768 Planarity : 0.004 0.069 4228 Dihedral : 19.354 119.380 7225 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.00 % Allowed : 9.04 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2682 helix: 0.59 (0.15), residues: 1094 sheet: -0.06 (0.32), residues: 260 loop : -0.80 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1005 HIS 0.008 0.001 HIS A 651 PHE 0.029 0.002 PHE B 320 TYR 0.021 0.002 TYR B 645 ARG 0.012 0.001 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1234) hydrogen bonds : angle 4.51139 ( 3193) covalent geometry : bond 0.00351 (30096) covalent geometry : angle 0.62478 (41970) *********************** 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 355 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 330 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7673 (tttp) cc_final: 0.7099 (ttmm) REVERT: A 30 GLU cc_start: 0.7661 (pm20) cc_final: 0.6933 (pm20) REVERT: A 103 LYS cc_start: 0.6229 (mppt) cc_final: 0.5965 (mppt) REVERT: A 277 ILE cc_start: 0.7251 (tp) cc_final: 0.6951 (mp) REVERT: A 337 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6667 (mm-40) REVERT: A 417 LYS cc_start: 0.5379 (mttt) cc_final: 0.4425 (ttmm) REVERT: A 429 GLN cc_start: 0.7477 (tp40) cc_final: 0.7202 (tp40) REVERT: A 460 PHE cc_start: 0.8389 (t80) cc_final: 0.7917 (t80) REVERT: A 498 ASN cc_start: 0.6056 (t0) cc_final: 0.5823 (m-40) REVERT: A 503 MET cc_start: 0.5838 (mmm) cc_final: 0.5516 (mmm) REVERT: A 695 LYS cc_start: 0.6933 (ttpp) cc_final: 0.6390 (mtpt) REVERT: A 941 ILE cc_start: 0.6146 (mm) cc_final: 0.5812 (tt) REVERT: A 1036 LEU cc_start: 0.8017 (tt) cc_final: 0.7777 (tm) REVERT: A 1037 ASP cc_start: 0.6945 (m-30) cc_final: 0.6643 (m-30) REVERT: A 1126 LYS cc_start: 0.7246 (ptmt) cc_final: 0.6955 (tttt) REVERT: A 1133 LYS cc_start: 0.7712 (tttt) cc_final: 0.6662 (tttp) REVERT: A 1145 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7618 (mtm110) REVERT: A 1163 THR cc_start: 0.8006 (m) cc_final: 0.7676 (p) REVERT: A 1167 LYS cc_start: 0.7756 (tmmt) cc_final: 0.7442 (ttpp) REVERT: A 1274 GLU cc_start: 0.7937 (tt0) cc_final: 0.7627 (pt0) REVERT: A 1302 GLU cc_start: 0.6974 (mp0) cc_final: 0.6773 (mp0) REVERT: A 1323 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7843 (ttt90) REVERT: B 21 LYS cc_start: 0.7334 (tptt) cc_final: 0.6297 (ttmm) REVERT: B 30 GLU cc_start: 0.7875 (pm20) cc_final: 0.7531 (pm20) REVERT: B 317 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 323 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7161 (mt-10) REVERT: B 331 LYS cc_start: 0.6782 (mppt) cc_final: 0.6494 (mttp) REVERT: B 498 ASN cc_start: 0.6666 (t0) cc_final: 0.5838 (m-40) REVERT: B 503 MET cc_start: 0.6368 (ttt) cc_final: 0.6025 (mtp) REVERT: B 587 MET cc_start: 0.6912 (mpp) cc_final: 0.6474 (mpp) REVERT: B 695 LYS cc_start: 0.6921 (ttpp) cc_final: 0.6620 (ptmm) REVERT: B 1133 LYS cc_start: 0.7885 (tttt) cc_final: 0.7392 (ttmt) REVERT: B 1173 VAL cc_start: 0.7681 (t) cc_final: 0.7426 (p) REVERT: B 1302 GLU cc_start: 0.5981 (pm20) cc_final: 0.5583 (pm20) REVERT: B 1323 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7680 (ptm-80) REVERT: B 1437 ILE cc_start: 0.7373 (mm) cc_final: 0.6940 (mm) REVERT: G 63 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7616 (mmtt) REVERT: G 90 LEU cc_start: 0.7967 (tp) cc_final: 0.7746 (mm) REVERT: H 110 ASN cc_start: 0.7860 (t0) cc_final: 0.7650 (t0) outliers start: 25 outliers final: 10 residues processed: 341 average time/residue: 1.4679 time to fit residues: 581.4917 Evaluate side-chains 303 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 293 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 19 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 216 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 GLN B 303 ASN B 306 GLN B 359 HIS B 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.226811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181163 restraints weight = 67671.237| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 3.01 r_work: 0.4102 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30096 Z= 0.174 Angle : 0.610 11.393 41970 Z= 0.327 Chirality : 0.041 0.234 4768 Planarity : 0.004 0.068 4228 Dihedral : 19.211 120.820 7219 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.81 % Allowed : 11.08 % Favored : 87.11 % 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: -0.21 (0.16), residues: 2682 helix: 0.64 (0.15), residues: 1096 sheet: 0.16 (0.33), residues: 260 loop : -0.82 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 230 HIS 0.006 0.001 HIS B1033 PHE 0.038 0.002 PHE A 990 TYR 0.022 0.002 TYR A 151 ARG 0.010 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 1234) hydrogen bonds : angle 4.35653 ( 3193) covalent geometry : bond 0.00385 (30096) covalent geometry : angle 0.61011 (41970) *********************** 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 362 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 317 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7643 (tttp) cc_final: 0.7103 (ttmm) REVERT: A 30 GLU cc_start: 0.7430 (pm20) cc_final: 0.6779 (pm20) REVERT: A 323 GLU cc_start: 0.7338 (tp30) cc_final: 0.6969 (tp30) REVERT: