Starting phenix.real_space_refine on Tue Apr 9 11:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdu_17621/04_2024/8pdu_17621_updated.pdb" } resolution = 3.22 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= 0.023 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 10586 2.51 5 N 2692 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16210 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8082 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 29, 'TRANS': 992} Chain breaks: 5 Chain: "B" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8082 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 29, 'TRANS': 992} Chain breaks: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.81, per 1000 atoms: 0.54 Number of scatterers: 16210 At special positions: 0 Unit cell: (115.486, 156.366, 126.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 2844 8.00 N 2692 7.00 C 10586 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: 6.73 Conformation dependent library (CDL) restraints added in 2.8 seconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 8 sheets defined 71.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 76 through 96 removed outlier: 3.731A pdb=" N ILE A 81 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 94 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 95 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 96 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.709A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.833A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.125A pdb=" N GLN A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 163 through 187 removed outlier: 3.583A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 211 through 220 removed outlier: 3.562A pdb=" N ALA A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.835A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.515A pdb=" N VAL A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 Processing helix chain 'A' and resid 297 through 317 Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 374 removed outlier: 3.576A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 382 through 412 removed outlier: 3.628A pdb=" N TRP A 385 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 395 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 404 " --> pdb=" O MET A 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 406 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 470 through 480 removed outlier: 5.283A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 572 through 599 removed outlier: 3.830A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 Processing helix chain 'A' and resid 628 through 635 removed outlier: 4.058A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.722A pdb=" N ASP A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 651 " --> pdb=" O LYS A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 670 through 676 removed outlier: 3.628A pdb=" N HIS A 676 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 705 removed outlier: 4.326A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 3.674A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 760 removed outlier: 3.647A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HIS A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 779 Processing helix chain 'A' and resid 798 through 857 removed outlier: 4.086A pdb=" N LEU A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.674A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 888 removed outlier: 3.801A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 919 Processing helix chain 'A' and resid 924 through 942 removed outlier: 3.579A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 959 removed outlier: 4.242A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 976 Processing helix chain 'A' and resid 1046 through 1049 No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1086 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1114 through 1122 Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'B' and resid 76 through 96 removed outlier: 3.732A pdb=" N ILE B 81 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 95 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 96 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.710A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.833A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 152 removed outlier: 4.125A pdb=" N GLN B 140 " --> pdb=" O HIS B 136 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 187 removed outlier: 3.584A pdb=" N LEU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.562A pdb=" N ALA B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.836A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.515A pdb=" N VAL B 271 " --> pdb=" O TYR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 343 through 374 removed outlier: 3.577A pdb=" N PHE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 382 through 412 removed outlier: 3.628A pdb=" N TRP B 385 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 395 " --> pdb=" O TYR B 392 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 404 " --> pdb=" O MET B 401 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 406 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 450 through 468 Processing helix chain 'B' and resid 470 through 480 removed outlier: 5.282A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 514 Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 572 through 599 removed outlier: 3.830A pdb=" N ASP B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 620 Processing helix chain 'B' and resid 628 through 635 removed outlier: 4.058A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.723A pdb=" N ASP B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 656 No H-bonds generated for 'chain 'B' and resid 654 through 656' Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.628A pdb=" N HIS B 676 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 705 removed outlier: 4.326A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix removed outlier: 3.674A pdb=" N PHE B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 760 removed outlier: 3.647A pdb=" N ALA B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HIS B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE B 759 " --> pdb=" O GLY B 755 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL B 760 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 779 Processing helix chain 'B' and resid 798 through 857 removed outlier: 4.086A pdb=" N LEU B 804 " --> pdb=" O LYS B 800 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 807 " --> pdb=" O ARG B 803 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.674A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 888 removed outlier: 3.801A pdb=" N GLN B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 887 " --> pdb=" O GLY B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 919 Processing helix chain 'B' and resid 924 through 942 removed outlier: 3.579A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 959 removed outlier: 4.242A pdb=" N LYS B 958 " --> pdb=" O GLU B 954 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 976 Processing helix chain 'B' and resid 1046 through 1049 No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1070 through 1079 Processing helix chain 'B' and resid 1086 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1114 through 1122 Processing helix chain 'B' and resid 1129 through 1131 No H-bonds generated for 'chain 'B' and resid 1129 through 1131' Processing sheet with id= A, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.512A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A1068 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE A 999 " --> pdb=" O ILE A1068 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1034 through 1036 removed outlier: 3.768A pdb=" N TYR A1009 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= D, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 3.708A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.512A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B1068 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE B 999 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1034 through 1036 removed outlier: 3.768A pdb=" N TYR B1009 " --> pdb=" O THR B1056 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1134 through 1136 Processing sheet with id= H, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 3.707A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 7.