Starting phenix.real_space_refine on Thu Jul 25 07:49:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_37657_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_37657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_37657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_37657_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmn_37657/07_2024/8wmn_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 Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 949": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 24.68, 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 - 3.50 Amino acid : False - 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: 13.22 Conformation dependent library (CDL) restraints added in 7.0 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: 11.79 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: 15.52 Time building geometry restraints manager: 14.25 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: 98.61 - 106.19: 2031 106.19 - 113.78: 17306 113.78 - 121.36: 15241 121.36 - 128.95: 6988 128.95 - 136.54: 404 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 2.440 nonbonded pdb=" O LYS B 109 " pdb=" OG1 THR B 112 " model vdw 2.239 2.440 nonbonded pdb=" OE2 GLU A 396 " pdb=" OH TYR A 648 " model vdw 2.250 2.440 ... (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 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: 2.560 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: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 101.140 Find NCS groups from input model: 1.190 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.820 ------------------------------------------------------------------------------- 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= 0.210 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 373 time to evaluate : 2.646 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: 1.3663 time to fit residues: 620.5081 Evaluate side-chains 312 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 304 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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: 0.6980 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 0.0370 chunk 232 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.0970 chunk 268 optimal weight: 0.9980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 GLN A1309 GLN B 57 GLN B 124 GLN B 178 ASN B 464 ASN ** B1006 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.1364 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= 0.185 Angle : 0.583 14.318 41970 Z= 0.314 Chirality : 0.039 0.236 4768 Planarity : 0.004 0.048 4228 Dihedral : 19.341 123.328 7225 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.04 % Allowed : 9.44 % Favored : 89.52 % 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: -0.20 (0.16), residues: 2682 helix: 0.67 (0.15), residues: 1094 sheet: -0.01 (0.32), residues: 250 loop : -0.80 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1005 HIS 0.006 0.001 HIS B1033 PHE 0.028 0.002 PHE A 425 TYR 0.020 0.002 TYR B 645 ARG 0.012 0.001 ARG A 318 *********************** 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 346 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 320 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.8338 (p0) cc_final: 0.8044 (p0) REVERT: A 21 LYS cc_start: 0.6873 (tttp) cc_final: 0.6134 (ttmm) REVERT: A 30 GLU cc_start: 0.7027 (pm20) cc_final: 0.6154 (pm20) REVERT: A 32 LEU cc_start: 0.8448 (mp) cc_final: 0.7984 (mp) REVERT: A 63 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7637 (mtmm) REVERT: A 103 LYS cc_start: 0.5884 (mppt) cc_final: 0.5573 (mppt) REVERT: A 151 TYR cc_start: 0.6184 (m-80) cc_final: 0.5933 (m-80) REVERT: A 182 LYS cc_start: 0.7233 (tptm) cc_final: 0.7007 (mmtp) REVERT: A 277 ILE cc_start: 0.6898 (tp) cc_final: 0.6620 (mp) REVERT: A 294 THR cc_start: 0.7468 (m) cc_final: 0.7059 (p) REVERT: A 323 GLU cc_start: 0.6939 (tp30) cc_final: 0.6227 (tp30) REVERT: A 337 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6903 (mm-40) REVERT: A 357 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6362 (mm-30) REVERT: A 417 LYS cc_start: 0.4601 (mttt) cc_final: 0.4085 (ttmm) REVERT: A 460 PHE cc_start: 0.8190 (t80) cc_final: 0.7743 (t80) REVERT: A 498 ASN cc_start: 0.5291 (t0) cc_final: 0.5036 (m-40) REVERT: A 503 MET cc_start: 0.5905 (mmm) cc_final: 0.5629 (mmm) REVERT: A 694 VAL cc_start: 0.5298 (p) cc_final: 0.4113 (m) REVERT: A 695 LYS cc_start: 0.6050 (ttpp) cc_final: 0.5595 (OUTLIER) REVERT: A 941 ILE cc_start: 0.5087 (mm) cc_final: 0.4848 (tt) REVERT: A 995 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6837 (tm130) REVERT: A 1036 LEU cc_start: 0.7710 (tt) cc_final: 0.7423 (tm) REVERT: A 1037 ASP cc_start: 0.6953 (m-30) cc_final: 0.6605 (m-30) REVERT: A 1118 LYS cc_start: 0.6985 (tttp) cc_final: 0.6580 (mtpt) REVERT: A 1126 LYS cc_start: 0.6901 (ptmt) cc_final: 0.6668 (tttt) REVERT: A 1133 LYS cc_start: 0.7134 (tttt) cc_final: 0.6149 (tttp) REVERT: A 1145 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.6526 (mtm110) REVERT: A 1167 LYS cc_start: 0.7415 (tmmt) cc_final: 0.6919 (ttpp) REVERT: A 1273 VAL cc_start: 0.8284 (m) cc_final: 0.8065 (t) REVERT: A 1302 GLU cc_start: 0.6603 (mp0) cc_final: 0.6215 (mp0) REVERT: A 1323 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7585 (ttt90) REVERT: A 1366 THR cc_start: 0.7930 (t) cc_final: 0.7651 (m) REVERT: A 1395 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6678 (tt0) REVERT: B 13 ASN cc_start: 0.8181 (p0) cc_final: 0.7950 (p0) REVERT: B 21 LYS cc_start: 0.6408 (tptt) cc_final: 0.5562 (ttmm) REVERT: B 30 GLU cc_start: 0.7161 (pm20) cc_final: 0.6326 (pm20) REVERT: B 63 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7772 (mtmm) REVERT: B 182 LYS cc_start: 0.7407 (tptm) cc_final: 0.7201 (mttt) REVERT: B 317 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 323 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6701 (mt-10) REVERT: B 331 LYS cc_start: 0.6629 (mppt) cc_final: 0.6305 (mttp) REVERT: B 397 PHE cc_start: 0.7555 (m-80) cc_final: 0.7252 (m-80) REVERT: B 498 ASN cc_start: 0.6569 (t0) cc_final: 0.5757 (m-40) REVERT: B 503 MET cc_start: 0.6485 (ttt) cc_final: 0.5947 (mtp) REVERT: B 587 MET cc_start: 0.7067 (mpp) cc_final: 0.6642 (mpp) REVERT: B 1036 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7311 (mm) REVERT: B 1110 LEU cc_start: 0.8274 (mm) cc_final: 0.8071 (mp) REVERT: B 1118 LYS cc_start: 0.7263 (tttp) cc_final: 0.7043 (tttm) REVERT: B 1133 LYS cc_start: 0.7251 (tttt) cc_final: 0.6846 (ttmt) REVERT: B 1173 VAL cc_start: 0.7564 (t) cc_final: 0.7281 (p) REVERT: B 1181 LEU cc_start: 0.8164 (mt) cc_final: 0.7927 (mt) REVERT: B 1256 LEU cc_start: 0.7464 (tt) cc_final: 0.7187 (tm) REVERT: B 1274 GLU cc_start: 0.7423 (tt0) cc_final: 0.7192 (tt0) REVERT: B 1296 GLU cc_start: 0.6422 (tp30) cc_final: 0.6144 (tm-30) REVERT: B 1302 GLU cc_start: 0.5813 (pm20) cc_final: 0.5473 (pm20) REVERT: B 1323 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7430 (ptm-80) REVERT: B 1395 GLU cc_start: 0.6834 (tt0) cc_final: 0.6534 (tt0) REVERT: B 1427 ASN cc_start: 0.6813 (m-40) cc_final: 0.6461 (p0) REVERT: B 1437 ILE cc_start: 0.6956 (mm) cc_final: 0.6473 (mm) REVERT: G 48 LYS cc_start: 0.7069 (tptp) cc_final: 0.6698 (tppt) REVERT: G 57 ASP cc_start: 0.6893 (p0) cc_final: 0.6627 (p0) REVERT: G 63 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7280 (mmtt) REVERT: G 90 LEU cc_start: 0.7696 (tp) cc_final: 0.7443 (mm) REVERT: H 110 ASN cc_start: 0.7519 (t0) cc_final: 0.7177 (t0) outliers start: 26 outliers final: 11 residues processed: 333 average time/residue: 1.4303 time to fit residues: 553.9890 Evaluate side-chains 307 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 296 time to evaluate : 2.517 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 700 LYS Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain G residue 10 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 74 optimal weight: 0.0060 chunk 269 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 239 optimal weight: 0.5980 chunk 267 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** A1309 GLN B 359 HIS B 429 GLN ** B1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30096 Z= 0.214 Angle : 0.571 11.128 41970 Z= 0.308 Chirality : 0.040 0.194 4768 Planarity : 0.004 0.075 4228 Dihedral : 19.158 123.977 7216 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer: Outliers : 1.73 % Allowed : 10.96 % Favored : 87.31 % 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: -0.10 (0.16), residues: 2682 helix: 0.78 (0.15), residues: 1096 sheet: 0.34 (0.33), residues: 250 loop : -0.83 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 230 HIS 0.006 0.001 HIS B1033 PHE 0.034 0.002 PHE B 669 TYR 0.022 0.002 TYR B 645 ARG 0.008 0.001 ARG B 80 *********************** 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 359 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 316 time to evaluate : 2.645 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 13 ASN cc_start: 0.8399 (p0) cc_final: 0.8145 (p0) REVERT: A 21 LYS cc_start: 0.6906 (tttp) cc_final: 0.6188 (ttmm) REVERT: A 30 GLU cc_start: 0.7013 (pm20) cc_final: 0.6162 (pm20) REVERT: A 32 LEU cc_start: 0.8519 (mp) cc_final: 0.8109 (mp) REVERT: A 63 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7622 (mtmm) REVERT: A 357 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6481 (mm-30) REVERT: A 417 LYS cc_start: 0.5087 (mttt) cc_final: 0.3836 (ttmt) REVERT: A 428 TRP cc_start: 0.7459 (m-10) cc_final: 0.7083 (m-90) REVERT: A 429 GLN cc_start: 0.7831 (tp40) cc_final: 0.7554 (tp40) REVERT: A 503 MET cc_start: 0.5907 (mmm) cc_final: 0.5631 (mmm) REVERT: A 695 LYS cc_start: 0.6090 (ttpp) cc_final: 0.5674 (ttpp) REVERT: A 941 ILE cc_start: 0.5207 (mm) cc_final: 0.4977 (tt) REVERT: A 986 ILE cc_start: 0.5977 (tp) cc_final: 0.5240 (pp) REVERT: A 995 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6770 (tm130) REVERT: A 1036 LEU cc_start: 0.7833 (tt) cc_final: 0.7608 (tm) REVERT: A 1037 ASP cc_start: 0.6972 (m-30) cc_final: 0.6670 (m-30) REVERT: A 1118 LYS cc_start: 0.7090 (tttp) cc_final: 0.6674 (mtmt) REVERT: A 1126 LYS cc_start: 0.7150 (ptmt) cc_final: 0.6909 (tttt) REVERT: A 1133 LYS cc_start: 0.7200 (tttt) cc_final: 0.6619 (ttmt) REVERT: A 1167 LYS cc_start: 0.7512 (tmmt) cc_final: 0.6998 (ttpp) REVERT: A 1296 GLU cc_start: 0.6718 (tp30) cc_final: 0.6472 (tp30) REVERT: A 1302 GLU cc_start: 0.6682 (mp0) cc_final: 0.6350 (mp0) REVERT: A 1323 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7684 (ttt90) REVERT: A 1365 LYS cc_start: 0.7740 (pttt) cc_final: 0.7404 (ptpt) REVERT: A 1395 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6585 (tt0) REVERT: A 1436 GLN cc_start: 0.7246 (mm110) cc_final: 0.6896 (mm110) REVERT: B 21 LYS cc_start: 0.6448 (tptt) cc_final: 0.5410 (ttmm) REVERT: B 30 GLU cc_start: 0.7190 (pm20) cc_final: 0.6680 (pm20) REVERT: B 63 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7769 (mtmm) REVERT: B 182 LYS cc_start: 0.7442 (tptm) cc_final: 0.7082 (mmtt) REVERT: B 317 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7211 (mm-30) REVERT: B 323 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6642 (mt-10) REVERT: B 331 LYS cc_start: 0.6682 (mppt) cc_final: 0.6394 (mmtp) REVERT: B 498 ASN cc_start: 0.6608 (t0) cc_final: 0.5597 (m-40) REVERT: B 503 MET cc_start: 0.6420 (ttt) cc_final: 0.5987 (mtp) REVERT: B 587 MET cc_start: 0.7054 (mpp) cc_final: 0.6589 (mpp) REVERT: B 1036 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7292 (mm) REVERT: B 1110 LEU cc_start: 0.8442 (mm) cc_final: 0.8060 (mp) REVERT: B 1118 LYS cc_start: 0.7269 (tttp) cc_final: 0.7068 (tttm) REVERT: B 1119 GLN cc_start: 0.7823 (tt0) cc_final: 0.7381 (tt0) REVERT: B 1121 LEU cc_start: 0.8171 (mm) cc_final: 0.7902 (mm) REVERT: B 1133 LYS cc_start: 0.7281 (tttt) cc_final: 0.6922 (ttmm) REVERT: B 1173 VAL cc_start: 0.7611 (t) cc_final: 0.7316 (p) REVERT: B 1181 LEU cc_start: 0.8142 (mt) cc_final: 0.7914 (mt) REVERT: B 1221 GLU cc_start: 0.7284 (mp0) cc_final: 0.7022 (mp0) REVERT: B 1256 LEU cc_start: 0.7462 (tt) cc_final: 0.7192 (tm) REVERT: B 1274 GLU cc_start: 0.7367 (tt0) cc_final: 0.7149 (tt0) REVERT: B 1302 GLU cc_start: 0.5839 (pm20) cc_final: 0.5500 (pm20) REVERT: B 1305 GLU cc_start: 0.6440 (tp30) cc_final: 0.6130 (tp30) REVERT: B 1312 THR cc_start: 0.7580 (m) cc_final: 0.7362 (p) REVERT: B 1323 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7341 (ptm-80) REVERT: B 1365 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7406 (ptpt) REVERT: B 1395 GLU cc_start: 0.7004 (tt0) cc_final: 0.6742 (tt0) REVERT: B 1427 ASN cc_start: 0.6823 (m-40) cc_final: 0.6567 (p0) REVERT: G 45 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: G 57 ASP cc_start: 0.6673 (p0) cc_final: 0.6466 (p0) REVERT: G 63 LYS cc_start: 0.7694 (mtpp) cc_final: 0.7224 (mmtt) REVERT: G 90 LEU cc_start: 0.7846 (tp) cc_final: 0.7531 (mm) outliers start: 43 outliers final: 22 residues processed: 343 average time/residue: 1.4630 time to fit residues: 583.3146 Evaluate side-chains 321 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 296 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 A residue 1000 LYS Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1382 ILE 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 665 ASP Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1107 LYS Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1225 SER Chi-restraints excluded: chain B residue 1365 LYS Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1403 THR Chi-restraints excluded: chain B residue 1405 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 346 ASN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN A1309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30096 Z= 0.343 Angle : 0.643 10.394 41970 Z= 0.344 Chirality : 0.043 0.231 4768 Planarity : 0.005 0.070 4228 Dihedral : 19.184 124.673 7216 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 2.09 % Allowed : 12.37 % 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: -0.41 (0.16), residues: 2682 helix: 0.43 (0.15), residues: 1104 sheet: 0.20 (0.34), residues: 250 loop : -0.93 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 230 HIS 0.006 0.001 HIS B 82 PHE 0.039 0.002 PHE A 990 TYR 0.025 0.002 