A 337 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6527 (mm-40) REVERT: A 357 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6580 (mm-30) REVERT: A 428 TRP cc_start: 0.7064 (m-10) cc_final: 0.6702 (m-90) REVERT: A 429 GLN cc_start: 0.7337 (tp40) cc_final: 0.7065 (tp40) REVERT: A 498 ASN cc_start: 0.6227 (t0) cc_final: 0.5995 (m-40) REVERT: A 503 MET cc_start: 0.5749 (mmm) cc_final: 0.5440 (mmm) REVERT: A 694 VAL cc_start: 0.6233 (p) cc_final: 0.5976 (t) REVERT: A 695 LYS cc_start: 0.6814 (ttpp) cc_final: 0.6429 (ttpp) REVERT: A 941 ILE cc_start: 0.6071 (mm) cc_final: 0.5869 (tt) REVERT: A 986 ILE cc_start: 0.5843 (tp) cc_final: 0.5380 (pp) REVERT: A 1037 ASP cc_start: 0.6698 (m-30) cc_final: 0.6485 (m-30) REVERT: A 1126 LYS cc_start: 0.7306 (ptmt) cc_final: 0.6994 (tttt) REVERT: A 1133 LYS cc_start: 0.7663 (tttt) cc_final: 0.7060 (ttmt) REVERT: A 1167 LYS cc_start: 0.7641 (tmmt) cc_final: 0.7349 (ttpp) REVERT: A 1323 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7852 (ttt90) REVERT: A 1352 LEU cc_start: 0.2235 (OUTLIER) cc_final: 0.1959 (mt) REVERT: A 1436 GLN cc_start: 0.7793 (mm110) cc_final: 0.7554 (mm110) REVERT: B 21 LYS cc_start: 0.7189 (tptt) cc_final: 0.6189 (ttmm) REVERT: B 30 GLU cc_start: 0.7582 (pm20) cc_final: 0.7339 (pm20) REVERT: B 32 LEU cc_start: 0.8709 (mp) cc_final: 0.8501 (mt) REVERT: B 318 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7739 (ttm-80) REVERT: B 320 PHE cc_start: 0.7442 (m-80) cc_final: 0.6892 (m-80) REVERT: B 323 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7005 (mt-10) REVERT: B 331 LYS cc_start: 0.6741 (mppt) cc_final: 0.6506 (mttp) REVERT: B 498 ASN cc_start: 0.6826 (t0) cc_final: 0.6054 (m-40) REVERT: B 587 MET cc_start: 0.6822 (mpp) cc_final: 0.6311 (mpp) REVERT: B 695 LYS cc_start: 0.6963 (ttpp) cc_final: 0.6684 (ttpp) REVERT: B 973 LYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4803 (mtmm) REVERT: B 1110 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 1133 LYS cc_start: 0.7764 (tttt) cc_final: 0.7460 (ttmm) REVERT: B 1173 VAL cc_start: 0.7366 (t) cc_final: 0.7121 (p) REVERT: B 1305 GLU cc_start: 0.6599 (tp30) cc_final: 0.6309 (tp30) REVERT: B 1323 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7646 (ptm-80) REVERT: B 1432 GLU cc_start: 0.6851 (tp30) cc_final: 0.6613 (tp30) REVERT: G 45 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: G 90 LEU cc_start: 0.8050 (tp) cc_final: 0.7803 (mm) outliers start: 45 outliers final: 20 residues processed: 339 average time/residue: 1.4915 time to fit residues: 586.1903 Evaluate side-chains 323 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1325 LEU Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 138 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 206 optimal weight: 40.0000 chunk 178 optimal weight: 2.9990 chunk 182 optimal weight: 40.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 433 ASN A1309 GLN B 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.230537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.182687 restraints weight = 90015.076| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 4.04 r_work: 0.4037 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30096 Z= 0.158 Angle : 0.600 10.912 41970 Z= 0.321 Chirality : 0.040 0.220 4768 Planarity : 0.004 0.058 4228 Dihedral : 19.160 120.887 7215 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.69 % Allowed : 12.77 % Favored : 85.54 % 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: -0.12 (0.16), residues: 2682 helix: 0.69 (0.15), residues: 1106 sheet: 0.20 (0.33), residues: 256 loop : -0.77 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 174 HIS 0.005 0.001 HIS B1033 PHE 0.024 0.002 PHE A 425 TYR 0.021 0.002 TYR B 156 ARG 0.012 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1234) hydrogen bonds : angle 4.24579 ( 3193) covalent geometry : bond 0.00350 (30096) covalent geometry : angle 0.59998 (41970) *********************** 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 354 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7699 (tttp) cc_final: 0.7168 (ttmm) REVERT: A 30 GLU cc_start: 0.7453 (pm20) cc_final: 0.6899 (pm20) REVERT: A 227 GLU cc_start: 0.7013 (pp20) cc_final: 0.6483 (mt-10) REVERT: A 330 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.5993 (mt-10) REVERT: A 337 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6649 (mm-40) REVERT: A 338 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: A 357 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6737 (mm-30) REVERT: A 428 TRP cc_start: 0.7291 (m-10) cc_final: 0.6881 (m-90) REVERT: A 498 ASN cc_start: 0.6251 (t0) cc_final: 0.5934 (m-40) REVERT: A 503 MET cc_start: 0.5841 (mmm) cc_final: 0.5449 (mmm) REVERT: A 694 VAL cc_start: 0.6434 (p) cc_final: 0.6112 (p) REVERT: A 941 ILE cc_start: 0.6090 (mm) cc_final: 0.5830 (tt) REVERT: A 986 ILE cc_start: 0.5903 (tp) cc_final: 0.5405 (pp) REVERT: A 1037 ASP cc_start: 0.6919 (m-30) cc_final: 0.6582 (m-30) REVERT: A 1126 LYS cc_start: 0.7419 (ptmt) cc_final: 0.7134 (tttt) REVERT: A 1133 LYS cc_start: 0.7727 (tttt) cc_final: 0.7163 (ttmt) REVERT: A 1167 LYS cc_start: 0.7778 (tmmt) cc_final: 