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5126 1.34 - 1.46: 3685 1.46 - 1.58: 7555 1.58 - 1.70: 4 1.70 - 1.82: 158 Bond restraints: 16528 Sorted by residual: bond pdb=" C2' PCG A1401 " pdb=" C3' PCG A1401 " ideal model delta sigma weight residual 1.200 1.523 -0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C2' PCG B1401 " pdb=" C3' PCG B1401 " ideal model delta sigma weight residual 1.200 1.523 -0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C3' PCG B1401 " pdb=" C4' PCG B1401 " ideal model delta sigma weight residual 1.808 1.505 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C3' PCG A1401 " pdb=" C4' PCG A1401 " ideal model delta sigma weight residual 1.808 1.505 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C1' PCG A1401 " pdb=" N9 PCG A1401 " ideal model delta sigma weight residual 1.216 1.473 -0.257 2.00e-02 2.50e+03 1.65e+02 ... (remaining 16523 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.84: 406 106.84 - 113.64: 9565 113.64 - 120.43: 6210 120.43 - 127.23: 6067 127.23 - 134.03: 172 Bond angle restraints: 22420 Sorted by residual: angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 112.96 107.11 5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" N VAL B 137 " pdb=" CA VAL B 137 " pdb=" C VAL B 137 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" N ILE B 657 " pdb=" CA ILE B 657 " pdb=" C ILE B 657 " ideal model delta sigma weight residual 111.62 108.84 2.78 7.90e-01 1.60e+00 1.24e+01 angle pdb=" N ILE A 657 " pdb=" CA ILE A 657 " pdb=" C ILE A 657 " ideal model delta sigma weight residual 111.62 108.85 2.77 7.90e-01 1.60e+00 1.23e+01 angle pdb=" O1A PCG A1401 " pdb=" PA PCG A1401 " pdb=" O2A PCG A1401 " ideal model delta sigma weight residual 109.32 118.89 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 22415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 9402 23.74 - 47.49: 426 47.49 - 71.23: 32 71.23 - 94.97: 4 94.97 - 118.72: 2 Dihedral angle restraints: 9866 sinusoidal: 3916 harmonic: 5950 Sorted by residual: dihedral pdb=" C5' PCG B1401 " pdb=" O5' PCG B1401 " pdb=" PA PCG B1401 " pdb=" O3' PCG B1401 " ideal model delta sinusoidal sigma weight residual -50.69 68.03 -118.72 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C5' PCG A1401 " pdb=" O5' PCG A1401 " pdb=" PA PCG A1401 " pdb=" O3' PCG A1401 " ideal model delta sinusoidal sigma weight residual -50.69 68.02 -118.71 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" CA GLN A 624 " pdb=" C GLN A 624 " pdb=" N PHE A 625 " pdb=" CA PHE A 625 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2663 0.111 - 0.222: 27 0.222 - 0.333: 4 0.333 - 0.443: 0 0.443 - 0.554: 2 Chirality restraints: 2696 Sorted by residual: chirality pdb=" C3' PCG B1401 " pdb=" C2' PCG B1401 " pdb=" C4' PCG B1401 " pdb=" O3' PCG B1401 " both_signs ideal model delta sigma weight residual False -2.10 -2.66 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" C3' PCG A1401 " pdb=" C2' PCG A1401 " pdb=" C4' PCG A1401 " pdb=" O3' PCG A1401 " both_signs ideal model delta sigma weight residual False -2.10 -2.66 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C2' PCG B1401 " pdb=" C1' PCG B1401 " pdb=" C3' PCG B1401 " pdb=" O2' PCG B1401 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 2693 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 693 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO B 694 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 693 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 694 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 295 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C ASN A 295 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 295 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 296 " 0.008 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2542 2.76 - 3.29: 17077 3.29 - 3.83: 26129 3.83 - 4.36: 30899 4.36 - 4.90: 53274 Nonbonded interactions: 129921 Sorted by model distance: nonbonded pdb=" SD MET B 602 " pdb=" CG GLU B1115 " model vdw 2.221 3.800 nonbonded pdb=" SD MET A 602 " pdb=" CG GLU A1115 " model vdw 2.221 3.800 nonbonded pdb=" O ASP A 534 " pdb=" OD1 ASP A 534 " model vdw 2.256 3.040 nonbonded pdb=" O ASP B 534 " pdb=" OD1 ASP B 534 " model vdw 2.256 3.040 nonbonded pdb=" O VAL B 115 " pdb=" OG SER B 118 " model vdw 2.262 2.440 ... (remaining 129916 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.250 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 45.830 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 : 0.008 0.323 16528 Z= 0.541 Angle : 0.562 9.573 22420 Z= 0.312 Chirality : 0.041 0.554 2696 Planarity : 0.003 0.049 2748 Dihedral : 13.023 118.717 6006 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: 0.82 (0.18), residues: 2020 helix: 0.96 (0.13), residues: 1464 sheet: -0.31 (0.80), residues: 48 loop : -0.36 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 278 HIS 0.007 0.001 HIS A1172 PHE 0.014 0.001 PHE B 457 TYR 0.007 0.001 TYR B 309 ARG 0.002 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 1.613 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 76 LYS cc_start: 0.7895 (mttm) cc_final: 0.7610 (mttm) REVERT: A 113 LEU cc_start: 0.7529 (mt) cc_final: 0.7162 (mp) REVERT: A 120 VAL cc_start: 0.6948 (t) cc_final: 0.6017 (p) REVERT: A 124 GLU cc_start: 0.6127 (tt0) cc_final: 0.5841 (mt-10) REVERT: A 125 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7081 (mp0) REVERT: A 154 MET cc_start: 0.8212 (tpp) cc_final: 0.7681 (mmt) REVERT: A 224 LYS cc_start: 0.7931 (pttt) cc_final: 0.7377 (pttt) REVERT: A 233 GLU cc_start: 0.7764 (tt0) cc_final: 0.6783 (pt0) REVERT: A 270 GLN cc_start: 0.7638 (mt0) cc_final: 0.7430 (mt0) REVERT: A 289 PHE cc_start: 0.8010 (m-80) cc_final: 0.7787 (m-80) REVERT: A 296 ASP cc_start: 0.7818 (t0) cc_final: 0.7466 (t0) REVERT: A 300 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 320 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7395 (mm-30) REVERT: A 337 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 377 LEU cc_start: 0.7971 (mt) cc_final: 0.7770 (mt) REVERT: A 384 ASP cc_start: 0.7009 (m-30) cc_final: 0.6709 (m-30) REVERT: A 406 PHE cc_start: 0.6637 (m-80) cc_final: 0.6393 (m-80) REVERT: A 444 ASN cc_start: 0.7251 (m-40) cc_final: 0.6961 (m110) REVERT: A 475 GLN cc_start: 0.7319 (tp40) cc_final: 0.7011 (tp40) REVERT: A 494 MET cc_start: 0.6833 (tpp) cc_final: 0.6542 (mmm) REVERT: A 499 ARG cc_start: 0.7085 (ttt180) cc_final: 0.6839 (ttt180) REVERT: A 503 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6936 (mt-10) REVERT: A 513 LYS cc_start: 0.7775 (mttt) cc_final: 0.7555 (mttp) REVERT: A 517 PHE cc_start: 0.7073 (m-10) cc_final: 0.6688 (m-10) REVERT: A 579 MET cc_start: 0.5493 (mtp) cc_final: 0.5243 (mtp) REVERT: A 580 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6192 (tp30) REVERT: A 608 LEU cc_start: 0.7462 (tp) cc_final: 0.7184 (tp) REVERT: A 609 ARG cc_start: 0.7480 (mtp-110) cc_final: 0.7148 (mtp180) REVERT: A 612 VAL cc_start: 0.6676 (t) cc_final: 0.6467 (m) REVERT: A 613 GLN cc_start: 0.6713 (tt0) cc_final: 0.6506 (tt0) REVERT: A 629 ASP cc_start: 0.7675 (m-30) cc_final: 0.7351 (m-30) REVERT: A 630 ASP cc_start: 0.7867 (m-30) cc_final: 0.7632 (m-30) REVERT: A 643 TRP cc_start: 0.7707 (t60) cc_final: 0.7503 (t60) REVERT: A 647 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7802 (mmtm) REVERT: A 650 ASP cc_start: 0.8099 (m-30) cc_final: 0.7818 (m-30) REVERT: A 678 MET cc_start: 0.7305 (mmm) cc_final: 0.6782 (mmm) REVERT: A 837 TYR cc_start: 0.7523 (m-80) cc_final: 0.7105 (m-80) REVERT: A 877 GLN cc_start: 0.7258 (mt0) cc_final: 0.7038 (mt0) REVERT: A 881 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 931 GLU cc_start: 0.7031 (tt0) cc_final: 0.6755 (tt0) REVERT: A 967 MET cc_start: 0.6351 (mtp) cc_final: 0.5912 (mtp) REVERT: A 971 ASP cc_start: 