TYR A 532 ARG 0.007 0.001 ARG B 104 *********************** 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 377 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 325 time to evaluate : 2.698 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 13 ASN cc_start: 0.8418 (p0) cc_final: 0.8216 (p0) REVERT: A 21 LYS cc_start: 0.6940 (tttp) cc_final: 0.6245 (ttmm) REVERT: A 30 GLU cc_start: 0.7111 (pm20) cc_final: 0.6225 (pm20) REVERT: A 32 LEU cc_start: 0.8600 (mp) cc_final: 0.8163 (mp) REVERT: A 63 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7646 (mtmm) REVERT: A 80 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7374 (mtt-85) REVERT: A 141 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6367 (tmmt) REVERT: A 182 LYS cc_start: 0.7448 (mmmt) cc_final: 0.7181 (mmtt) REVERT: A 186 TYR cc_start: 0.7180 (t80) cc_final: 0.6682 (t80) REVERT: A 227 GLU cc_start: 0.6825 (pp20) cc_final: 0.6015 (mt-10) REVERT: A 270 SER cc_start: 0.7845 (t) cc_final: 0.7256 (p) REVERT: A 323 GLU cc_start: 0.7230 (tp30) cc_final: 0.6596 (tp30) REVERT: A 337 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6921 (mm-40) REVERT: A 338 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: A 357 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6492 (mm-30) REVERT: A 428 TRP cc_start: 0.7520 (m-10) cc_final: 0.7105 (m-90) REVERT: A 429 GLN cc_start: 0.7848 (tp40) cc_final: 0.7647 (tp40) REVERT: A 995 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6793 (tm130) REVERT: A 1036 LEU cc_start: 0.7917 (tt) cc_final: 0.7686 (tm) REVERT: A 1037 ASP cc_start: 0.6954 (m-30) cc_final: 0.6660 (m-30) REVERT: A 1118 LYS cc_start: 0.7186 (tttp) cc_final: 0.6982 (ttpp) REVERT: A 1133 LYS cc_start: 0.7262 (tttt) cc_final: 0.6875 (ttmm) REVERT: A 1241 ASP cc_start: 0.6433 (m-30) cc_final: 0.6157 (m-30) REVERT: A 1256 LEU cc_start: 0.7386 (tt) cc_final: 0.7028 (tm) REVERT: A 1273 VAL cc_start: 0.8368 (t) cc_final: 0.8073 (p) REVERT: A 1274 GLU cc_start: 0.7475 (tt0) cc_final: 0.6958 (pt0) REVERT: A 1296 GLU cc_start: 0.6767 (tp30) cc_final: 0.6566 (tp30) REVERT: A 1302 GLU cc_start: 0.6701 (mp0) cc_final: 0.6388 (mp0) REVERT: A 1323 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7624 (ptm-80) REVERT: A 1365 LYS cc_start: 0.7786 (pttt) cc_final: 0.7425 (ptpt) REVERT: A 1393 GLU cc_start: 0.6768 (tp30) cc_final: 0.6166 (tp30) REVERT: A 1395 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6552 (tt0) REVERT: A 1433 LYS cc_start: 0.7558 (tttp) cc_final: 0.7274 (tttp) REVERT: A 1436 GLN cc_start: 0.7040 (mm110) cc_final: 0.6676 (mm110) REVERT: B 21 LYS cc_start: 0.6372 (tptt) cc_final: 0.5519 (ttmm) REVERT: B 30 GLU cc_start: 0.7174 (pm20) cc_final: 0.6662 (pm20) REVERT: B 63 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7723 (mtmm) REVERT: B 93 GLU cc_start: 0.7026 (pm20) cc_final: 0.6774 (pm20) REVERT: B 182 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7267 (mmtt) REVERT: B 323 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6747 (mt-10) REVERT: B 331 LYS cc_start: 0.6807 (mppt) cc_final: 0.6553 (mttp) REVERT: B 363 LEU cc_start: 0.7325 (mt) cc_final: 0.7115 (mp) REVERT: B 498 ASN cc_start: 0.6860 (t0) cc_final: 0.5970 (m-40) REVERT: B 503 MET cc_start: 0.6478 (ttt) cc_final: 0.6090 (mtt) REVERT: B 587 MET cc_start: 0.7028 (mpp) cc_final: 0.6601 (mpp) REVERT: B 991 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 1036 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7537 (mm) REVERT: B 1110 LEU cc_start: 0.8494 (mm) cc_final: 0.8016 (mp) REVERT: B 1118 LYS cc_start: 0.7358 (tttp) cc_final: 0.7126 (tttm) REVERT: B 1121 LEU cc_start: 0.8040 (mm) cc_final: 0.7801 (mm) REVERT: B 1133 LYS cc_start: 0.7317 (tttt) cc_final: 0.7064 (ttmm) REVERT: B 1173 VAL cc_start: 0.7378 (t) cc_final: 0.7067 (p) REVERT: B 1181 LEU cc_start: 0.8169 (mt) cc_final: 0.7958 (mt) REVERT: B 1221 GLU cc_start: 0.7343 (mp0) cc_final: 0.6994 (mp0) REVERT: B 1256 LEU cc_start: 0.7463 (tt) cc_final: 0.7162 (tm) REVERT: B 1302 GLU cc_start: 0.5976 (pm20) cc_final: 0.5658 (pm20) REVERT: B 1305 GLU cc_start: 0.6404 (tp30) cc_final: 0.6064 (tp30) REVERT: B 1323 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7480 (ptm-80) REVERT: B 1393 GLU cc_start: 0.6794 (tp30) cc_final: 0.6305 (tp30) REVERT: B 1395 GLU cc_start: 0.7107 (tt0) cc_final: 0.6835 (tt0) REVERT: B 1427 ASN cc_start: 0.6719 (m-40) cc_final: 0.6454 (p0) REVERT: G 45 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: G 57 ASP cc_start: 0.6748 (p0) cc_final: 0.6525 (p0) REVERT: G 63 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7262 (mmtt) REVERT: G 90 LEU cc_start: 0.7925 (tp) cc_final: 0.7599 (mm) REVERT: H 56 MET cc_start: 0.5660 (mpp) cc_final: 0.5407 (ttm) outliers start: 52 outliers final: 27 residues processed: 351 average time/residue: 1.4770 time to fit residues: 604.9379 Evaluate side-chains 340 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 308 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 343 ASP 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 1165 SER Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1298 ILE 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 182 LYS Chi-restraints excluded: chain B residue 197 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 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 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 100 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.0050 chunk 162 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 213 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 433 ASN A1309 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30096 Z= 0.161 Angle : 0.538 10.354 41970 Z= 0.292 Chirality : 0.038 0.214 4768 Planarity : 0.004 0.059 4228 Dihedral : 19.047 124.890 7212 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 1.97 % Allowed : 14.06 % Favored : 83.98 % 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: -0.04 (0.16), residues: 2682 helix: 0.81 (0.16), residues: 1116 sheet: 0.58 (0.36), residues: 232 loop : -0.85 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 230 HIS 0.005 0.001 HIS B 651 PHE 0.035 0.001 PHE B 669 TYR 0.021 0.001 TYR B 645 ARG 0.007 0.000 ARG B 80 *********************** 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 359 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 310 time to evaluate : 2.533 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 13 ASN cc_start: 0.8358 (p0) cc_final: 0.8150 (p0) REVERT: A 21 LYS cc_start: 0.6918 (tttp) cc_final: 0.6463 (tttp) REVERT: A 30 GLU cc_start: 0.6917 (pm20) cc_final: 0.6158 (pm20) REVERT: A 32 LEU cc_start: 0.8571 (mp) cc_final: 0.8200 (mp) REVERT: A 63 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7594 (mtmm) REVERT: A 186 TYR cc_start: 0.7159 (t80) cc_final: 0.6675 (t80) REVERT: A 323 GLU cc_start: 0.7140 (tp30) cc_final: 0.6486 (tp30) REVERT: A 330 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5867 (tt0) REVERT: A 338 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: A 357 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 428 TRP cc_start: 0.7492 (m-10) cc_final: 0.7069 (m-90) REVERT: A 498 ASN cc_start: 