0.7449 (ttpp) REVERT: A 1256 LEU cc_start: 0.7624 (tt) cc_final: 0.7353 (tm) REVERT: A 1323 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7954 (ptm-80) REVERT: A 1436 GLN cc_start: 0.7792 (mm110) cc_final: 0.7516 (mm110) REVERT: B 21 LYS cc_start: 0.7296 (tptt) cc_final: 0.6248 (ttmm) REVERT: B 30 GLU cc_start: 0.7742 (pm20) cc_final: 0.7166 (pm20) REVERT: B 93 GLU cc_start: 0.7043 (pm20) cc_final: 0.6835 (pp20) REVERT: B 182 LYS cc_start: 0.7447 (mttt) cc_final: 0.7187 (mmtt) REVERT: B 317 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7256 (mm-30) REVERT: B 318 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7751 (ttm-80) REVERT: B 331 LYS cc_start: 0.6919 (mppt) cc_final: 0.6657 (mmtp) REVERT: B 498 ASN cc_start: 0.6944 (t0) cc_final: 0.6150 (m-40) REVERT: B 587 MET cc_start: 0.6863 (mpp) cc_final: 0.6434 (mpp) REVERT: B 695 LYS cc_start: 0.6993 (ttpp) cc_final: 0.6717 (ttpp) REVERT: B 973 LYS cc_start: 0.4927 (OUTLIER) cc_final: 0.4691 (mtmm) REVERT: B 1036 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7947 (mm) REVERT: B 1133 LYS cc_start: 0.7855 (tttt) cc_final: 0.7574 (ttmm) REVERT: B 1173 VAL cc_start: 0.7453 (t) cc_final: 0.7170 (p) REVERT: B 1305 GLU cc_start: 0.6720 (tp30) cc_final: 0.6406 (tp30) REVERT: B 1323 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7581 (ptm-80) REVERT: G 45 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: G 90 LEU cc_start: 0.8094 (tp) cc_final: 0.7800 (mm) outliers start: 42 outliers final: 20 residues processed: 334 average time/residue: 1.4760 time to fit residues: 572.2230 Evaluate side-chains 324 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 45 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 80 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1006 ASN A1309 GLN B 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.225276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.178823 restraints weight = 83978.326| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 3.82 r_work: 0.4028 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4021 r_free = 0.4021 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30096 Z= 0.192 Angle : 0.624 10.284 41970 Z= 0.334 Chirality : 0.042 0.299 4768 Planarity : 0.004 0.072 4228 Dihedral : 19.133 121.117 7215 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 1.97 % Allowed : 14.10 % Favored : 83.94 % 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: -0.23 (0.16), residues: 2682 helix: 0.58 (0.15), residues: 1106 sheet: 0.30 (0.34), residues: 242 loop : -0.83 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.028 0.002 PHE A 425 TYR 0.024 0.002 TYR B 156 ARG 0.018 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 1234) hydrogen bonds : angle 4.26318 ( 3193) covalent geometry : bond 0.00423 (30096) covalent geometry : angle 0.62442 (41970) *********************** 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 365 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7648 (tttp) cc_final: 0.7096 (ttmm) REVERT: A 30 GLU cc_start: 0.7735 (pm20) cc_final: 0.7189 (pm20) REVERT: A 182 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7201 (tptt) REVERT: A 186 TYR cc_start: 0.7248 (t80) cc_final: 0.6956 (t80) REVERT: A 277 ILE cc_start: 0.7427 (tp) cc_final: 0.7187 (mp) REVERT: A 330 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6028 (mt-10) REVERT: A 337 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6587 (mm-40) REVERT: A 338 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: A 357 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6777 (mm-30) REVERT: A 428 TRP cc_start: 0.7303 (m-10) cc_final: 0.6828 (m-90) REVERT: A 429 GLN cc_start: 0.7472 (tp40) cc_final: 0.7222 (tp40) REVERT: A 498 ASN cc_start: 0.6350 (t0) cc_final: 0.5948 (m-40) REVERT: A 503 MET cc_start: 0.6038 (mmm) cc_final: 0.5627 (mmm) REVERT: A 694 VAL cc_start: 0.6443 (p) cc_final: 0.6131 (t) REVERT: A 986 ILE cc_start: 0.6082 (tp) cc_final: 0.5646 (pp) REVERT: A 1005 TRP cc_start: 0.7250 (t-100) cc_final: 0.6369 (t-100) REVERT: A 1006 ASN cc_start: 0.6797 (m-40) cc_final: 0.5023 (p0) REVERT: A 1126 LYS cc_start: 0.7499 (ptmt) cc_final: 0.7191 (tttt) REVERT: A 1133 LYS cc_start: 0.7714 (tttt) cc_final: 0.7239 (ttmt) REVERT: A 1163 THR cc_start: 0.7819 (m) cc_final: 0.7523 (p) REVERT: A 1256 LEU cc_start: 0.7752 (tt) cc_final: 0.7461 (tm) REVERT: A 1436 GLN cc_start: 0.7795 (mm110) cc_final: 0.7289 (mm110) REVERT: B 21 LYS cc_start: 0.7313 (tptt) cc_final: 0.6244 (ttmm) REVERT: B 30 GLU cc_start: 0.7660 (pm20) cc_final: 0.7100 (pm20) REVERT: B 32 LEU cc_start: 0.8752 (mp) cc_final: 0.8508 (mt) REVERT: B 317 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 323 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 357 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7236 (mp0) REVERT: B 498 ASN cc_start: 0.6948 (t0) cc_final: 0.6070 (m-40) REVERT: B 503 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5790 (mtt) REVERT: B 587 MET cc_start: 0.6913 (mpp) cc_final: 0.6443 (mpp) REVERT: B 973 LYS cc_start: 0.5071 (OUTLIER) cc_final: 0.4852 (mtmm) REVERT: B 1036 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 1133 LYS