0.7117 (m-30) cc_final: 0.6662 (m-30) REVERT: A 976 ARG cc_start: 0.7858 (mpt180) cc_final: 0.7262 (mmt-90) REVERT: A 982 PHE cc_start: 0.6890 (m-80) cc_final: 0.6645 (m-10) REVERT: A 986 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6291 (mt-10) REVERT: A 1003 SER cc_start: 0.7970 (t) cc_final: 0.7624 (t) REVERT: A 1122 GLU cc_start: 0.7003 (tp30) cc_final: 0.6351 (tp30) REVERT: A 1125 TYR cc_start: 0.6207 (p90) cc_final: 0.5594 (p90) REVERT: B 76 LYS cc_start: 0.7857 (mttm) cc_final: 0.7573 (mttm) REVERT: B 125 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7306 (mp0) REVERT: B 128 ARG cc_start: 0.7117 (ttp-170) cc_final: 0.6812 (ptm160) REVERT: B 154 MET cc_start: 0.8053 (tpp) cc_final: 0.7448 (mmt) REVERT: B 187 ASN cc_start: 0.6975 (m-40) cc_final: 0.6752 (m110) REVERT: B 205 MET cc_start: 0.7630 (tpp) cc_final: 0.7205 (mpp) REVERT: B 214 VAL cc_start: 0.7931 (p) cc_final: 0.7675 (m) REVERT: B 224 LYS cc_start: 0.7900 (pttt) cc_final: 0.7368 (pttt) REVERT: B 344 GLU cc_start: 0.7713 (tt0) cc_final: 0.7372 (tm-30) REVERT: B 475 GLN cc_start: 0.7244 (tp40) cc_final: 0.6920 (tp-100) REVERT: B 503 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 513 LYS cc_start: 0.7820 (mttt) cc_final: 0.7605 (mttp) REVERT: B 579 MET cc_start: 0.5597 (mtp) cc_final: 0.5170 (mtp) REVERT: B 580 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6209 (tp30) REVERT: B 584 LEU cc_start: 0.7802 (mt) cc_final: 0.7597 (mm) REVERT: B 608 LEU cc_start: 0.7430 (tp) cc_final: 0.7152 (tp) REVERT: B 609 ARG cc_start: 0.7434 (mtp-110) cc_final: 0.7102 (mtp180) REVERT: B 612 VAL cc_start: 0.6706 (t) cc_final: 0.6492 (m) REVERT: B 630 ASP cc_start: 0.7902 (m-30) cc_final: 0.7656 (m-30) REVERT: B 647 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8023 (mmtm) REVERT: B 650 ASP cc_start: 0.8161 (m-30) cc_final: 0.7871 (m-30) REVERT: B 678 MET cc_start: 0.6973 (mmm) cc_final: 0.6574 (mmm) REVERT: B 684 ILE cc_start: 0.8114 (mp) cc_final: 0.7913 (pt) REVERT: B 810 MET cc_start: 0.6669 (mmm) cc_final: 0.6428 (mmm) REVERT: B 832 GLN cc_start: 0.7293 (tp40) cc_final: 0.6907 (tp40) REVERT: B 866 GLU cc_start: 0.7542 (tt0) cc_final: 0.7141 (tp30) REVERT: B 881 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6957 (mm-30) REVERT: B 923 ASP cc_start: 0.7151 (m-30) cc_final: 0.6792 (p0) REVERT: B 931 GLU cc_start: 0.7058 (tt0) cc_final: 0.6620 (mt-10) REVERT: B 946 SER cc_start: 0.7974 (p) cc_final: 0.7695 (m) REVERT: B 967 MET cc_start: 0.6514 (mtp) cc_final: 0.6237 (mtp) REVERT: B 976 ARG cc_start: 0.7571 (mpt180) cc_final: 0.7306 (tpt170) REVERT: B 986 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6740 (mt-10) REVERT: B 988 ILE cc_start: 0.8241 (mt) cc_final: 0.8032 (mp) REVERT: B 994 GLU cc_start: 0.7380 (tt0) cc_final: 0.7067 (tp30) REVERT: B 999 PHE cc_start: 0.6910 (m-80) cc_final: 0.6627 (m-80) REVERT: B 1003 SER cc_start: 0.7793 (t) cc_final: 0.7355 (t) REVERT: B 1040 ASN cc_start: 0.7280 (m110) cc_final: 0.6704 (m110) REVERT: B 1060 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7070 (tp30) REVERT: B 1125 TYR cc_start: 0.6170 (p90) cc_final: 0.5472 (p90) REVERT: B 1128 ASP cc_start: 0.6943 (m-30) cc_final: 0.5835 (t0) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.3242 time to fit residues: 218.8769 Evaluate side-chains 414 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0000 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.5980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 190 ASN A 597 GLN A 600 HIS A 636 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 190 ASN B 444 ASN B 600 HIS B 636 GLN B 886 GLN B 981 HIS ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16528 Z= 0.177 Angle : 0.530 7.207 22420 Z= 0.281 Chirality : 0.040 0.181 2696 Planarity : 0.004 0.042 2748 Dihedral : 5.562 89.844 2200 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.99 % Allowed : 11.26 % Favored : 86.75 % 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: 1.33 (0.19), residues: 2020 helix: 1.33 (0.13), residues: 1468 sheet: 0.01 (0.66), residues: 62 loop : -0.16 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS B1172 PHE 0.014 0.001 PHE B 982 TYR 0.020 0.001 TYR B 984 ARG 0.006 0.000 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 421 time to evaluate : 2.498 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 125 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6645 (mm-30) REVERT: A 128 ARG cc_start: 0.7043 (ptp-110) cc_final: 0.5844 (ptp-170) REVERT: A 154 MET cc_start: 0.8214 (tpp) cc_final: 0.7883 (mmt) REVERT: A 289 PHE cc_start: 0.8062 (m-80) cc_final: 0.7805 (m-80) REVERT: A 320 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 337 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 377 LEU cc_start: 0.7931 (mt) cc_final: 0.7377 (mt) REVERT: A 384 ASP cc_start: 0.6748 (m-30) cc_final: 0.6389 (m-30) REVERT: A 420 ARG cc_start: 0.7498 (ptp90) cc_final: 0.7246 (mtt90) REVERT: A 475 GLN cc_start: 0.7268 (tp40) cc_final: 0.7002 (tp40) REVERT: A 503 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 517 PHE cc_start: 0.7303 (m-10) cc_final: 0.7006 (m-10) REVERT: A 579 MET cc_start: 0.5824 (mtp) cc_final: 0.5405 (mtp) REVERT: A 580 GLU cc_start: 0.6700 (mm-30) cc_final: 0.6137 (tp30) REVERT: A 590 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6816 (mt-10) REVERT: A 591 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6971 (mtpp) REVERT: A 608 LEU cc_start: 0.7449 (tp) cc_final: 0.7215 (tp) REVERT: A 609 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.7050 (mtp180) REVERT: A 629 ASP cc_start: 0.7334 (m-30) cc_final: 0.7107 (m-30) REVERT: A 634 SER cc_start: 0.8193 (t) cc_final: 0.7741 (p) REVERT: A 643 TRP cc_start: 0.7781 (t60) cc_final: 0.7561 (t60) REVERT: A 647 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7830 (mmtm) REVERT: A 650 ASP cc_start: 0.8098 (m-30) cc_final: 0.7828 (m-30) REVERT: A 678 MET cc_start: 0.7169 (mmm) cc_final: 0.6683 (mmm) REVERT: A 841 LYS cc_start: 0.7083 (tttt) cc_final: 0.6714 (mmmt) REVERT: A 847 GLU cc_start: 0.6702 (tp30) cc_final: 0.6467 (tp30) REVERT: A 849 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 872 GLU cc_start: 0.6240 (tp30) cc_final: 0.5755 (mm-30) REVERT: A 925 MET cc_start: 0.6394 (ttp) cc_final: 0.6099 (ttp) REVERT: A 931 GLU cc_start: 0.7231 (tt0) cc_final: 0.6890 (mt-10) REVERT: A 955 ASN cc_start: 0.7504 (t0) cc_final: 0.7235 (t0) REVERT: A 958 LYS cc_start: 0.7182 (ttpp) cc_final: 0.6783 (ttpp) REVERT: A 967 MET cc_start: 0.6540 (mtp) cc_final: 0.6012 (mtp) REVERT: A 971 ASP cc_start: 0.7222 (m-30) cc_final: 0.6828 (m-30) REVERT: A 982 PHE cc_start: 0.6707 (m-80) cc_final: 0.6227 (m-10) REVERT: A 986 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6425 (mt-10) REVERT: A 989 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6715 (m) REVERT: A 1034 ASP cc_start: 0.6816 (t0) cc_final: 0.6542 (t0) REVERT: A 1038 VAL cc_start: 0.7841 (t) cc_final: 0.7547 (p) REVERT: A 1057 VAL cc_start: 0.6374 (t) cc_final: 0.6103 (p) REVERT: A 1060 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 1078 ASP cc_start: 0.7916 (m-30) cc_final: 0.7697 (m-30) REVERT: A 1122 GLU cc_start: 0.7162 (tp30) cc_final: 0.6919 (tm-30) REVERT: B 76 LYS cc_start: 0.7770 (mttm) cc_final: 0.7518 (mttm) REVERT: B 125 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7033 (mp0) REVERT: B 128 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6805 (ptm160) REVERT: B 154 MET cc_start: 0.8022 (tpp) cc_final: 0.7687 (mmt) REVERT: B 186 MET cc_start: 0.5583 (mpp) cc_final: 0.5225 (mpp) REVERT: B 205 MET cc_start: 0.7650 (tpp) cc_final: 0.7235 (tpp) REVERT: B 236 LEU cc_start: 0.7492 (mm) cc_final: 0.7222 (mp) REVERT: B 251 MET cc_start: 0.7814 (mtm) cc_final: 0.7571 (mtm) REVERT: B 338 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7369 (mtmt) REVERT: B 344 GLU cc_start: 0.7612 (tt0) cc_final: 0.7255 (tm-30) REVERT: B 346 GLU cc_start: 0.7105 (tt0) cc_final: 0.6806 (tp30) REVERT: B 407 SER cc_start: 0.7070 (t) cc_final: 0.6765 (m) REVERT: B 475 GLN cc_start: 0.7172 (tp40) cc_final: 0.6817 (tp-100) REVERT: B 579 MET cc_start: 0.5828 (mtp) cc_final: 0.5365 (mtp) REVERT: B 580 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6362 (tp30) REVERT: B 608 LEU cc_start: 0.7384 (tp) cc_final: 0.7146 (tp) REVERT: B 609 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.7097 (mtp180) REVERT: B 630 ASP cc_start: 0.7821 (m-30) cc_final: 0.7555 (m-30) REVERT: B 633 LYS cc_start: 0.7882 (mttt) cc_final: 0.7214 (mmtp) REVERT: B 634 SER cc_start: 0.8154 (m) cc_final: 0.7870 (p) REVERT: B 650 ASP cc_start: 0.8141 (m-30) cc_final: 0.7929 (m-30) REVERT: B 678 MET cc_start: 0.6820 (mmm) cc_final: 0.6415 (mmm) REVERT: B 810 MET cc_start: 0.6809 (mmm) cc_final: 0.6533 (mmm) REVERT: B 881 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6982 (mm-30) REVERT: B 887 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.7027 (mmm-85) REVERT: B 931 GLU cc_start: 0.7224 (tt0) cc_final: 0.6868 (mt-10) REVERT: B 946 SER cc_start: 0.7998 (p) cc_final: 0.7743 (m) REVERT: B 955 ASN cc_start: 0.7156 (t0) cc_final: 0.6889 (t0) REVERT: B 958 LYS cc_start: 0.7193 (ttpp) cc_final: 0.6847 (ttpp) REVERT: B 986 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6935 (mt-10) REVERT: B 994 GLU cc_start: 0.7295 (tt0) cc_final: 0.6994 (tp30) REVERT: B 1007 LYS cc_start: 0.7276 (tttt) cc_final: 0.6771 (tttp) REVERT: B 1038 VAL cc_start: 0.7817 (t) cc_final: 0.7549 (p) REVERT: B 1040 ASN cc_start: 0.7410 (m110) cc_final: 0.6927 (m110) REVERT: B 1060 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7044 (tp30) REVERT: B 1115 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6631 (mm-30) REVERT: B 1128 ASP cc_start: 0.6941 (m-30) cc_final: 0.5877 (t0) outliers start: 35 outliers final: 18 residues processed: 435 average time/residue: 0.3004 time to fit residues: 192.2508 Evaluate side-chains 415 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 396 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 0.0000 chunk 126 optimal weight: 0.0170 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 184 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 0.4980 overall best weight: 0.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 190 ASN A 295 ASN A 877 GLN A 886 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 270 GLN B 886 GLN ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16528 Z= 0.141 Angle : 0.468 6.369 22420 Z= 0.249 Chirality : 0.038 0.196 2696 Planarity : 0.004 0.042 2748 Dihedral : 5.362 91.805 2200 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.22 % Allowed : 13.31 % Favored : 84.47 % 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: 1.63 (0.19), residues: 2020 helix: 1.53 (0.13), residues: 1472 sheet: 0.66 (0.65), residues: 62 loop : -0.09 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.003 0.001 HIS A 292 PHE 0.014 0.001 PHE A 999 TYR 0.020 0.001 TYR B 984 ARG 0.004 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 410 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.7607 (p) cc_final: 0.7373 (p) REVERT: A 125 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6812 (mm-30) REVERT: A 128 ARG cc_start: 0.7154 (ptp-170) cc_final: 0.5942 (ptp-110) REVERT: A 154 MET cc_start: 0.8062 (tpp) cc_final: 0.7552 (tpp) REVERT: A 199 MET cc_start: 0.7527 (mmm) cc_final: 0.7225 (mmm) REVERT: A 205 MET cc_start: 0.7487 (tpp) cc_final: 0.6927 (mmt) REVERT: A 337 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 346 GLU cc_start: 0.7226 (tt0) cc_final: 0.6834 (tt0) REVERT: A 475 GLN cc_start: 0.7312 (tp40) cc_final: 0.7025 (tp40) REVERT: A 503 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6842 (mt-10) REVERT: A 517 PHE cc_start: 0.7245 (m-10) cc_final: 0.6515 (m-10) REVERT: A 520 ASP cc_start: 0.7856 (p0) cc_final: 0.7600 (p0) REVERT: A 579 MET cc_start: 0.5781 (mtp) cc_final: 0.5459 (mtp) REVERT: A 580 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6090 (tp30) REVERT: A 591 LYS cc_start: 0.7376 (mtpp) cc_final: 0.6981 (mtpp) REVERT: A 629 ASP cc_start: 0.7373 (m-30) cc_final: 0.6804 (m-30) REVERT: A 633 LYS cc_start: 0.7709 (mttt) cc_final: 0.6901 (mmtm) REVERT: A 634 SER cc_start: 0.8150 (t) cc_final: 0.7666 (p) REVERT: A 647 LYS cc_start: 0.8267 (mmtm) cc_final: 0.8016 (mtmm) REVERT: A 650 ASP cc_start: 0.8093 (m-30) cc_final: 0.7836 (m-30) REVERT: A 678 MET cc_start: 0.7149 (mmm) cc_final: 0.6654 (mmm) REVERT: A 841 LYS cc_start: 0.7075 (tttt) cc_final: 0.6586 (mmmt) REVERT: A 877 GLN cc_start: 0.7427 (mt0) cc_final: 0.7105 (mt0) REVERT: A 881 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6946 (mm-30) REVERT: A 931 GLU cc_start: 0.7272 (tt0) cc_final: 0.6952 (mt-10) REVERT: A 955 ASN cc_start: 0.7520 (t0) cc_final: 0.7229 (t0) REVERT: A 958 LYS cc_start: 0.7211 (ttpp) cc_final: 0.6817 (ttpp) REVERT: A 967 MET cc_start: 0.6533 (mtp) cc_final: 0.6011 (mtp) REVERT: A 971 ASP cc_start: 0.7273 (m-30) cc_final: 0.6866 (m-30) REVERT: A 982 PHE cc_start: 0.6683 (m-80) cc_final: 0.6326 (m-10) REVERT: A 986 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6615 (mt-10) REVERT: A 999 PHE cc_start: 0.6785 (m-10) cc_final: 0.6567 (m-80) REVERT: A 1038 VAL cc_start: 0.7669 (t) cc_final: 0.7455 (p) REVERT: A 1040 ASN cc_start: 0.7524 (m110) cc_final: 0.6955 (m110) REVERT: A 1060 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 76 LYS cc_start: 0.7714 (mttm) cc_final: 0.7491 (mttm) REVERT: B 103 THR cc_start: 0.7675 (p) cc_final: 0.7428 (p) REVERT: B 125 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7038 (mp0) REVERT: B 128 ARG cc_start: 0.7154 (ttp-170) cc_final: 0.6844 (ptp-110) REVERT: B 197 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6533 (mp0) REVERT: B 236 LEU cc_start: 0.7496 (mm) cc_final: 0.7240 (mp) REVERT: B 319 LEU cc_start: 0.8033 (mt) cc_final: 0.7802 (mp) REVERT: B 344 GLU cc_start: 0.7627 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 346 GLU cc_start: 0.7250 (tt0) cc_final: 0.6838 (tt0) REVERT: B 407 SER cc_start: 0.7042 (t) cc_final: 0.6741 (m) REVERT: B 475 GLN cc_start: 0.7215 (tp40) cc_final: 0.6940 (tp-100) REVERT: B 579 MET cc_start: 0.5851 (mtp) cc_final: 0.5422 (mtp) REVERT: B 580 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6226 (tp30) REVERT: B 591 LYS cc_start: 0.7270 (mtpp) cc_final: 0.6864 (mtpp) REVERT: B 605 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6590 (mtp-110) REVERT: B 609 ARG cc_start: 0.7325 (mtp-110) cc_final: 0.7066 (mtp180) REVERT: B 630 ASP cc_start: 0.7828 (m-30) cc_final: 0.7579 (m-30) REVERT: B 633 LYS cc_start: 0.7868 (mttt) cc_final: 0.7153 (mmtp) REVERT: B 647 LYS cc_start: 0.8343 (mmmm) cc_final: 0.8055 (mtmt) REVERT: B 650 ASP cc_start: 0.8190 (m-30) cc_final: 0.7909 (m-30) REVERT: B 678 MET cc_start: 0.6707 (mmm) cc_final: 0.6311 (mmm) REVERT: B 810 MET cc_start: 0.6766 (mmm) cc_final: 0.6476 (mmm) REVERT: B 832 GLN cc_start: 0.7446 (tp40) cc_final: 0.7045 (tp40) REVERT: B 841 LYS cc_start: 0.7026 (tttt) cc_final: 0.6532 (mmmt) REVERT: B 881 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 887 ARG cc_start: 0.7512 (mmm-85) cc_final: 0.7003 (mmm-85) REVERT: B 931 GLU cc_start: 0.7225 (tt0) cc_final: 0.6931 (mt-10) REVERT: B 946 SER cc_start: 0.8043 (p) cc_final: 0.7796 (m) REVERT: B 955 ASN cc_start: 0.7167 (t0) cc_final: 0.6916 (t0) REVERT: B 958 LYS cc_start: 0.7231 (ttpp) cc_final: 0.6896 (ttpp) REVERT: B 967 MET cc_start: 0.6438 (mtp) cc_final: 0.6106 (mmm) REVERT: B 994 GLU cc_start: 0.7229 (tt0) cc_final: 0.6950 (tp30) REVERT: B 1007 LYS cc_start: 0.7177 (tttt) cc_final: 0.6534 (tmtt) REVERT: B 1034 ASP cc_start: 0.7080 (t0) cc_final: 0.6816 (t70) REVERT: B 1040 ASN cc_start: 0.7635 (m110) cc_final: 0.7067 (m110) REVERT: B 1057 VAL cc_start: 0.5996 (t) cc_final: 0.5736 (p) REVERT: B 1060 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6806 (tm-30) REVERT: B 1115 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6424 (mm-30) REVERT: B 1128 ASP cc_start: 0.6968 (m-30) cc_final: 0.5895 (t0) outliers start: 39 outliers final: 23 residues processed: 429 average time/residue: 0.2855 time to fit residues: 180.7693 Evaluate side-chains 406 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 383 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1033 GLU Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.4980 chunk 197 optimal weight: 0.0670 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 190 ASN A 295 ASN