0.5683 (t0) cc_final: 0.5238 (m-40) REVERT: A 986 ILE cc_start: 0.6031 (tp) cc_final: 0.5436 (pp) REVERT: A 995 GLN cc_start: 0.7037 (tm-30) cc_final: 0.6776 (tm130) REVERT: A 1036 LEU cc_start: 0.7892 (tt) cc_final: 0.7664 (tm) REVERT: A 1037 ASP cc_start: 0.6905 (m-30) cc_final: 0.6605 (m-30) REVERT: A 1118 LYS cc_start: 0.7018 (tttp) cc_final: 0.6564 (mtmt) REVERT: A 1133 LYS cc_start: 0.7144 (tttt) cc_final: 0.6804 (ttmm) REVERT: A 1256 LEU cc_start: 0.7322 (tt) cc_final: 0.6995 (tm) REVERT: A 1273 VAL cc_start: 0.8406 (t) cc_final: 0.8112 (p) REVERT: A 1274 GLU cc_start: 0.7509 (tt0) cc_final: 0.7039 (pt0) REVERT: A 1296 GLU cc_start: 0.6702 (tp30) cc_final: 0.6483 (tp30) REVERT: A 1302 GLU cc_start: 0.6660 (mp0) cc_final: 0.6349 (mp0) REVERT: A 1309 GLN cc_start: 0.6128 (OUTLIER) cc_final: 0.5865 (mt0) REVERT: A 1323 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7557 (ttt90) REVERT: A 1365 LYS cc_start: 0.7733 (pttt) cc_final: 0.7463 (ptpt) REVERT: A 1383 LYS cc_start: 0.7500 (tttp) cc_final: 0.7200 (ttpm) REVERT: A 1393 GLU cc_start: 0.6601 (tp30) cc_final: 0.6024 (tp30) REVERT: A 1395 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6536 (tt0) REVERT: A 1436 GLN cc_start: 0.7058 (mm110) cc_final: 0.6692 (mm110) REVERT: B 21 LYS cc_start: 0.6353 (tptt) cc_final: 0.5339 (ttmm) REVERT: B 30 GLU cc_start: 0.7122 (pm20) cc_final: 0.6270 (pm20) REVERT: B 32 LEU cc_start: 0.8511 (mp) cc_final: 0.8283 (mt) REVERT: B 63 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7748 (mtmm) REVERT: B 64 TYR cc_start: 0.7240 (m-80) cc_final: 0.6869 (m-80) REVERT: B 182 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6958 (mmtp) REVERT: B 317 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 318 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7663 (ttm-80) REVERT: B 323 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6688 (mt-10) REVERT: B 331 LYS cc_start: 0.6750 (mppt) cc_final: 0.6513 (mttp) REVERT: B 357 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6809 (mp0) REVERT: B 495 TYR cc_start: 0.4763 (m-10) cc_final: 0.4502 (m-10) REVERT: B 503 MET cc_start: 0.6409 (ttt) cc_final: 0.6040 (mtt) REVERT: B 587 MET cc_start: 0.7059 (mpp) cc_final: 0.6619 (mpp) REVERT: B 623 ARG cc_start: -0.0562 (OUTLIER) cc_final: -0.1064 (mtt-85) REVERT: B 695 LYS cc_start: 0.6440 (ttpp) cc_final: 0.6137 (ttpt) REVERT: B 700 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6645 (tttt) REVERT: B 1036 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7514 (mm) REVERT: B 1110 LEU cc_start: 0.8501 (mm) cc_final: 0.8023 (mp) REVERT: B 1118 LYS cc_start: 0.7240 (tttp) cc_final: 0.7033 (tttm) REVERT: B 1121 LEU cc_start: 0.8155 (mm) cc_final: 0.7904 (mm) REVERT: B 1133 LYS cc_start: 0.7260 (tttt) cc_final: 0.6996 (ttmm) REVERT: B 1173 VAL cc_start: 0.7311 (t) cc_final: 0.7005 (p) REVERT: B 1181 LEU cc_start: 0.8115 (mt) cc_final: 0.7905 (mt) REVERT: B 1224 PHE cc_start: 0.5477 (m-10) cc_final: 0.4439 (m-10) REVERT: B 1256 LEU cc_start: 0.7363 (tt) cc_final: 0.7089 (tm) REVERT: B 1274 GLU cc_start: 0.7325 (tt0) cc_final: 0.6991 (pt0) REVERT: B 1305 GLU cc_start: 0.6376 (tp30) cc_final: 0.6062 (tp30) REVERT: B 1323 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7299 (ptm-80) REVERT: B 1389 THR cc_start: 0.6283 (m) cc_final: 0.6003 (t) REVERT: B 1393 GLU cc_start: 0.6569 (tp30) cc_final: 0.6113 (tp30) REVERT: B 1395 GLU cc_start: 0.6990 (tt0) cc_final: 0.6758 (tt0) REVERT: B 1436 GLN cc_start: 0.7092 (tp40) cc_final: 0.6827 (mm110) REVERT: G 45 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: G 57 ASP cc_start: 0.6563 (p0) cc_final: 0.6333 (p0) REVERT: G 63 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7219 (mmtt) REVERT: G 90 LEU cc_start: 0.7865 (tp) cc_final: 0.7525 (mm) REVERT: H 56 MET cc_start: 0.5232 (tpp) cc_final: 0.4402 (ttp) outliers start: 49 outliers final: 26 residues processed: 338 average time/residue: 1.4471 time to fit residues: 570.6770 Evaluate side-chains 333 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 299 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS 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 564 LYS Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1309 GLN Chi-restraints excluded: chain A residue 1366 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 700 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 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 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 Chi-restraints excluded: chain H residue 21 ASP 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 96 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 286 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 477 HIS B1108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2850 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= 0.245 Angle : 0.581 9.896 41970 Z= 0.314 Chirality : 0.040 0.220 4768 Planarity : 0.004 0.062 4228 Dihedral : 19.024 124.077 7212 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 2.01 % Allowed : 14.66 % Favored : 83.33 % 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: 0.73 (0.15), residues: 1114 sheet: 0.54 (0.36), residues: 234 loop : -0.88 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 230 HIS 0.005 0.001 HIS B 651 PHE 0.029 0.002 PHE A 669 TYR 0.025 0.002 TYR B 156 ARG 0.005 0.001 ARG B 183 *********************** 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 366 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 316 time to evaluate : 2.535 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 13 ASN cc_start: 0.8388 (p0) cc_final: 0.8170 (p0) REVERT: A 21 LYS cc_start: 0.6946 (tttp) cc_final: 0.6253 (ttmm) REVERT: A 30 GLU cc_start: 0.7039 (pm20) cc_final: 0.6206 (pm20) REVERT: A 32 LEU cc_start: 0.8646 (mp) cc_final: 0.8260 (mp) REVERT: A 63 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7616 (mtmm) REVERT: A 93 GLU cc_start: 0.6911 (pm20) cc_final: 0.6656 (pm20) REVERT: A 186 TYR cc_start: 0.7165 (t80) cc_final: 0.6719 (t80) REVERT: A 277 ILE cc_start: 0.7153 (tp) cc_final: 0.6916 (mp) REVERT: A 330 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5896 (mt-10) REVERT: A 338 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: A 357 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6507 (mm-30) REVERT: A 428 TRP cc_start: 0.7567 (m-10) cc_final: 0.7044 (m-90) REVERT: A 429 GLN cc_start: 0.7636 (tp40) cc_final: 0.7389 (tp40) REVERT: A 498 ASN cc_start: 0.5964 (t0) cc_final: 0.5523 (m-40) REVERT: A 503 MET cc_start: 0.6134 (mmm) cc_final: 0.5682 (mmm) REVERT: A 995 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6856 (tm130) REVERT: A 1036 LEU cc_start: 0.7926 (tt) cc_final: 0.7676 (tm) REVERT: A 1037 ASP cc_start: 0.6941 (m-30) cc_final: 0.6645 (m-30) REVERT: A 1133 LYS cc_start: 0.7192 (tttt) cc_final: 0.6862 (ttmm) REVERT: A 1241 ASP cc_start: 0.6320 (m-30) cc_final: 0.6036 (m-30) REVERT: A 1256 LEU cc_start: 0.7415 (tt) cc_final: 0.7059 (tm) REVERT: A 1302 GLU cc_start: 0.6678 (mp0) cc_final: 0.6285 (mp0) REVERT: A 1323 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7640 (ptt90) REVERT: A 1365 LYS cc_start: 0.7758 (pttt) cc_final: 0.7508 (ptpt) REVERT: A 1383 LYS cc_start: 0.7723 (tttp) cc_final: 0.7176 (ttpp) REVERT: A 1393 GLU cc_start: 0.6596 (tp30) cc_final: 0.6006 (tp30) REVERT: A 1395 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6711 (tt0) REVERT: B 21 LYS cc_start: 0.6410 (tptt) cc_final: 0.5439 (ttmm) REVERT: B 30 GLU cc_start: 0.7144 (pm20) cc_final: 0.6318 (pm20) REVERT: B 63 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7735 (mtmm) REVERT: B 64 TYR cc_start: 0.7193 (m-80) cc_final: 0.6784 (m-80) REVERT: B 93 GLU cc_start: 0.7035 (pm20) cc_final: 0.6812 (pm20) REVERT: B 182 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7222 (mmtt) REVERT: B 317 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 323 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6643 (mt-10) REVERT: B 331 LYS cc_start: 0.6794 (mppt) cc_final: 0.6552 (mttp) REVERT: B 357 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6790 (mp0) REVERT: B 495 TYR cc_start: 0.5014 (m-10) cc_final: 0.4716 (m-10) REVERT: B 503 MET cc_start: 0.6319 (ttt) cc_final: 0.5952 (mtt) REVERT: B 587 MET cc_start: 0.7127 (mpp) cc_final: 0.6663 (mpp) REVERT: B 623 ARG cc_start: -0.0601 (OUTLIER) cc_final: -0.1121 (mtt-85) REVERT: B 695 LYS cc_start: 0.6250 (ttpp) cc_final: 0.5743 (ttpp) REVERT: B 986 ILE cc_start: 0.5859 (tp) cc_final: 0.5335 (pp) REVERT: B 1036 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7579 (mm) REVERT: B 1118 LYS cc_start: 0.7280 (tttp) cc_final: 0.7047 (tttm) REVERT: B 1121 LEU cc_start: 0.8010 (mm) cc_final: 0.7757 (mm) REVERT: B 1133 LYS cc_start: 0.7312 (tttt) cc_final: 0.7035 (ttmm) REVERT: B 1173 VAL cc_start: 0.7375 (t) cc_final: 0.7065 (p) REVERT: B 1181 LEU cc_start: 0.8124 (mt) cc_final: 0.7916 (mt) REVERT: B 1224 PHE cc_start: 0.5594 (m-10) cc_final: 0.5311 (m-10) REVERT: B 1256 LEU cc_start: 0.7414 (tt) cc_final: 0.7114 (tm) REVERT: B 1274 GLU cc_start: 0.7320 (tt0) cc_final: 0.6884 (pt0) REVERT: B 1305 GLU cc_start: 0.6412 (tp30) cc_final: 0.6099 (tp30) REVERT: B 1323 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7371 (ptm-80) REVERT: B 1365 LYS cc_start: 0.7671 (ptpt) cc_final: 0.7453 (ptpt) REVERT: B 1389 THR cc_start: 0.6361 (m) cc_final: 0.6051 (t) REVERT: B 1393 GLU cc_start: 0.6587 (tp30) cc_final: 0.6145 (tp30) REVERT: B 1395 GLU cc_start: 0.7093 (tt0) cc_final: 0.6817 (tt0) REVERT: B 1436 GLN cc_start: 0.7121 (tp40) cc_final: 0.6875 (mm110) REVERT: G 45 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: G 57 ASP cc_start: 0.6653 (p0) cc_final: 0.6421 (p0) REVERT: G 63 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7246 (mmtt) REVERT: G 90 LEU cc_start: 0.7898 (tp) cc_final: 0.7557 (mm) REVERT: H 56 MET cc_start: 0.5397 (tpp) cc_final: 0.4546 (ttm) outliers start: 50 outliers final: 25 residues processed: 344 average time/residue: 1.4766 time to fit residues: 591.1399 Evaluate side-chains 336 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 305 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 665 ASP Chi-restraints excluded: chain A residue 1000 LYS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1165 SER 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 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 623 ARG Chi-restraints excluded: chain B residue 1036 LEU 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 1352 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 Chi-restraints excluded: chain H residue 30 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 241 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 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 983 ASN A1309 GLN B1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30096 Z= 0.213 Angle : 0.558 9.751 41970 Z= 0.303 Chirality : 0.039 0.191 4768 Planarity : 0.004 0.107 4228 Dihedral : 18.979 124.489 7208 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 2.21 % Allowed : 14.94 % Favored : 82.85 % 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: -0.10 (0.16), residues: 2682 helix: 0.79 (0.16), residues: 1116 sheet: 0.53 (0.35), residues: 234 loop : -0.90 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.036 0.002 PHE B 669 TYR 0.020 0.002 TYR A 156 ARG 0.008 0.000 ARG A 80 *********************** 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 361 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 306 time to evaluate : 2.461 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: 0.6949 (tttp) cc_final: 0.6503 (tttp) REVERT: A 30 GLU cc_start: 0.7030 (pm20) cc_final: 0.6235 (pm20) REVERT: A 32 LEU cc_start: 0.8688 (mp) cc_final: 0.8356 (mp) REVERT: A 63 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7608 (mtmm) REVERT: A 93 GLU cc_start: 0.6920 (pm20) cc_final: 0.6562 (pp20) REVERT: A 186 TYR cc_start: 0.7161 (t80) cc_final: 0.6688 (t80) REVERT: A 323 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6737 (tp30) REVERT: A 330 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5947 (mt-10) REVERT: A 338 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: A 357 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6504 (mm-30) REVERT: A 428 TRP cc_start: 0.7520 (m-10) cc_final: 0.6990 (m-90) REVERT: A 498 ASN cc_start: 0.5938 (t0) cc_final: 0.5482 (m-40) REVERT: A 503 MET cc_start: 0.5783 (mmm) cc_final: 0.5379 (mmm) REVERT: A 986 ILE cc_start: 0.5874 (tp) cc_final: 0.5331 (pp) REVERT: A 991 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 995 GLN cc_start: 0.7126 (tm-30) cc_final: 0.6894 (tm130) REVERT: A 996 LEU cc_start: 0.7339 (tp) cc_final: 0.7098 (tt) REVERT: A 1036 LEU cc_start: 0.7937 (tt) cc_final: 0.7682 (tm) REVERT: A 1037 ASP cc_start: 0.6939 (m-30) cc_final: 0.6635 (m-30) REVERT: A 1133 LYS cc_start: 0.7162 (tttt) cc_final: 0.6869 (ttmm) REVERT: A 1256 LEU cc_start: 0.7420 (tt) cc_final: 0.7075 (tm) REVERT: A 1274 GLU cc_start: 0.7600 (tt0) cc_final: 0.7148 (tt0) REVERT: A 1302 GLU cc_start: 0.6645 (mp0) cc_final: 0.6299 (mp0) REVERT: A 1309 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.6031 (mt0) REVERT: A 1323 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7602 (ptt90) REVERT: A 1365 LYS cc_start: 0.7763 (pttt) cc_final: 0.7407 (ptpt) REVERT: A 1383 LYS cc_start: 0.7622 (tttp) cc_final: 0.7131 (ttpp) REVERT: A 1393 GLU cc_start: 0.6657 (tp30) cc_final: 0.6084 (tp30) REVERT: A 1395 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6705 (tt0) REVERT: B 21 LYS cc_start: 0.6325 (tptt) cc_final: 0.5343 (ttmm) REVERT: B 30 GLU cc_start: 0.7129 (pm20) cc_final: 0.6278 (pm20) REVERT: B 63 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7727 (mtmm) REVERT: B 64 TYR cc_start: 0.7296 (m-80) cc_final: 0.6896 (m-80) REVERT: B 93 GLU cc_start: 0.7102 (pm20) cc_final: 0.6879 (pm20) REVERT: B 182 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7211 (mmtt) REVERT: B 317 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7116 (mm-30) REVERT: B 331 LYS cc_start: 0.6783 (mppt) cc_final: 0.6532 (mttp) REVERT: B 357 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6766 (mp0) REVERT: B 495 TYR cc_start: 0.5006 (m-10) cc_final: 0.4702 (m-10) REVERT: B 503 MET cc_start: 0.6307 (ttt) cc_final: 0.5947 (mtt) REVERT: B 587 MET