cc_start: 0.7860 (tttt) cc_final: 0.7587 (ttmm) REVERT: B 1173 VAL cc_start: 0.7466 (t) cc_final: 0.7181 (p) REVERT: B 1182 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (p) REVERT: B 1224 PHE cc_start: 0.6526 (m-10) cc_final: 0.5870 (m-10) REVERT: B 1305 GLU cc_start: 0.6718 (tp30) cc_final: 0.6432 (tp30) REVERT: B 1323 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7537 (ptm-80) REVERT: B 1436 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7597 (mm110) REVERT: G 45 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: G 56 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6802 (ttm) REVERT: G 90 LEU cc_start: 0.8128 (tp) cc_final: 0.7860 (mm) REVERT: H 30 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6906 (pm20) outliers start: 49 outliers final: 24 residues processed: 342 average time/residue: 1.5258 time to fit residues: 617.7621 Evaluate side-chains 334 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1436 GLN Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 102 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.225429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.179255 restraints weight = 85573.317| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.85 r_work: 0.4033 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30096 Z= 0.183 Angle : 0.623 10.037 41970 Z= 0.332 Chirality : 0.042 0.407 4768 Planarity : 0.004 0.056 4228 Dihedral : 19.091 121.522 7212 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 2.05 % Allowed : 15.18 % Favored : 82.77 % 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: -0.27 (0.16), residues: 2682 helix: 0.53 (0.15), residues: 1116 sheet: 0.32 (0.34), residues: 242 loop : -0.85 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.025 0.002 PHE A 425 TYR 0.022 0.002 TYR B 156 ARG 0.012 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 1234) hydrogen bonds : angle 4.24241 ( 3193) covalent geometry : bond 0.00408 (30096) covalent geometry : angle 0.62295 (41970) *********************** 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 358 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 2.839 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 21 LYS cc_start: 0.7666 (tttp) cc_final: 0.7105 (ttmm) REVERT: A 30 GLU cc_start: 0.7681 (pm20) cc_final: 0.7194 (pm20) REVERT: A 186 TYR cc_start: 0.7274 (t80) cc_final: 0.6965 (t80) REVERT: A 330 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.5955 (mt-10) REVERT: A 337 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6564 (mm-40) REVERT: A 338 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: A 357 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6709 (mm-30) REVERT: A 428 TRP cc_start: 0.7323 (m-10) cc_final: 0.6848 (m-90) REVERT: A 498 ASN cc_start: 0.6403 (t0) cc_final: 0.5980 (m-40) REVERT: A 503 MET cc_start: 0.5958 (mmm) cc_final: 0.5521 (mmm) REVERT: A 549 ARG cc_start: 0.6845 (ttp80) cc_final: 0.6423 (ttp80) REVERT: A 694 VAL cc_start: 0.6489 (p) cc_final: 0.6175 (t) REVERT: A 986 ILE cc_start: 0.6067 (tp) cc_final: 0.5653 (pp) REVERT: A 991 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 1005 TRP cc_start: 0.7403 (t-100) cc_final: 0.7021 (t-100) REVERT: A 1107 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7451 (tmtt) REVERT: A 1126 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7336 (tttt) REVERT: A 1133 LYS cc_start: 0.7696 (tttt) cc_final: 0.7257 (ttmt) REVERT: A 1256 LEU cc_start: 0.7722 (tt) cc_final: 0.7430 (tm) REVERT: A 1365 LYS cc_start: 0.8025 (ptpt) cc_final: 0.7788 (ptpp) REVERT: B 21 LYS cc_start: 0.7307 (tptt) cc_final: 0.6240 (ttmm) REVERT: B 30 GLU cc_start: 0.7639 (pm20) cc_final: 0.7071 (pm20) REVERT: B 182 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7293 (tptt) REVERT: B 317 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 318 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7846 (ttm-80) REVERT: B 331 LYS cc_start: 0.6941 (mttp) cc_final: 0.6588 (mtmt) REVERT: B 357 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7223 (mp0) REVERT: B 495 TYR cc_start: 0.5451 (m-10) cc_final: 0.5159 (m-10) REVERT: B 498 ASN cc_start: 0.6985 (t0) cc_final: 0.6111 (m-40) REVERT: B 503 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5834 (mtt) REVERT: B 587 MET cc_start: 0.6932 (mpp) cc_final: 0.6428 (mpp) REVERT: B 695 LYS cc_start: 0.6771 (ttpt) cc_final: 0.6514 (ttpp) REVERT: B 973 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.4860 (mtmm) REVERT: B 986 ILE cc_start: 0.6027 (tp) cc_final: 0.5617 (pp) REVERT: B 1036 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 1133 LYS cc_start: 0.7891 (tttt) cc_final: 0.7585 (ttmm) REVERT: B 1173 VAL cc_start: 0.7484 (t) cc_final: 0.7197 (p) REVERT: B 1224 PHE cc_start: 0.6385 (m-10) cc_final: 0.5048 (m-10) REVERT: B 1305 GLU cc_start: 0.6617 (tp30) cc_final: 0.6332 (tp30) REVERT: B 1323 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7404 (ptm-80) REVERT: G 45 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: G 56 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6720 (ttm) REVERT: G 90 LEU cc_start: 0.8141 (tp) cc_final: 0.7879 (mm) REVERT: H 56 MET cc_start: 0.5491 (mmt) cc_final: 