A 597 GLN A 886 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 295 ASN B 600 HIS ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16528 Z= 0.182 Angle : 0.485 7.221 22420 Z= 0.255 Chirality : 0.039 0.227 2696 Planarity : 0.004 0.043 2748 Dihedral : 5.363 92.471 2200 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.05 % Allowed : 15.02 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2020 helix: 1.48 (0.14), residues: 1468 sheet: 0.95 (0.64), residues: 62 loop : 0.03 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS B1120 PHE 0.014 0.001 PHE B 254 TYR 0.018 0.001 TYR B 984 ARG 0.008 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 384 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6840 (mm-30) REVERT: A 128 ARG cc_start: 0.7175 (ptp-110) cc_final: 0.5974 (ptp-110) REVERT: A 199 MET cc_start: 0.7541 (mmm) cc_final: 0.7249 (mmm) REVERT: A 205 MET cc_start: 0.7585 (tpp) cc_final: 0.7177 (mpp) REVERT: A 269 LEU cc_start: 0.7239 (mt) cc_final: 0.6989 (mm) REVERT: A 337 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 346 GLU cc_start: 0.7247 (tt0) cc_final: 0.6691 (tm-30) REVERT: A 407 SER cc_start: 0.6748 (t) cc_final: 0.6465 (m) REVERT: A 475 GLN cc_start: 0.7340 (tp40) cc_final: 0.7053 (tp-100) REVERT: A 503 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 517 PHE cc_start: 0.7358 (m-10) cc_final: 0.6578 (m-10) REVERT: A 579 MET cc_start: 0.5755 (mtp) cc_final: 0.5450 (mtp) REVERT: A 580 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6125 (tp30) REVERT: A 591 LYS cc_start: 0.7372 (mtpp) cc_final: 0.6997 (mtpp) REVERT: A 629 ASP cc_start: 0.7374 (m-30) cc_final: 0.6769 (m-30) REVERT: A 632 LYS cc_start: 0.7187 (ttmm) cc_final: 0.6983 (ttmm) REVERT: A 633 LYS cc_start: 0.7753 (mttt) cc_final: 0.6938 (mmtm) REVERT: A 634 SER cc_start: 0.8114 (t) cc_final: 0.7708 (p) REVERT: A 643 TRP cc_start: 0.7963 (t60) cc_final: 0.7732 (t60) REVERT: A 647 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7942 (mmmm) REVERT: A 650 ASP cc_start: 0.8077 (m-30) cc_final: 0.7836 (m-30) REVERT: A 678 MET cc_start: 0.7026 (mmm) cc_final: 0.6573 (mmm) REVERT: A 832 GLN cc_start: 0.7431 (tp40) cc_final: 0.6942 (tp-100) REVERT: A 841 LYS cc_start: 0.7138 (tttt) cc_final: 0.6623 (mmmt) REVERT: A 881 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 931 GLU cc_start: 0.7308 (tt0) cc_final: 0.6975 (mt-10) REVERT: A 955 ASN cc_start: 0.7553 (t0) cc_final: 0.7285 (t0) REVERT: A 958 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6852 (ttpp) REVERT: A 967 MET cc_start: 0.6538 (mtp) cc_final: 0.6025 (mtp) REVERT: A 971 ASP cc_start: 0.7249 (m-30) cc_final: 0.6817 (m-30) REVERT: A 982 PHE cc_start: 0.6684 (m-80) cc_final: 0.6354 (m-10) REVERT: A 986 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 999 PHE cc_start: 0.6843 (m-10) cc_final: 0.6553 (m-80) REVERT: A 1034 ASP cc_start: 0.6839 (t0) cc_final: 0.6602 (t0) REVERT: A 1040 ASN cc_start: 0.7573 (m110) cc_final: 0.7036 (m110) REVERT: A 1058 THR cc_start: 0.7100 (t) cc_final: 0.6709 (t) REVERT: A 1060 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 76 LYS cc_start: 0.7703 (mttm) cc_final: 0.7494 (mttm) REVERT: B 103 THR cc_start: 0.7684 (p) cc_final: 0.7475 (p) REVERT: B 125 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7051 (mp0) REVERT: B 128 ARG cc_start: 0.7300 (ttp-170) cc_final: 0.6968 (ptp-110) REVERT: B 197 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6549 (mp0) REVERT: B 236 LEU cc_start: 0.7531 (mm) cc_final: 0.7264 (mp) REVERT: B 256 GLN cc_start: 0.7429 (mt0) cc_final: 0.7052 (mt0) REVERT: B 269 LEU cc_start: 0.7372 (mt) cc_final: 0.7085 (mm) REVERT: B 280 TYR cc_start: 0.7920 (t80) cc_final: 0.7661 (t80) REVERT: B 319 LEU cc_start: 0.8051 (mt) cc_final: 0.7818 (mp) REVERT: B 344 GLU cc_start: 0.7630 (tt0) cc_final: 0.7314 (tm-30) REVERT: B 346 GLU cc_start: 0.7293 (tt0) cc_final: 0.6835 (tt0) REVERT: B 407 SER cc_start: 0.7048 (t) cc_final: 0.6738 (m) REVERT: B 475 GLN cc_start: 0.7247 (tp40) cc_final: 0.6961 (tp-100) REVERT: B 579 MET cc_start: 0.5839 (mtp) cc_final: 0.5419 (mtp) REVERT: B 580 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6246 (tp30) REVERT: B 591 LYS cc_start: 0.7362 (mtpp) cc_final: 0.6963 (mtpp) REVERT: B 605 ARG cc_start: 0.7003 (ttm-80) cc_final: 0.6669 (mtp-110) REVERT: B 630 ASP cc_start: 0.7842 (m-30) cc_final: 0.7588 (m-30) REVERT: B 632 LYS cc_start: 0.7274 (ttmm) cc_final: 0.7018 (ttmm) REVERT: B 633 LYS cc_start: 0.7884 (mttt) cc_final: 0.7167 (mmtm) REVERT: B 647 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7991 (mtmt) REVERT: B 650 ASP cc_start: 0.8200 (m-30) cc_final: 0.7928 (m-30) REVERT: B 678 MET cc_start: 0.6721 (mmm) cc_final: 0.6302 (mmm) REVERT: B 810 MET cc_start: 0.6785 (mmm) cc_final: 0.6495 (mmm) REVERT: B 832 GLN cc_start: 0.7489 (tp40) cc_final: 0.7261 (tp-100) REVERT: B 841 LYS cc_start: 0.6978 (tttt) cc_final: 0.6319 (mmmt) REVERT: B 881 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7054 (mm-30) REVERT: B 931 GLU cc_start: 0.7234 (tt0) cc_final: 0.6954 (mt-10) REVERT: B 946 SER cc_start: 0.7999 (p) cc_final: 0.7790 (m) REVERT: B 955 ASN cc_start: 0.7195 (t0) cc_final: 0.6954 (t0) REVERT: B 958 LYS cc_start: 0.7294 (ttpp) cc_final: 0.6923 (ttpp) REVERT: B 994 GLU cc_start: 0.7288 (tt0) cc_final: 0.6983 (tp30) REVERT: B 1007 LYS cc_start: 0.7198 (tttt) cc_final: 0.6746 (tttm) REVERT: B 1034 ASP cc_start: 0.7095 (t0) cc_final: 0.6859 (t70) REVERT: B 1040 ASN cc_start: 0.7584 (m110) cc_final: 0.7036 (m110) REVERT: B 1057 VAL cc_start: 0.6035 (t) cc_final: 0.5764 (p) REVERT: B 1060 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6910 (tm-30) REVERT: B 1115 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 1128 ASP cc_start: 0.6956 (m-30) cc_final: 0.5887 (t0) outliers start: 36 outliers final: 24 residues processed: 402 average time/residue: 0.2924 time to fit residues: 172.3220 Evaluate side-chains 405 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 381 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 636 GLN A1156 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS B 636 GLN B1156 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16528 Z= 0.285 Angle : 0.526 8.757 22420 Z= 0.278 Chirality : 0.041 0.247 2696 Planarity : 0.004 0.048 2748 Dihedral : 5.460 95.212 2200 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.96 % Allowed : 14.73 % Favored : 82.31 % 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: 1.23 (0.19), residues: 2020 helix: 1.20 (0.13), residues: 1480 sheet: 0.85 (0.62), residues: 62 loop : -0.19 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 635 HIS 0.008 0.001 HIS A1120 PHE 0.017 0.001 PHE A 288 TYR 0.016 0.001 TYR B 984 ARG 0.012 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 391 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7047 (mp0) REVERT: A 128 ARG cc_start: 0.7226 (ptp-110) cc_final: 0.6706 (ptp-170) REVERT: A 199 MET cc_start: 0.7575 (mmm) cc_final: 0.7205 (mmm) REVERT: A 205 MET cc_start: 0.7752 (tpp) cc_final: 0.7463 (tpp) REVERT: A 251 MET cc_start: 0.7583 (mtp) cc_final: 0.7377 (mtm) REVERT: A 269 LEU cc_start: 0.7228 (mt) cc_final: 0.6996 (mm) REVERT: A 337 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 384 ASP cc_start: 0.6981 (m-30) cc_final: 0.6769 (m-30) REVERT: A 475 GLN cc_start: 0.7397 (tp40) cc_final: 0.7094 (tp-100) REVERT: A 499 ARG cc_start: 0.7116 (ttt180) cc_final: 0.6832 (ttt180) REVERT: A 503 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 517 PHE cc_start: 0.7463 (m-10) cc_final: 0.7263 (m-10) REVERT: A 534 ASP cc_start: 0.6416 (p0) cc_final: 0.6130 (p0) REVERT: A 591 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7062 (mtpp) REVERT: A 629 ASP cc_start: 0.7428 (m-30) cc_final: 0.7185 (m-30) REVERT: A 633 LYS cc_start: 0.7835 (mttt) cc_final: 0.7156 (mmtm) REVERT: A 634 SER cc_start: 0.8070 (t) cc_final: 0.7696 (p) REVERT: A 643 TRP cc_start: 0.7962 (t60) cc_final: 0.7694 (t60) REVERT: A 647 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7769 (mmtm) REVERT: A 650 ASP cc_start: 0.8086 (m-30) cc_final: 0.7859 (m-30) REVERT: A 671 MET cc_start: 0.5933 (mpp) cc_final: 0.5718 (mpp) REVERT: A 678 MET cc_start: 0.7050 (mmm) cc_final: 