cc_start: 0.7146 (mpp) cc_final: 0.6664 (mpp) REVERT: B 695 LYS cc_start: 0.6309 (ttpp) cc_final: 0.5806 (ttpp) REVERT: B 986 ILE cc_start: 0.5849 (tp) cc_final: 0.5348 (pp) REVERT: B 1036 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 1118 LYS cc_start: 0.7266 (tttp) cc_final: 0.7035 (tttm) REVERT: B 1121 LEU cc_start: 0.8004 (mm) cc_final: 0.7744 (mm) REVERT: B 1133 LYS cc_start: 0.7293 (tttt) cc_final: 0.7026 (ttmm) REVERT: B 1173 VAL cc_start: 0.7344 (t) cc_final: 0.7042 (p) REVERT: B 1224 PHE cc_start: 0.5501 (m-10) cc_final: 0.5235 (m-10) REVERT: B 1256 LEU cc_start: 0.7412 (tt) cc_final: 0.7105 (tm) REVERT: B 1274 GLU cc_start: 0.7317 (tt0) cc_final: 0.6965 (pt0) REVERT: B 1305 GLU cc_start: 0.6421 (tp30) cc_final: 0.6113 (tp30) REVERT: B 1323 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7372 (ptm-80) REVERT: B 1393 GLU cc_start: 0.6501 (tp30) cc_final: 0.6082 (tp30) REVERT: B 1395 GLU cc_start: 0.7068 (tt0) cc_final: 0.6806 (tt0) REVERT: B 1436 GLN cc_start: 0.7044 (tp40) cc_final: 0.6843 (mm110) REVERT: G 30 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: G 45 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: G 56 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6190 (ttm) REVERT: G 57 ASP cc_start: 0.6625 (p0) cc_final: 0.6305 (p0) REVERT: G 63 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7232 (mmtt) REVERT: G 80 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7197 (tpt-90) REVERT: H 56 MET cc_start: 0.5109 (tpp) cc_final: 0.4329 (ttm) outliers start: 55 outliers final: 28 residues processed: 339 average time/residue: 1.4824 time to fit residues: 583.0945 Evaluate side-chains 336 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1039 LEU Chi-restraints excluded: chain A residue 1152 ASN Chi-restraints excluded: chain A residue 1165 SER Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1309 GLN 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 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain B residue 1036 LEU 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 1352 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 56 MET Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 95 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 B 471 GLN B1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30096 Z= 0.324 Angle : 0.638 9.328 41970 Z= 0.343 Chirality : 0.043 0.219 4768 Planarity : 0.005 0.092 4228 Dihedral : 19.030 124.297 7208 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 2.05 % Allowed : 15.66 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.16), residues: 2682 helix: 0.48 (0.15), residues: 1116 sheet: 0.43 (0.34), residues: 238 loop : -0.96 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 174 HIS 0.006 0.001 HIS A 82 PHE 0.038 0.002 PHE B 669 TYR 0.028 0.002 TYR A 156 ARG 0.012 0.001 ARG B 623 *********************** 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 368 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 317 time to evaluate : 2.707 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 21 LYS cc_start: 0.6937 (tttp) cc_final: 0.6470 (tttp) REVERT: A 30 GLU cc_start: 0.7132 (pm20) cc_final: 0.6390 (pm20) REVERT: A 32 LEU cc_start: 0.8771 (mp) cc_final: 0.8381 (mp) REVERT: A 63 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7632 (mtmm) REVERT: A 186 TYR cc_start: 0.7220 (t80) cc_final: 0.6759 (t80) REVERT: A 270 SER cc_start: 0.7914 (t) cc_final: 0.7364 (p) REVERT: A 277 ILE cc_start: 0.7086 (tp) cc_final: 0.6880 (mp) REVERT: A 323 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: A 330 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5925 (tt0) REVERT: A 338 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: A 357 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 428 TRP cc_start: 0.7562 (m-10) cc_final: 0.7095 (m-90) REVERT: A 498 ASN cc_start: 0.6075 (t0) cc_final: 0.5551 (m-40) REVERT: A 991 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 995 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6915 (tm-30) REVERT: A 1036 LEU cc_start: 0.8012 (tt) cc_final: 0.7728 (tm) REVERT: A 1133 LYS cc_start: 0.7229 (tttt) cc_final: 0.6956 (ttmm) REVERT: A 1241 ASP cc_start: 0.6535 (m-30) cc_final: 0.6245 (m-30) REVERT: A 1256 LEU cc_start: 0.7553 (tt) cc_final: 0.7184 (tm) REVERT: A 1302 GLU cc_start: 0.6683 (mp0) cc_final: 0.6268 (mp0) REVERT: A 1305 GLU cc_start: 0.6294 (tp30) cc_final: 0.6068 (tp30) REVERT: A 1309 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5991 (mt0) REVERT: A 1323 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7612 (ptt90) REVERT: A 1365 LYS cc_start: 0.7795 (pttt) cc_final: 0.7431 (ptpt) REVERT: A 1383 LYS cc_start: 0.7781 (tttp) cc_final: 0.7337 (ttpm) REVERT: A 1395 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6781 (tt0) REVERT: A 1408 ARG cc_start: 0.6970 (mtp-110) cc_final: 0.6703 (mmm-85) REVERT: B 21 LYS cc_start: 0.6364 (tptt) cc_final: 0.5782 (ttmm) REVERT: B 30 GLU cc_start: 0.7128 (pm20) cc_final: 0.6661 (pm20) REVERT: B 63 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7710 (mtmm) REVERT: B 64 TYR cc_start: 0.7259 (m-80) cc_final: 0.6869 (m-80) REVERT: B 93 GLU cc_start: 0.7169 (pm20) cc_final: 0.6946 (pm20) REVERT: B 182 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7308 (tptt) REVERT: B 317 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 320 PHE cc_start: 0.7464 (m-80) cc_final: 0.6813 (m-80) REVERT: B 331 LYS cc_start: 0.6721 (mppt) cc_final: 0.6471 (mttp) REVERT: B 357 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6799 (mp0) REVERT: B 498 ASN cc_start: 0.6891 (t0) cc_final: 0.5823 (m-40) REVERT: B 503 MET cc_start: 0.6207 (ttt) cc_final: 0.5913 (mtt) REVERT: B 587 MET cc_start: 0.7152 (mpp) cc_final: 0.6694 (mpp) REVERT: B 695 LYS cc_start: 0.6252 (ttpp) cc_final: 0.5822 (ttpp) REVERT: B 986 ILE cc_start: 0.6052 (tp) cc_final: 0.5540 (pp) REVERT: B 991 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 1036 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7656 (mm) REVERT: B 1118 LYS cc_start: 0.7333 (tttp) cc_final: 0.7088 (tttm) REVERT: B 1121 LEU cc_start: 0.8015 (mm) cc_final: 0.7745 (mm) REVERT: B 1133 LYS cc_start: 0.7350 (tttt) cc_final: 0.7053 (ttmm) REVERT: B 1173 VAL cc_start: 0.7388 (t) cc_final: 0.7090 (p) REVERT: B 1224 PHE cc_start: 0.5684 (m-10) cc_final: 0.5482 (m-10) REVERT: B 1256 LEU cc_start: 0.7631 (tt) cc_final: 0.7330 (tm) REVERT: B 1274 GLU cc_start: 0.7351 (tt0) cc_final: 0.6980 (pt0) REVERT: B 1302 GLU cc_start: 0.6028 (pm20) cc_final: 0.5786 (pm20) REVERT: B 1305 GLU cc_start: 0.6444 (tp30) cc_final: 0.6123 (tp30) REVERT: B 1323 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7438 (ptm-80) REVERT: B 1380 TYR cc_start: 0.4328 (m-80) cc_final: 0.4105 (m-80) REVERT: B 1395 GLU cc_start: 0.7149 (tt0) cc_final: 0.6843 (tt0) REVERT: B 1436 GLN cc_start: 0.7057 (tp40) cc_final: 0.6838 (mm110) REVERT: G 45 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: G 57 ASP cc_start: 0.6696 (p0) cc_final: 0.6488 (p0) REVERT: G 63 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7205 (mmtt) REVERT: G 80 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7177 (tpt-90) REVERT: G 90 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7601 (mm) REVERT: G 129 LEU cc_start: 0.7882 (tp) cc_final: 0.7625 (tt) REVERT: H 56 MET cc_start: 0.5130 (tpp) cc_final: 0.4356 (ttm) REVERT: H 90 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7619 (tt) outliers start: 51 outliers final: 28 residues processed: 338 average time/residue: 1.4962 time to fit residues: 587.1675 Evaluate side-chains 355 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 323 GLU 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 1039 LEU Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1309 GLN 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 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 319 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 1352 LEU 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 80 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 95 PHE Chi-restraints excluded: chain H residue 100 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.2980 chunk 273 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 265 optimal weight: 0.3980 chunk 160 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 240 optimal weight: 0.5980 chunk 251 optimal weight: 1.9990 chunk 264 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** B1108 HIS G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30096 Z= 0.190 Angle : 0.562 9.679 41970 Z= 0.307 Chirality : 0.039 0.188 4768 Planarity : 0.004 0.073 4228 Dihedral : 18.974 124.902 7208 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 1.77 % Allowed : 16.51 % Favored : 81.73 % 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: 0.76 (0.16), residues: 1114 sheet: 0.54 (0.35), residues: 234 loop : -0.89 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.036 0.001 PHE A 669 TYR 0.026 0.001 TYR A 151 ARG 0.010 0.001 ARG B 623 *********************** 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 355 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 311 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.6954 (tttp) cc_final: 0.6484 (tttp) REVERT: A 30 GLU cc_start: 0.7096 (pm20) cc_final: 0.6374 (pm20) REVERT: A 31 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7987 (pp) REVERT: A 32 LEU cc_start: 0.8786 (mp) cc_final: 0.8435 (mp) REVERT: A 63 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7608 (mtmm) REVERT: A 186 TYR cc_start: 0.7207 (t80) cc_final: 0.6744 (t80) REVERT: A 330 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: A 338 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: A 357 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6481 (mm-30) REVERT: A 428 TRP cc_start: 0.7467 (m-10) cc_final: 0.6991 (m-90) REVERT: A 498 ASN cc_start: 0.5986 (t0) cc_final: 0.5444 (m-40) REVERT: A 503 MET cc_start: 0.5805 (mmm) cc_final: 0.5392 (mmm) REVERT: A 991 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 996 LEU cc_start: 0.7263 (tp) cc_final: 0.7032 (tt) REVERT: A 1036 LEU cc_start: 0.7986 (tt) cc_final: 0.7701 (tm) REVERT: A 1133 LYS cc_start: 0.7100 (tttt) cc_final: 0.6866 (ttmm) REVERT: A 1256 LEU cc_start: 0.7468 (tt) cc_final: 0.7117 (tm) REVERT: A 1274 GLU cc_start: 0.7633 (tt0) cc_final: 0.7188 (tt0) REVERT: A 1302 GLU cc_start: 0.6670 (mp0) cc_final: 0.6303 (mp0) REVERT: A 1323 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7581 (ptt90) REVERT: A 1365 LYS cc_start: 0.7760 (pttt) cc_final: 0.7397 (ptpt) REVERT: A 1383 LYS cc_start: 0.7570 (tttp) cc_final: 0.7225 (ttpm) REVERT: A 1395 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6786 (tt0) REVERT: B 21 LYS cc_start: 0.6403 (tptt) cc_final: 0.5722 (ttmm) REVERT: B 30 GLU cc_start: 0.7085 (pm20) cc_final: 0.6632 (pm20) REVERT: B 63 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7687 (mtmm) REVERT: B 64 TYR cc_start: 0.7278 (m-80) cc_final: 0.6892 (m-80) REVERT: B 93 GLU cc_start: 0.7134 (pm20) cc_final: 0.6893 (pm20) REVERT: B 182 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7061 (mmtt) REVERT: B 317 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7281 (mm-30) REVERT: B 320 PHE cc_start: 0.7350 (m-80) cc_final: 0.6778 (m-80) REVERT: B 331 LYS cc_start: 0.6779 (mppt) cc_final: 0.6533 (mttp) REVERT: B 357 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6760 (mp0) REVERT: B 495 TYR cc_start: 0.5162 (m-10) cc_final: 0.4829 (m-10) REVERT: B 503 MET cc_start: 0.6113 (ttt) cc_final: 0.5803 (mtt) REVERT: B 587 MET cc_start: 0.7154 (mpp) cc_final: 0.6692 (mpp) REVERT: B 695 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5793 (ttpp) REVERT: B 986 ILE cc_start: 0.5933 (tp) cc_final: 0.5440 (pp) REVERT: B 1036 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7699 (mm) REVERT: B 1118 LYS cc_start: 0.7260 (tttp) cc_final: 0.7033 (tttm) REVERT: B 1121 LEU cc_start: 0.7982 (mm) cc_final: 0.7725 (mm) REVERT: B 1133 LYS cc_start: 0.7294 (tttt) cc_final: 0.6983 (ttmm) REVERT: B 1173 VAL cc_start: 0.7358 (t) cc_final: 0.7057 (p) REVERT: B 1224 PHE cc_start: 0.5473 (m-10) cc_final: 0.5178 (m-10) REVERT: B 1256 LEU cc_start: 0.7439 (tt) cc_final: 0.7172 (tm) REVERT: B 1274 GLU cc_start: 0.7312 (tt0) cc_final: 0.6980 (pt0) REVERT: B 1305 GLU cc_start: 0.6469 (tp30) cc_final: 0.6152 (tp30) REVERT: B 1323 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7249 (ptm-80) REVERT: B 1395 GLU cc_start: 0.7058 (tt0) cc_final: 0.6785 (tt0) REVERT: B 1433 LYS cc_start: 0.7711 (tptt) cc_final: 0.7454 (tptt) REVERT: B 1436 GLN cc_start: 0.6925 (tp40) cc_final: 0.6714 (mm110) REVERT: G 45 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: G 57 ASP cc_start: 0.6604 (p0) cc_final: 0.6358 (p0) REVERT: G 63 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7235 (mmtt) REVERT: G 80 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7172 (tpt-90) REVERT: G 90 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7519 (mm) REVERT: G 129 LEU cc_start: 0.7863 (tp) cc_final: 0.7611 (tt) REVERT: H 56 MET cc_start: 0.5113 (tpp) cc_final: 0.4325 (ttm) REVERT: H 90 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7612 (tt) outliers start: 44 outliers final: 27 residues processed: 332 average time/residue: 1.4784 time to fit residues: 572.2820 Evaluate side-chains 339 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 302 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 323 GLU 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 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 1420 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 319 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 1352 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 80 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 95 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.0970 chunk 281 optimal weight: 0.7980 chunk 171 optimal weight: 0.0020 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 181 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 overall best weight: 0.3564 ------------------------------------------------------------------------------- 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 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 306 GLN B1108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30096 