0.4963 (ttp) outliers start: 51 outliers final: 23 residues processed: 334 average time/residue: 1.3987 time to fit residues: 544.2382 Evaluate side-chains 330 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 100 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 276 optimal weight: 0.3980 chunk 293 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 ASN A1309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.229718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183025 restraints weight = 83944.071| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.81 r_work: 0.4036 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30096 Z= 0.164 Angle : 0.610 9.925 41970 Z= 0.327 Chirality : 0.041 0.227 4768 Planarity : 0.004 0.054 4228 Dihedral : 19.038 121.559 7208 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 1.69 % Allowed : 16.27 % Favored : 82.05 % 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: -0.21 (0.16), residues: 2682 helix: 0.61 (0.15), residues: 1112 sheet: 0.35 (0.34), residues: 242 loop : -0.85 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.040 0.002 PHE B 669 TYR 0.022 0.002 TYR B 156 ARG 0.011 0.001 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1234) hydrogen bonds : angle 4.18627 ( 3193) covalent geometry : bond 0.00366 (30096) covalent geometry : angle 0.61026 (41970) *********************** 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 354 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7664 (tttp) cc_final: 0.7063 (ttmm) REVERT: A 30 GLU cc_start: 0.7701 (pm20) cc_final: 0.7202 (pm20) REVERT: A 182 LYS cc_start: 0.7296 (mmtt) cc_final: 0.7065 (mmtt) REVERT: A 186 TYR cc_start: 0.7292 (t80) cc_final: 0.7002 (t80) REVERT: A 330 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.5946 (mt-10) REVERT: A 337 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6494 (mm-40) REVERT: A 338 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: A 428 TRP cc_start: 0.7449 (m-10) cc_final: 0.6978 (m-90) REVERT: A 429 GLN cc_start: 0.7459 (tp40) cc_final: 0.7182 (tp40) REVERT: A 498 ASN cc_start: 0.6508 (t0) cc_final: 0.6049 (m-40) REVERT: A 503 MET cc_start: 0.5816 (mmm) cc_final: 0.5402 (mmm) REVERT: A 694 VAL cc_start: 0.6482 (p) cc_final: 0.6173 (t) REVERT: A 973 LYS cc_start: 0.4758 (mppt) cc_final: 0.4454 (mppt) REVERT: A 991 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 1005 TRP cc_start: 0.7415 (t-100) cc_final: 0.6712 (t-100) REVERT: A 1006 ASN cc_start: 0.6924 (m-40) cc_final: 0.6596 (m-40) REVERT: A 1126 LYS cc_start: 0.7607 (ptmt) cc_final: 0.7371 (tttt) REVERT: A 1133 LYS cc_start: 0.7637 (tttt) cc_final: 0.7402 (ttmm) REVERT: A 1163 THR cc_start: 0.7678 (m) cc_final: 0.7338 (p) REVERT: A 1241 ASP cc_start: 0.6632 (m-30) cc_final: 0.6288 (m-30) REVERT: A 1255 GLU cc_start: 0.7556 (tt0) cc_final: 0.7234 (tt0) REVERT: A 1256 LEU cc_start: 0.7750 (tt) cc_final: 0.7491 (tm) REVERT: B 21 LYS cc_start: 0.7348 (tptt) cc_final: 0.6288 (ttmm) REVERT: B 30 GLU cc_start: 0.7646 (pm20) cc_final: 0.7233 (pm20) REVERT: B 93 GLU cc_start: 0.7166 (pm20) cc_final: 0.6964 (pp20) REVERT: B 317 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7254 (mm-30) REVERT: B 331 LYS cc_start: 0.6961 (mttp) cc_final: 0.6652 (mttp) REVERT: B 357 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7224 (mp0) REVERT: B 495 TYR cc_start: 0.5494 (m-10) cc_final: 0.5184 (m-10) REVERT: B 498 ASN cc_start: 0.6899 (t0) cc_final: 0.5887 (m-40) REVERT: B 587 MET cc_start: 0.6950 (mpp) cc_final: 0.6400 (mpp) REVERT: B 695 LYS cc_start: 0.6771 (ttpt) cc_final: 0.6082 (ttpp) REVERT: B 700 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7282 (tttt) REVERT: B 973 LYS cc_start: 0.5055 (OUTLIER) cc_final: 0.4833 (mtmm) REVERT: B 986 ILE cc_start: 0.6052 (tp) cc_final: 0.5662 (pp) REVERT: B 1133 LYS cc_start: 0.7882 (tttt) cc_final: 0.7581 (ttmm) REVERT: B 1173 VAL cc_start: 0.7429 (t) cc_final: 0.7159 (p) REVERT: B 1182 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7859 (p) REVERT: B 1224 PHE cc_start: 0.6315 (m-10) cc_final: 0.5675 (m-80) REVERT: B 1305 GLU cc_start: 0.6723 (tp30) cc_final: 0.6458 (tp30) REVERT: B 1323 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7394 (ptm-80) REVERT: G 45 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: G 80 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7502 (tpt-90) REVERT: G 129 LEU cc_start: 0.8131 (tp) cc_final: 0.7918 (tt) REVERT: H 30 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: H 56 MET cc_start: 0.5550 (mmt) cc_final: 0.4993 (ttp) outliers start: 42 outliers final: 23 residues processed: 335 average time/residue: 1.4692 time to fit residues: 574.2729 Evaluate side-chains 331 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 700 LYS Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1262 VAL Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 100 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 223 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 241 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A1309 GLN B1240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.223771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.177571 