0.6574 (mmm) REVERT: A 822 ILE cc_start: 0.7206 (tp) cc_final: 0.6880 (pt) REVERT: A 841 LYS cc_start: 0.7188 (tttt) cc_final: 0.6558 (mmmt) REVERT: A 863 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5399 (tt) REVERT: A 881 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6929 (mm-30) REVERT: A 931 GLU cc_start: 0.7322 (tt0) cc_final: 0.6955 (mt-10) REVERT: A 955 ASN cc_start: 0.7660 (t0) cc_final: 0.7409 (t0) REVERT: A 958 LYS cc_start: 0.7426 (ttpp) cc_final: 0.7027 (ttpp) REVERT: A 967 MET cc_start: 0.6535 (mtp) cc_final: 0.6016 (mtp) REVERT: A 971 ASP cc_start: 0.7198 (m-30) cc_final: 0.6776 (m-30) REVERT: A 982 PHE cc_start: 0.6742 (m-80) cc_final: 0.6362 (m-10) REVERT: A 986 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 1034 ASP cc_start: 0.6998 (t0) cc_final: 0.6705 (t0) REVERT: A 1040 ASN cc_start: 0.7381 (m110) cc_final: 0.6833 (m110) REVERT: A 1060 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7180 (mm-30) REVERT: B 125 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7068 (mp0) REVERT: B 128 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6805 (ptp-110) REVERT: B 191 TYR cc_start: 0.8236 (m-80) cc_final: 0.7975 (m-80) REVERT: B 205 MET cc_start: 0.7712 (tpp) cc_final: 0.7421 (tpp) REVERT: B 256 GLN cc_start: 0.7575 (mt0) cc_final: 0.7171 (mt0) REVERT: B 269 LEU cc_start: 0.7378 (mt) cc_final: 0.7089 (mm) REVERT: B 280 TYR cc_start: 0.7928 (t80) cc_final: 0.7623 (t80) REVERT: B 337 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7171 (mm-30) REVERT: B 475 GLN cc_start: 0.7290 (tp40) cc_final: 0.6978 (tp-100) REVERT: B 503 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6866 (mt-10) REVERT: B 579 MET cc_start: 0.5779 (mtp) cc_final: 0.5481 (mtp) REVERT: B 580 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6314 (tp30) REVERT: B 591 LYS cc_start: 0.7425 (mtpp) cc_final: 0.7035 (mtpp) REVERT: B 605 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6802 (ttm-80) REVERT: B 633 LYS cc_start: 0.7895 (mttt) cc_final: 0.7199 (mmtm) REVERT: B 647 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7784 (mtmm) REVERT: B 650 ASP cc_start: 0.8215 (m-30) cc_final: 0.7929 (m-30) REVERT: B 678 MET cc_start: 0.6825 (mmm) cc_final: 0.6393 (mmm) REVERT: B 810 MET cc_start: 0.6837 (mmm) cc_final: 0.6510 (mmm) REVERT: B 832 GLN cc_start: 0.7486 (tp40) cc_final: 0.7270 (tp-100) REVERT: B 885 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7689 (tt) REVERT: B 887 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.7001 (mmm-85) REVERT: B 931 GLU cc_start: 0.7264 (tt0) cc_final: 0.6942 (mt-10) REVERT: B 958 LYS cc_start: 0.7328 (ttpp) cc_final: 0.6977 (ttpp) REVERT: B 967 MET cc_start: 0.6527 (mtp) cc_final: 0.6227 (mmm) REVERT: B 983 ASP cc_start: 0.7304 (t0) cc_final: 0.7073 (t0) REVERT: B 994 GLU cc_start: 0.7451 (tt0) cc_final: 0.7110 (tp30) REVERT: B 1007 LYS cc_start: 0.7194 (tttt) cc_final: 0.6796 (tttm) REVERT: B 1040 ASN cc_start: 0.7521 (m110) cc_final: 0.7034 (m110) REVERT: B 1057 VAL cc_start: 0.6194 (t) cc_final: 0.5917 (p) REVERT: B 1060 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7603 (tp30) REVERT: B 1110 GLN cc_start: 0.5451 (mp10) cc_final: 0.5062 (mp10) REVERT: B 1115 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6555 (mm-30) REVERT: B 1126 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6802 (pt) REVERT: B 1128 ASP cc_start: 0.6965 (m-30) cc_final: 0.5917 (t0) REVERT: B 1185 ARG cc_start: 0.6164 (mmt180) cc_final: 0.4978 (mmt180) outliers start: 52 outliers final: 37 residues processed: 419 average time/residue: 0.3086 time to fit residues: 189.6644 Evaluate side-chains 417 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 377 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 984 TYR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 115 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 295 ASN A 600 HIS A 636 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 292 HIS B 600 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16528 Z= 0.186 Angle : 0.496 10.078 22420 Z= 0.258 Chirality : 0.040 0.244 2696 Planarity : 0.004 0.046 2748 Dihedral : 5.343 93.111 2200 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.39 % Allowed : 16.72 % Favored : 80.89 % 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: 1.41 (0.19), residues: 2020 helix: 1.35 (0.13), residues: 1476 sheet: 0.83 (0.60), residues: 62 loop : -0.18 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS B 292 PHE 0.017 0.001 PHE A 999 TYR 0.015 0.001 TYR B 267 ARG 0.008 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 385 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7022 (mp0) REVERT: A 128 ARG cc_start: 0.7262 (ptp-110) cc_final: 0.6708 (ptp-170) REVERT: A 186 MET cc_start: 0.5877 (mpp) cc_final: 0.5598 (mpp) REVERT: A 199 MET cc_start: 0.7659 (mmm) cc_final: 0.7278 (mmm) REVERT: A 205 MET cc_start: 0.7706 (tpp) cc_final: 0.7392 (tpp) REVERT: A 269 LEU cc_start: 0.7244 (mt) cc_final: 0.7005 (mm) REVERT: A 337 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 475 GLN cc_start: 0.7390 (tp40) cc_final: 0.7089 (tp-100) REVERT: A 503 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6831 (mt-10) REVERT: A 517 PHE cc_start: 0.7371 (m-10) cc_final: 0.7134 (m-10) REVERT: A 534 ASP cc_start: 0.6395 (p0) cc_final: 0.6113 (p0) REVERT: A 629 ASP cc_start: 0.7476 (m-30) cc_final: 0.7003 (m-30) REVERT: A 633 LYS cc_start: 0.7836 (mttt) cc_final: 0.7017 (mmtm) REVERT: A 634 SER cc_start: 0.8118 (t) cc_final: 0.7775 (p) REVERT: A 647 LYS cc_start: 0.8222 (mmtm) cc_final: 0.8012 (mtmm) REVERT: A 671 MET cc_start: 0.5931 (mpp) cc_final: 0.5702 (mpp) REVERT: A 678 MET cc_start: 0.7009 (mmm) cc_final: 0.6538 (mmm) REVERT: A 822 ILE cc_start: 0.7187 (tp) cc_final: 0.6871 (pt) REVERT: A 881 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6838 (mm-30) REVERT: A 931 GLU cc_start: 0.7308 (tt0) cc_final: 0.6938 (mt-10) REVERT: A 955 ASN cc_start: 0.7639 (t0) cc_final: 0.7400 (t0) REVERT: A 958 LYS cc_start: 0.7410 (ttpp) cc_final: 0.7013 (ttpp) REVERT: A 967 MET cc_start: 0.6512 (mtp) cc_final: 0.6019 (mtp) REVERT: A 971 ASP cc_start: 0.7213 (m-30) cc_final: 0.6788 (m-30) REVERT: A 982 PHE cc_start: 0.6708 (m-80) cc_final: 0.6374 (m-10) REVERT: A 986 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 1033 GLU cc_start: 0.6171 (mp0) cc_final: 0.5901 (mp0) REVERT: A 1040 ASN cc_start: 0.7451 (m110) cc_final: 0.6860 (m110) REVERT: A 1057 VAL cc_start: 0.6608 (t) cc_final: 0.6365 (p) REVERT: A 1060 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 1110 GLN cc_start: 0.5673 (mp10) cc_final: 0.5263 (mp10) REVERT: B 125 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6922 (mp0) REVERT: B 128 ARG cc_start: 0.7180 (ttp-170) cc_final: 0.6818 (ptp-110) REVERT: B 186 MET cc_start: 0.5642 (mpp) cc_final: 0.5409 (mpp) REVERT: B 236 LEU cc_start: 0.7553 (mm) cc_final: 0.7269 (mp) REVERT: B 269 LEU cc_start: 0.7382 (mt) cc_final: 0.7112 (mm) REVERT: B 280 TYR cc_start: 0.7944 (t80) cc_final: 0.7659 (t80) REVERT: B 346 GLU cc_start: 0.7561 (tt0) cc_final: 0.7014 (tt0) REVERT: B 475 GLN cc_start: 0.7274 (tp40) cc_final: 0.6957 (tp-100) REVERT: B 503 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6857 (mt-10) REVERT: B 579 MET cc_start: 0.5901 (mtp) cc_final: 0.5509 (mtp) REVERT: B 580 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6122 (tp30) REVERT: B 591 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7016 (mtpp) REVERT: B 605 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6836 (ttm-80) REVERT: B 633 LYS cc_start: 0.7902 (mttt) cc_final: 0.7189 (mmtm) REVERT: B 647 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7924 (mtmt) REVERT: B 650 ASP cc_start: 0.8191 (m-30) cc_final: 0.7908 (m-30) REVERT: B 678 MET cc_start: 0.6807 (mmm) cc_final: 0.6349 (mmm) REVERT: B 810 MET cc_start: 0.6816 (mmm) cc_final: 0.6506 (mmm) REVERT: B 832 GLN cc_start: 0.7516 (tp40) cc_final: 0.7221 (tp-100) REVERT: B 881 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 885 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 931 GLU cc_start: 0.7234 (tt0) cc_final: 0.6899 (mt-10) REVERT: B 958 LYS cc_start: 0.7344 (ttpp) cc_final: 0.7007 (ttpp) REVERT: B 983 ASP