Z= 0.174 Angle : 0.553 9.635 41970 Z= 0.303 Chirality : 0.038 0.190 4768 Planarity : 0.004 0.063 4228 Dihedral : 18.924 123.771 7208 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.49 % Allowed : 16.99 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2682 helix: 0.85 (0.16), residues: 1116 sheet: 0.58 (0.35), residues: 234 loop : -0.87 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.037 0.001 PHE A 425 TYR 0.026 0.001 TYR A 151 ARG 0.009 0.000 ARG B 623 ********************** 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 348 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 311 time to evaluate : 2.594 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: 0.6919 (tttp) cc_final: 0.6480 (tttp) REVERT: A 30 GLU cc_start: 0.7079 (pm20) cc_final: 0.6359 (pm20) REVERT: A 31 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 32 LEU cc_start: 0.8782 (mp) cc_final: 0.8506 (mp) REVERT: A 63 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7566 (mtmm) REVERT: A 186 TYR cc_start: 0.7200 (t80) cc_final: 0.6683 (t80) REVERT: A 277 ILE cc_start: 0.7157 (tp) cc_final: 0.6917 (mp) REVERT: A 290 LYS cc_start: 0.7386 (ttmm) cc_final: 0.7075 (ttmm) REVERT: A 330 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5879 (mt-10) REVERT: A 338 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: A 357 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6497 (mm-30) REVERT: A 428 TRP cc_start: 0.7464 (m-10) cc_final: 0.6946 (m-90) REVERT: A 429 GLN cc_start: 0.7662 (tp40) cc_final: 0.7462 (tp40) REVERT: A 498 ASN cc_start: 0.5879 (t0) cc_final: 0.5320 (m-40) REVERT: A 991 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: A 1036 LEU cc_start: 0.7966 (tt) cc_final: 0.7679 (tm) REVERT: A 1133 LYS cc_start: 0.7071 (tttt) cc_final: 0.6826 (ttmm) REVERT: A 1221 GLU cc_start: 0.7215 (mp0) cc_final: 0.6809 (mp0) REVERT: A 1240 ASN cc_start: 0.7088 (t0) cc_final: 0.6759 (t0) REVERT: A 1256 LEU cc_start: 0.7497 (tt) cc_final: 0.7146 (tm) REVERT: A 1274 GLU cc_start: 0.7489 (tt0) cc_final: 0.7035 (tt0) REVERT: A 1323 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7580 (ptt90) REVERT: A 1365 LYS cc_start: 0.7738 (pttt) cc_final: 0.7480 (ptpt) REVERT: A 1383 LYS cc_start: 0.7671 (tttp) cc_final: 0.7307 (ttpm) REVERT: A 1395 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6791 (tt0) REVERT: B 21 LYS cc_start: 0.6280 (tptt) cc_final: 0.5562 (ttmm) REVERT: B 30 GLU cc_start: 0.7057 (pm20) cc_final: 0.6499 (pm20) REVERT: B 63 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7673 (mtmm) REVERT: B 64 TYR cc_start: 0.7271 (m-80) cc_final: 0.6898 (m-80) REVERT: B 118 TRP cc_start: 0.7776 (m100) cc_final: 0.7541 (m100) REVERT: B 182 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7228 (mmtt) REVERT: B 317 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7376 (tp30) REVERT: B 318 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7759 (ttm-80) REVERT: B 320 PHE cc_start: 0.7247 (m-80) cc_final: 0.6703 (m-80) REVERT: B 331 LYS cc_start: 0.6688 (mppt) cc_final: 0.6447 (mttp) REVERT: B 357 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6792 (mp0) REVERT: B 495 TYR cc_start: 0.5167 (m-10) cc_final: 0.4835 (m-10) REVERT: B 498 ASN cc_start: 0.6811 (t0) cc_final: 0.5760 (m-40) REVERT: B 503 MET cc_start: 0.6149 (ttt) cc_final: 0.5805 (mtt) REVERT: B 587 MET cc_start: 0.7261 (mpp) cc_final: 0.6787 (mpp) REVERT: B 695 LYS cc_start: 0.6291 (ttpp) cc_final: 0.5780 (ttpp) REVERT: B 986 ILE cc_start: 0.5891 (tp) cc_final: 0.5420 (pp) REVERT: B 1036 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7689 (mm) REVERT: B 1118 LYS cc_start: 0.7229 (tttp) cc_final: 0.7008 (tttm) REVERT: B 1121 LEU cc_start: 0.7978 (mm) cc_final: 0.7736 (mm) REVERT: B 1133 LYS cc_start: 0.7274 (tttt) cc_final: 0.6966 (ttmm) REVERT: B 1173 VAL cc_start: 0.7369 (t) cc_final: 0.7058 (p) REVERT: B 1224 PHE cc_start: 0.5282 (m-10) cc_final: 0.4997 (m-10) REVERT: B 1240 ASN cc_start: 0.7251 (t0) cc_final: 0.6994 (t0) REVERT: B 1256 LEU cc_start: 0.7474 (tt) cc_final: 0.7176 (tm) REVERT: B 1274 GLU cc_start: 0.7290 (tt0) cc_final: 0.6970 (pt0) REVERT: B 1305 GLU cc_start: 0.6444 (tp30) cc_final: 0.6148 (tp30) REVERT: B 1323 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7206 (ptm-80) REVERT: B 1380 TYR cc_start: 0.4280 (m-80) cc_final: 0.4074 (m-80) REVERT: B 1395 GLU cc_start: 0.7014 (tt0) cc_final: 0.6763 (tt0) REVERT: B 1433 LYS cc_start: 0.7635 (tptt) cc_final: 0.7408 (tptt) REVERT: G 45 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: G 57 ASP cc_start: 0.6573 (p0) cc_final: 0.6145 (p0) REVERT: G 63 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7192 (mmtt) REVERT: G 80 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7190 (tpt-90) REVERT: G 90 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7508 (mm) REVERT: G 110 ASN cc_start: 0.8192 (t0) cc_final: 0.7818 (m110) REVERT: G 129 LEU cc_start: 0.7841 (tp) cc_final: 0.7592 (tt) REVERT: H 56 MET cc_start: 0.5107 (tpp) cc_final: 0.4334 (ttm) REVERT: H 90 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7569 (tt) outliers start: 37 outliers final: 23 residues processed: 328 average time/residue: 1.4741 time to fit residues: 562.5186 Evaluate side-chains 335 residues out of total 2486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 302 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 323 GLU 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 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 B residue 126 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 319 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 1438 PHE 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 80 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain H residue 30 GLU Chi-restraints excluded: chain H residue 90 LEU 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 186 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 65 optimal weight: 20.0000 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 241 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 303 ASN A 306 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 HIS ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.230823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.183758 restraints weight = 82315.751| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 3.84 r_work: 0.4050 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3467 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= 0.208 Angle : 0.571 9.555 41970 Z= 0.310 Chirality : 0.039 0.184 4768 Planarity : 0.004 0.067 4228 Dihedral : 18.907 123.052 7208 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.45 % Allowed : 17.27 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.05 (0.16), residues: 2682 helix: 0.84 (0.16), residues: 1112 sheet: 0.31 (0.33), residues: 258 loop : -0.84 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 174 HIS 0.005 0.001 HIS B 651 PHE 0.027 0.002 PHE B 249 TYR 0.031 0.002 TYR B1239 ARG 0.012 0.001 ARG H 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11010.65 seconds wall clock time: 193 minutes 34.09 seconds (11614.09 seconds total)