restraints weight = 70417.040| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.11 r_work: 0.4057 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30096 Z= 0.231 Angle : 0.673 16.690 41970 Z= 0.359 Chirality : 0.044 0.247 4768 Planarity : 0.005 0.055 4228 Dihedral : 19.072 120.586 7208 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 1.89 % Allowed : 16.43 % Favored : 81.69 % 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: -0.47 (0.16), residues: 2682 helix: 0.36 (0.15), residues: 1112 sheet: 0.06 (0.33), residues: 264 loop : -0.94 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 174 HIS 0.005 0.001 HIS B 82 PHE 0.029 0.002 PHE A1020 TYR 0.025 0.002 TYR A 151 ARG 0.012 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 1234) hydrogen bonds : angle 4.35080 ( 3193) covalent geometry : bond 0.00515 (30096) covalent geometry : angle 0.67291 (41970) *********************** 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 372 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7551 (tttp) cc_final: 0.7001 (ttmm) REVERT: A 30 GLU cc_start: 0.7637 (pm20) cc_final: 0.7206 (pm20) REVERT: A 186 TYR cc_start: 0.7226 (t80) cc_final: 0.6978 (t80) REVERT: A 277 ILE cc_start: 0.7380 (tp) cc_final: 0.7159 (mp) REVERT: A 330 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6046 (mt-10) REVERT: A 337 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6466 (mm-40) REVERT: A 338 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: A 428 TRP cc_start: 0.7188 (m-10) cc_final: 0.6770 (m-90) REVERT: A 429 GLN cc_start: 0.7429 (tp40) cc_final: 0.7152 (tp40) REVERT: A 498 ASN cc_start: 0.6493 (t0) cc_final: 0.6029 (m-40) REVERT: A 503 MET cc_start: 0.5851 (mmm) cc_final: 0.5429 (mmm) REVERT: A 549 ARG cc_start: 0.6914 (ttp80) cc_final: 0.6497 (ttp80) REVERT: A 694 VAL cc_start: 0.6517 (p) cc_final: 0.6265 (t) REVERT: A 695 LYS cc_start: 0.7166 (tppp) cc_final: 0.6823 (tppp) REVERT: A 973 LYS cc_start: 0.4754 (mppt) cc_final: 0.4507 (mppt) REVERT: A 991 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 1005 TRP cc_start: 0.7403 (t-100) cc_final: 0.6444 (t-100) REVERT: A 1006 ASN cc_start: 0.7003 (m-40) cc_final: 0.5425 (p0) REVERT: A 1163 THR cc_start: 0.7594 (m) cc_final: 0.7282 (p) REVERT: A 1173 VAL cc_start: 0.7599 (t) cc_final: 0.7366 (p) REVERT: A 1182 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7647 (t) REVERT: A 1241 ASP cc_start: 0.6785 (m-30) cc_final: 0.6532 (m-30) REVERT: A 1255 GLU cc_start: 0.7532 (tt0) cc_final: 0.7264 (tt0) REVERT: A 1256 LEU cc_start: 0.7822 (tt) cc_final: 0.7544 (tm) REVERT: B 21 LYS cc_start: 0.7198 (tptt) cc_final: 0.6247 (ttmm) REVERT: B 30 GLU cc_start: 0.7510 (pm20) cc_final: 0.7109 (pm20) REVERT: B 280 LYS cc_start: 0.7668 (tttp) cc_final: 0.7348 (tttp) REVERT: B 331 LYS cc_start: 0.6940 (mttp) cc_final: 0.6638 (mttp) REVERT: B 357 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7111 (mp0) REVERT: B 495 TYR cc_start: 0.5712 (m-10) cc_final: 0.5330 (m-10) REVERT: B 498 ASN cc_start: 0.6855 (t0) cc_final: 0.6031 (m-40) REVERT: B 503 MET cc_start: 0.6090 (OUTLIER) cc_final: 0.5836 (mtt) REVERT: B 587 MET cc_start: 0.6866 (mpp) cc_final: 0.6405 (mpp) REVERT: B 695 LYS cc_start: 0.6718 (ttpt) cc_final: 0.6056 (mtpt) REVERT: B 700 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7298 (tttt) REVERT: B 973 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4858 (mtmm) REVERT: B 986 ILE cc_start: 0.6046 (tp) cc_final: 0.5706 (pp) REVERT: B 1133 LYS cc_start: 0.7856 (tttt) cc_final: 0.7627 (ttmm) REVERT: B 1173 VAL cc_start: 0.7435 (t) cc_final: 0.7185 (p) REVERT: B 1224 PHE cc_start: 0.6360 (m-10) cc_final: 0.5828 (m-10) REVERT: B 1305 GLU cc_start: 0.6669 (tp30) cc_final: 0.6399 (tp30) REVERT: B 1433 LYS cc_start: 0.7588 (tptt) cc_final: 0.7385 (tptt) REVERT: G 45 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: G 80 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7418 (tpt-90) REVERT: G 90 LEU cc_start: 0.8207 (tp) cc_final: 0.7919 (mm) REVERT: H 51 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: H 56 MET cc_start: 0.5692 (mmt) cc_final: 0.5182 (ttp) outliers start: 47 outliers final: 24 residues processed: 351 average time/residue: 1.4453 time to fit residues: 588.8751 Evaluate side-chains 347 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 700 LYS Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 128 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 277 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 GLN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.229691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.182792 restraints weight = 74865.568| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 3.62 r_work: 0.4052 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4038 r_free = 0.4038 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30096 Z= 0.163 Angle : 0.630 14.804 41970 Z= 0.337 Chirality : 0.041 0.253 4768 Planarity : 0.005 0.088 4228 Dihedral : 19.035 121.363 7208 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 1.61 % Allowed : 17.15 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.16), residues: 2682 helix: 0.53 (0.15), residues: 1108 sheet: 0.10 (0.33), residues: 262 loop : -0.85 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.036 0.002 PHE B 669 TYR 0.027 0.002 TYR A 151 ARG 0.012 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1234) hydrogen bonds : angle 4.21763 ( 3193) covalent geometry : bond 0.00364 (30096) covalent geometry : angle 0.62951 (41970) *********************** 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 344 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 2.725 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 21 LYS cc_start: 0.7633 (tttp) cc_final: 0.7030 (ttmm) REVERT: A 30 GLU cc_start: 0.7681 (pm20) cc_final: 0.7202 (pm20) REVERT: A 182 LYS cc_start: 0.7304 (mmtt) cc_final: 0.7085 (tptm) REVERT: A 186 TYR cc_start: 0.7273 (t80) cc_final: 0.6953 (t80) REVERT: A 330 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6035 (mt-10) REVERT: A 337 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6463 (mm-40) REVERT: A 338 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: A 428 TRP cc_start: 0.7293 (m-10) cc_final: 0.6871 (m-90) REVERT: A 429 GLN cc_start: 0.7527 (tp40) cc_final: 0.7240 (tp40) REVERT: A 498 ASN cc_start: 0.6550 (t0) cc_final: 0.6015 (m-40) REVERT: A 503 MET cc_start: 0.5818 (mmm) cc_final: 0.5384 (mmm) REVERT: A 549 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6523 (ttp80) REVERT: A 694 VAL cc_start: 0.6445 (p) cc_final: 0.6164 (t) REVERT: A 695 LYS cc_start: 0.7145 (tppp) cc_final: 0.6831 (tppp) REVERT: A 991 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 1005 TRP cc_start: 0.7427 (t-100) cc_final: 0.6474 (t-100) REVERT: A 1006 ASN cc_start: 0.7034 (m-40) cc_final: 0.5527 (p0) REVERT: A 1163 THR cc_start: 0.7626 (m) cc_final: 0.7292 (p) REVERT: A 1241 ASP cc_start: 0.6759 (m-30) cc_final: 0.6430 (m-30) REVERT: A 1255 GLU cc_start: 0.7507 (tt0) cc_final: 0.7233 (tt0) REVERT: A 1256 LEU cc_start: 0.7845 (tt) cc_final: 0.7554 (tm) REVERT: A 1406 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30) REVERT: B 21 LYS cc_start: 0.7325 (tptt) cc_final: 0.6266 (ttmm) REVERT: B 30 GLU cc_start: 0.7618 (pm20) cc_final: 0.7148 (pm20) REVERT: B 182 LYS cc_start: 0.7672 (mttt) cc_final: 0.7253 (mtpt) REVERT: B 317 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 331 LYS cc_start: 0.7000 (mttp) cc_final: 0.6655 (mttp) REVERT: B 357 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7149 (mp0) REVERT: B 495 TYR cc_start: 0.5525 (m-10) cc_final: 0.5175 (m-10) REVERT: B 498 ASN cc_start: 0.6866 (t0) cc_final: 0.5953 (m-40) REVERT: B 587 MET cc_start: 0.6913 (mpp) cc_final: 0.6430 (mpp) REVERT: B 695 LYS cc_start: 0.6796 (ttpt) cc_final: 0.6167 (ttpp) REVERT: B 700 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7312 (tttt) REVERT: B 973 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4984 (mtmm) REVERT: B 986 ILE cc_start: 0.6172 (tp) cc_final: 0.5763 (pp) REVERT: B 1133 LYS cc_start: 0.7858 (tttt) cc_final: 0.7652 (ttmm) REVERT: B 1173 VAL cc_start: 0.7426 (t) cc_final: 0.7163 (p) REVERT: B 1182 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (p) REVERT: B 1224 PHE cc_start: 0.6300 (m-10) cc_final: 0.5657 (m-10) REVERT: B 1305 GLU cc_start: 0.6739 (tp30) cc_final: 0.6459 (tp30) REVERT: G 30 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: G 45 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: G 80 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7423 (tpt-90) REVERT: G 90 LEU cc_start: 0.8180 (tp) cc_final: 0.7895 (mm) REVERT: G 129 LEU cc_start: 0.8130 (tp) cc_final: 0.7914 (tt) REVERT: H 30 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: H 56 MET cc_start: 0.5689 (mmt) cc_final: 0.5090 (ttp) outliers start: 40 outliers final: 22 residues processed: 326 average time/residue: 1.5303 time to fit residues: 581.7307 Evaluate side-chains 335 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 303 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 700 LYS Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1409 ILE Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 280 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 174 optimal weight: 0.0370 chunk 269 optimal weight: 0.8980 chunk 271 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 279 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 GLN B 346 ASN B1108 HIS B1245 HIS ** G 110 ASN ** 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 = 0.4766 r_free = 0.4766 target = 0.231689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.185459 restraints weight = 83046.594| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 3.79 r_work: 0.4072 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30096 Z= 0.132 Angle : 0.609 12.891 41970 Z= 0.326 Chirality : 0.039 0.239 4768 Planarity : 0.004 0.080 4228 Dihedral : 18.988 120.863 7208 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 1.29 % Allowed : 18.11 % Favored : 80.60 % 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: -0.12 (0.16), residues: 2682 helix: 0.66 (0.16), residues: 1116 sheet: 0.42 (0.35), residues: 238 loop : -0.78 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.034 0.001 PHE B 669 TYR 0.028 0.002 TYR A 151 ARG 0.012 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1234) hydrogen bonds : angle 4.09651 ( 3193) covalent geometry : bond 0.00291 (30096) covalent geometry : angle 0.60932 (41970) ********************** 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 334 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 2.833 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: A 21 LYS cc_start: 0.7655 (tttp) cc_final: 0.7043 (ttmm) REVERT: A 30 GLU cc_start: 0.7691 (pm20) cc_final: 0.7205 (pm20) REVERT: A 182 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6973 (mmtt) REVERT: A 186 TYR cc_start: 0.7276 (t80) cc_final: 0.6912 (t80) REVERT: A 277 ILE cc_start: 0.7494 (tp) cc_final: 0.7245 (mp) REVERT: A 330 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5923 (mt-10) REVERT: A 337 GLN cc_start: 0.6787 (mm-40) cc_final: 0.6568 (mm-40) REVERT: A 338 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: A 428 TRP cc_start: 0.7283 (m-10) cc_final: 0.6869 (m-90) REVERT: A 429 GLN cc_start: 0.7535 (tp40) cc_final: 0.7246 (tp40) REVERT: A 498 ASN cc_start: 0.6482 (t0) cc_final: 0.5929 (m-40) REVERT: A 503 MET cc_start: 0.5767 (mmm) cc_final: 0.5353 (mmm) REVERT: A 694 VAL cc_start: 0.6369 (p) cc_final: 0.6136 (p) REVERT: A 695 LYS cc_start: 0.7164 (tppp) cc_final: 0.6842 (tppp) REVERT: A 991 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 1005 TRP cc_start: 0.7398 (t-100) cc_final: 0.6439 (t-100) REVERT: A 1006 ASN cc_start: 0.7074 (m-40) cc_final: 0.5490 (p0) REVERT: A 1163 THR cc_start: 0.7590 (m) cc_final: 0.7244 (p) REVERT: A 1182 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7648 (t) REVERT: A 1215 PHE cc_start: 0.6962 (t80) cc_final: 0.6603 (t80) REVERT: A 1255 GLU cc_start: 0.7470 (tt0) cc_final: 0.7199 (tt0) REVERT: A 1256 LEU cc_start: 0.7803 (tt) cc_final: 0.7521 (tm) REVERT: B 21 LYS cc_start: 0.7329 (tptt) cc_final: 0.6257 (ttmm) REVERT: B 30 GLU cc_start: 0.7559 (pm20) cc_final: 0.7126 (pm20) REVERT: B 32 LEU cc_start: 0.8826 (mm) cc_final: 0.8616 (mt) REVERT: B 317 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 331 LYS cc_start: 0.6986 (mttp) cc_final: 0.6657 (mttp) REVERT: B 357 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7188 (mp0) REVERT: B 495 TYR cc_start: 0.5415 (m-10) cc_final: 0.5213 (m-10) REVERT: B 498 ASN cc_start: 0.6845 (t0) cc_final: 0.5949 (m-40) REVERT: B 587 MET cc_start: 0.6924 (mpp) cc_final: 0.6437 (mpp) REVERT: B 695 LYS cc_start: 0.6723 (ttpt) cc_final: 0.6027 (ttpp) REVERT: B 973 LYS cc_start: 0.5113 (OUTLIER) cc_final: 0.4892 (mtmm) REVERT: B 986 ILE cc_start: 0.6127 (tp) cc_final: 0.5730 (pp) REVERT: B 1032 ARG cc_start: 0.7842 (mpp80) cc_final: 0.7593 (mtp180) REVERT: B 1110 LEU cc_start: 0.8227 (pt) cc_final: 0.7601 (tm) REVERT: B 1173 VAL cc_start: 0.7388 (t) cc_final: 0.7125 (p) REVERT: B 1182 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7835 (p) REVERT: B 1197 ILE cc_start: 0.7890 (mt) cc_final: 0.7435 (tp) REVERT: B 1224 PHE cc_start: 0.6037 (m-10) cc_final: 0.5487 (m-10) REVERT: B 1305 GLU cc_start: 0.6646 (tp30) cc_final: 0.6387 (tp30) REVERT: G 30 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: G 45 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: G 80 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7441 (tpt-90) REVERT: G 90 LEU cc_start: 0.8142 (tp) cc_final: 0.7838 (mm) REVERT: G 110 ASN cc_start: 0.8418 (t0) cc_final: 0.8191 (m110) REVERT: G 129 LEU cc_start: 0.8131 (tp) cc_final: 0.7919 (tt) REVERT: H 56 MET cc_start: 0.5650 (mmt) cc_final: 0.5090 (ttp) outliers start: 32 outliers final: 17 residues processed: 320 average time/residue: 1.4741 time to fit residues: 548.1663 Evaluate side-chains 322 residues out of total 2486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain A residue 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 973 LYS Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1182 THR Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 117 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 HIS B1245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.223981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177223 restraints weight = 96255.540| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 4.06 r_work: 0.4002 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30096 Z= 0.251 Angle : 0.695 13.444 41970 Z= 0.368 Chirality : 0.044 0.265 4768 Planarity : 0.005 0.086 4228 Dihedral : 19.037 119.238 7200 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 1.41 % Allowed : 18.19 % Favored : 80.40 % 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: -0.43 (0.16), residues: 2682 helix: 0.36 (0.15), residues: 1114 sheet: 0.09 (0.34), residues: 260 loop : -0.88 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 174 HIS 0.005 0.001 HIS B 82 PHE 0.038 0.002 PHE B 669 TYR 0.036 0.003 TYR B1239 ARG 0.014 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 1234) hydrogen bonds : angle 4.29165 ( 3193) covalent geometry : bond 0.00559 (30096) covalent geometry : angle 0.69476 (41970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31771.08 seconds wall clock time: 544 minutes 37.69 seconds (32677.69 seconds total)