cc_start: 0.7351 (t0) cc_final: 0.7068 (t0) REVERT: B 986 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6948 (mt-10) REVERT: B 994 GLU cc_start: 0.7438 (tt0) cc_final: 0.7106 (tp30) REVERT: B 1001 ILE cc_start: 0.7783 (mm) cc_final: 0.7486 (mt) REVERT: B 1007 LYS cc_start: 0.7086 (tttt) cc_final: 0.6657 (tttm) REVERT: B 1040 ASN cc_start: 0.7597 (m110) cc_final: 0.7116 (m110) REVERT: B 1057 VAL cc_start: 0.6199 (t) cc_final: 0.5922 (p) REVERT: B 1060 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7388 (tp30) REVERT: B 1110 GLN cc_start: 0.5372 (mp10) cc_final: 0.4916 (mp10) REVERT: B 1115 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6542 (mm-30) REVERT: B 1128 ASP cc_start: 0.6976 (m-30) cc_final: 0.5941 (t0) REVERT: B 1185 ARG cc_start: 0.5991 (mmt180) cc_final: 0.5321 (mmt180) outliers start: 42 outliers final: 32 residues processed: 407 average time/residue: 0.3227 time to fit residues: 196.2642 Evaluate side-chains 421 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 388 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 600 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16528 Z= 0.234 Angle : 0.514 8.408 22420 Z= 0.268 Chirality : 0.041 0.262 2696 Planarity : 0.004 0.048 2748 Dihedral : 5.380 93.864 2200 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 17.80 % Favored : 79.64 % 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: 1.31 (0.19), residues: 2020 helix: 1.28 (0.13), residues: 1478 sheet: 0.91 (0.61), residues: 62 loop : -0.24 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.005 0.001 HIS B1120 PHE 0.013 0.001 PHE B 159 TYR 0.013 0.001 TYR A 358 ARG 0.009 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 396 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7199 (mm-30) REVERT: A 186 MET cc_start: 0.5899 (mpp) cc_final: 0.5659 (mpp) REVERT: A 199 MET cc_start: 0.7635 (mmm) cc_final: 0.7366 (mmm) REVERT: A 205 MET cc_start: 0.7738 (tpp) cc_final: 0.7513 (tpp) REVERT: A 233 GLU cc_start: 0.7847 (tt0) cc_final: 0.6836 (pt0) REVERT: A 269 LEU cc_start: 0.7279 (mt) cc_final: 0.7044 (mm) REVERT: A 300 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 385 TRP cc_start: 0.7471 (m100) cc_final: 0.7224 (m100) REVERT: A 475 GLN cc_start: 0.7414 (tp40) cc_final: 0.7110 (tp-100) REVERT: A 499 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6841 (ttt180) REVERT: A 503 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6874 (mt-10) REVERT: A 517 PHE cc_start: 0.7317 (m-10) cc_final: 0.6785 (m-10) REVERT: A 629 ASP cc_start: 0.7531 (m-30) cc_final: 0.7116 (m-30) REVERT: A 633 LYS cc_start: 0.7867 (mttt) cc_final: 0.7066 (mmtm) REVERT: A 634 SER cc_start: 0.8088 (t) cc_final: 0.7763 (p) REVERT: A 647 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7812 (mmtm) REVERT: A 671 MET cc_start: 0.5940 (mpp) cc_final: 0.5714 (mpp) REVERT: A 678 MET cc_start: 0.7004 (mmm) cc_final: 0.6531 (mmm) REVERT: A 822 ILE cc_start: 0.7190 (tp) cc_final: 0.6864 (pt) REVERT: A 841 LYS cc_start: 0.7164 (tttt) cc_final: 0.6620 (mmmt) REVERT: A 849 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 863 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.5401 (tt) REVERT: A 881 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6976 (mm-30) REVERT: A 931 GLU cc_start: 0.7296 (tt0) cc_final: 0.6798 (mt-10) REVERT: A 955 ASN cc_start: 0.7654 (t0) cc_final: 0.7424 (t0) REVERT: A 958 LYS cc_start: 0.7466 (ttpp) cc_final: 0.7072 (ttpp) REVERT: A 967 MET cc_start: 0.6584 (mtp) cc_final: 0.6105 (mtp) REVERT: A 971 ASP cc_start: 0.7199 (m-30) cc_final: 0.6781 (m-30) REVERT: A 972 PHE cc_start: 0.7455 (t80) cc_final: 0.6948 (t80) REVERT: A 1033 GLU cc_start: 0.6239 (mp0) cc_final: 0.5981 (mp0) REVERT: A 1040 ASN cc_start: 0.7360 (m110) cc_final: 0.6752 (m110) REVERT: A 1110 GLN cc_start: 0.5677 (mp10) cc_final: 0.5467 (mp10) REVERT: B 125 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6931 (mp0) REVERT: B 128 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6827 (ptp-110) REVERT: B 154 MET cc_start: 0.8079 (mtp) cc_final: 0.7860 (mtp) REVERT: B 205 MET cc_start: 0.7658 (tpp) cc_final: 0.7128 (mmt) REVERT: B 236 LEU cc_start: 0.7583 (mm) cc_final: 0.7293 (mp) REVERT: B 256 GLN cc_start: 0.7557 (mt0) cc_final: 0.7185 (mt0) REVERT: B 269 LEU cc_start: 0.7395 (mt) cc_final: 0.7122 (mm) REVERT: B 280 TYR cc_start: 0.7961 (t80) cc_final: 0.7681 (t80) REVERT: B 337 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 346 GLU cc_start: 0.7542 (tt0) cc_final: 0.7060 (tt0) REVERT: B 475 GLN cc_start: 0.7291 (tp40) cc_final: 0.6971 (tp-100) REVERT: B 503 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6809 (mt-10) REVERT: B 579 MET cc_start: 0.5895 (mtp) cc_final: 0.5505 (mtp) REVERT: B 580 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6142 (tp30) REVERT: B 591 LYS cc_start: 0.7405 (mtpp) cc_final: 0.7065 (mtpp) REVERT: B 605 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6855 (ttm-80) REVERT: B 633 LYS cc_start: 0.7951 (mttt) cc_final: 0.7261 (mmtm) REVERT: B 647 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7745 (mtmm) REVERT: B 678 MET cc_start: 0.6798 (mmm) cc_final: 0.6316 (mmm) REVERT: B 810 MET cc_start: 0.6776 (mmm) cc_final: 0.6482 (mmm) REVERT: B 832 GLN cc_start: 0.7509 (tp40) cc_final: 0.7215 (tp-100) REVERT: B 841 LYS cc_start: 0.7002 (mttt) cc_final: 0.6255 (mmmt) REVERT: B 849 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6613 (mt-10) REVERT: B 885 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7618 (tt) REVERT: B 887 ARG cc_start: 0.7419 (mmm-85) cc_final: 0.7109 (mmm-85) REVERT: B 931 GLU cc_start: 0.7254 (tt0) cc_final: 0.6919 (mt-10) REVERT: B 958 LYS cc_start: 0.7471 (ttpp) cc_final: 0.7101 (ttpp) REVERT: B 967 MET cc_start: 0.6876 (mmm) cc_final: 0.6481 (mmm) REVERT: B 983 ASP cc_start: 0.7351 (t0) cc_final: 0.7142 (t0) REVERT: B 1001 ILE cc_start: 0.7806 (mm) cc_final: 0.7508 (mt) REVERT: B 1007 LYS cc_start: 0.7048 (tttt) cc_final: 0.6631 (tttm) REVERT: B 1040 ASN cc_start: 0.7543 (m110) cc_final: 0.6971 (m110) REVERT: B 1060 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7585 (tp30) REVERT: B 1110 GLN cc_start: 0.5487 (mp10) cc_final: 0.5006 (mp10) REVERT: B 1115 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6552 (mm-30) REVERT: B 1128 ASP cc_start: 0.6957 (m-30) cc_final: 0.5920 (t0) REVERT: B 1185 ARG cc_start: 0.6022 (mmt180) cc_final: 0.5435 (mmt180) outliers start: 45 outliers final: 37 residues processed: 421 average time/residue: 0.2953 time to fit residues: 184.2071 Evaluate side-chains 415 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 376 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 838 ASP Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1126 LEU Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 600 HIS A1074 ASN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS B1114 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16528 Z= 0.234 Angle : 0.520 9.306 22420 Z= 0.269 Chirality : 0.041 0.271 2696 Planarity : 0.004 0.048 2748 Dihedral : 5.372 93.351 2200 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.73 % Allowed : 18.43 % Favored : 78.84 % 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: 1.35 (0.19), residues: 2020 helix: 1.31 (0.13), residues: 1478 sheet: 1.00 (0.61), residues: 62 loop : -0.23 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 635 HIS 0.005 0.001 HIS B1120 PHE 0.018 0.001 PHE A 268 TYR 0.013 0.001 TYR B 984 ARG 0.009 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 388 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.7637 (mmm) cc_final: 0.7362 (mmm) REVERT: A 205 MET cc_start: 0.7732 (tpp) cc_final: 0.7499 (tpp) REVERT: A 218 LYS cc_start: 0.8084 (tttt) cc_final: 0.7673 (tttt) REVERT: A 233 GLU cc_start: 0.7833 (tt0) cc_final: 0.6930 (tm-30) REVERT: A 269 LEU cc_start: 0.7278 (mt) cc_final: 0.7044 (mm) REVERT: A 300 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7124 (mt-10) REVERT: A 337 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 385 TRP cc_start: 0.7462 (m100) cc_final: 0.7250 (m100) REVERT: A 475 GLN cc_start: 0.7409 (tp40) cc_final: 0.7100 (tp-100) REVERT: A 499 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6857 (ttt180) REVERT: A 503 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 517 PHE cc_start: 0.7383 (m-10) cc_final: 0.6836 (m-10) REVERT: A 633 LYS cc_start: 0.7860 (mttt) cc_final: 0.7064 (mmtm) REVERT: A 634 SER cc_start: 0.8100 (t) cc_final: 0.7741 (p) REVERT: A 647 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7823 (mmtm) REVERT: A 671 MET cc_start: 0.5940 (mpp) cc_final: 0.5719 (mpp) REVERT: A 678 MET cc_start: 0.6984 (mmm) cc_final: 0.6513 (mmm) REVERT: A 688 ILE cc_start: 0.8191 (mt) cc_final: 0.7930 (tp) REVERT: A 841 LYS cc_start: 0.7154 (tttt) cc_final: 0.6641 (mmmt) REVERT: A 849 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6711 (mt-10) REVERT: A 881 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 931 GLU cc_start: 0.7277 (tt0) cc_final: 0.7020 (tt0) REVERT: A 955 ASN cc_start: 0.7676 (t0) cc_final: 0.7454 (t0) REVERT: A 958 LYS cc_start: 0.7474 (ttpp) cc_final: 0.7072 (ttpp) REVERT: A 967 MET cc_start: 0.6586 (mtp) cc_final: 0.6113 (mtp) REVERT: A 971 ASP cc_start: 0.7209 (m-30) cc_final: 0.6787 (m-30) REVERT: A 972 PHE cc_start: 0.7461 (t80) cc_final: 0.6957 (t80) REVERT: A 1033 GLU cc_start: 0.6294 (mp0) cc_final: 0.6025 (mp0) REVERT: A 1034 ASP cc_start: 0.6951 (t0) cc_final: 0.6579 (t70) REVERT: A 1040 ASN cc_start: 0.7356 (m110) cc_final: 0.6747 (m110) REVERT: A 1128 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6649 (m-30) REVERT: B 76 LYS cc_start: 0.7620 (mttm) cc_final: 0.7162 (mmtm) REVERT: B 125 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6930 (mp0) REVERT: B 128 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6823 (ptp-110) REVERT: B 154 MET cc_start: 0.8097 (mtp) cc_final: 0.7808 (mtp) REVERT: B 205 MET cc_start: 0.7660 (tpp) cc_final: 0.6993 (mmp) REVERT: B 236 LEU cc_start: 0.7583 (mm) cc_final: 0.7299 (mp) REVERT: B 256 GLN cc_start: 0.7579 (mt0) cc_final: 0.7180 (mt0) REVERT: B 269 LEU cc_start: 0.7349 (mt) cc_final: 0.7090 (mm) REVERT: B 280 TYR cc_start: 0.7967 (t80) cc_final: 0.7730 (t80) REVERT: B 337 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 475 GLN cc_start: 0.7276 (tp40) cc_final: 0.6954 (tp-100) REVERT: B 503 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6804 (mt-10) REVERT: B 579 MET cc_start: 0.5790 (mtp) cc_final: 0.5406 (mtp) REVERT: B 580 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6109 (tp30) REVERT: B 591 LYS cc_start: 0.7416 (mtpp) cc_final: 0.7073 (mtpp) REVERT: B 605 ARG cc_start: 0.7142 (ttm-80) cc_final: 0.6848 (ttm-80) REVERT: B 633 LYS cc_start: 0.7892 (mttt) cc_final: 0.7224 (mmtm) REVERT: B 647 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7883 (mtmt) REVERT: B 678 MET cc_start: 0.6852 (mmm) cc_final: 0.6371 (mmm) REVERT: B 810 MET cc_start: 0.6819 (mmm) cc_final: 0.6504 (mmm) REVERT: B 832 GLN cc_start: 0.7513 (tp40) cc_final: 0.7228 (tp-100) REVERT: B 841 LYS cc_start: 0.7064 (mttt) cc_final: 0.6319 (mmmt) REVERT: B 885 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7605 (tt) REVERT: B 887 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7083 (mmm-85) REVERT: B 931 GLU cc_start: 0.7248 (tt0) cc_final: 0.6907 (mt-10) REVERT: B 958 LYS cc_start: 0.7522 (ttpp) cc_final: 0.7206 (ttpp) REVERT: B 983 ASP cc_start: 0.7358 (t0) cc_final: 0.7151 (t0) REVERT: B 1001 ILE cc_start: 0.7783 (mm) cc_final: 0.7517 (mt) REVERT: B 1007 LYS cc_start: 0.7096 (tttt) cc_final: 0.6697 (tttm) REVERT: B 1040 ASN cc_start: 0.7551 (m110) cc_final: 0.6984 (m110) REVERT: B 1057 VAL cc_start: 0.6346 (t) cc_final: 0.6079 (p) REVERT: B 1060 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7499 (tp30) REVERT: B 1110 GLN cc_start: 0.5430 (mp10) cc_final: 0.4968 (mp10) REVERT: B 1115 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6514 (mm-30) REVERT: B 1128 ASP cc_start: 0.6961 (m-30) cc_final: 0.5923 (t0) REVERT: B 1185 ARG cc_start: 0.6063 (mmt180) cc_final: 0.5856 (mmt180) outliers start: 48 outliers final: 37 residues processed: 417 average time/residue: 0.2989 time to fit residues: 182.8945 Evaluate side-chains 424 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 385 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 838 ASP Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 183 optimal weight: 0.0370 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 0.0770 chunk 56 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 0.4980 chunk 120 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 600 HIS A1120 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16528 Z= 0.157 Angle : 0.502 8.724 22420 Z= 0.257 Chirality : 0.039 0.261 2696 Planarity : 0.004 0.046 2748 Dihedral : 5.268 92.594 2200 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.50 % Allowed : 18.71 % Favored : 78.78 % 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: 1.60 (0.19), residues: 2020 helix: 1.51 (0.14), residues: 1476 sheet: 0.98 (0.60), residues: 62 loop : -0.17 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.003 0.001 HIS A 292 PHE 0.010 0.001 PHE A 254 TYR 0.013 0.001 TYR B 191 ARG 0.009 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 394 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6990 (m-40) cc_final: 0.6703 (m110) REVERT: A 199 MET cc_start: 0.7653 (mmm) cc_final: 0.7308 (mmm) REVERT: A 205 MET cc_start: 0.7710 (tpp) cc_final: 0.7445 (tpp) REVERT: A 218 LYS cc_start: 0.8092 (tttt) cc_final: 0.7661 (tttt) REVERT: A 233 GLU cc_start: 0.7729 (tt0) cc_final: 0.7456 (tt0) REVERT: A 269 LEU cc_start: 0.7248 (mt) cc_final: 0.7015 (mm) REVERT: A 300 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 337 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 385 TRP cc_start: 0.7414 (m100) cc_final: 0.7156 (m100) REVERT: A 475 GLN cc_start: 0.7405 (tp40) cc_final: 0.7110 (tp-100) REVERT: A 503 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6828 (mt-10) REVERT: A 517 PHE cc_start: 0.7238 (m-10) cc_final: 0.7028 (m-10) REVERT: A 633 LYS cc_start: 0.7808 (mttt) cc_final: 0.7016 (mmtm) REVERT: A 634 SER cc_start: 0.8094 (t) cc_final: 0.7821 (p) REVERT: A 647 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7948 (mtmm) REVERT: A 678 MET cc_start: 0.6919 (mmm) cc_final: 0.6457 (mmm) REVERT: A 688 ILE cc_start: 0.8179 (mt) cc_final: 0.7926 (tp) REVERT: A 822 ILE cc_start: 0.7230 (tp) cc_final: 0.6915 (pt) REVERT: A 841 LYS cc_start: 0.7120 (tttt) cc_final: 0.6660 (mmmt) REVERT: A 847 GLU cc_start: 0.6325 (tp30) cc_final: 0.6094 (tp30) REVERT: A 849 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6581 (mt-10) REVERT: A 881 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6929 (mm-30) REVERT: A 931 GLU cc_start: 0.7256 (tt0) cc_final: 0.7000 (tt0) REVERT: A 955 ASN cc_start: 0.7625 (t0) cc_final: 0.7401 (t0) REVERT: A 958 LYS cc_start: 0.7444 (ttpp) cc_final: 0.7042 (ttpp) REVERT: A 967 MET cc_start: 0.6658 (mtp) cc_final: 0.6199 (mtp) REVERT: A 971 ASP cc_start: 0.7259 (m-30) cc_final: 0.6829 (m-30) REVERT: A 972 PHE cc_start: 0.7420 (t80) cc_final: 0.6940 (t80) REVERT: A 986 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 1033 GLU cc_start: 0.6282 (mp0) cc_final: 0.5992 (mp0) REVERT: A 1034 ASP cc_start: 0.6792 (t0) cc_final: 0.6579 (t0) REVERT: A 1040 ASN cc_start: 0.7395 (m110) cc_final: 0.6751 (m110) REVERT: A 1122 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6984 (pp20) REVERT: B 76 LYS cc_start: 0.7596 (mttm) cc_final: 0.7134 (mmtm) REVERT: B 125 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6923 (mp0) REVERT: B 128 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6877 (ptp-110) REVERT: B 154 MET cc_start: 0.8072 (mtp) cc_final: 0.7827 (mtp) REVERT: B 205 MET cc_start: 0.7609 (tpp) cc_final: 0.7040 (mmp) REVERT: B 236 LEU cc_start: 0.7511 (mm) cc_final: 0.7254 (mp) REVERT: B 256 GLN cc_start: 0.7580 (mt0) cc_final: 0.7169 (mt0) REVERT: B 269 LEU cc_start: 0.7342 (mt) cc_final: 0.7074 (mm) REVERT: B 280 TYR cc_start: 0.7956 (t80) cc_final: 0.7702 (t80) REVERT: B 337 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 366 MET cc_start: 0.7692 (mtp) cc_final: 0.7490 (mmm) REVERT: B 475 GLN cc_start: 0.7267 (tp40) cc_final: 0.6939 (tp-100) REVERT: B 503 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6791 (mt-10) REVERT: B 579 MET cc_start: 0.5899 (mtp) cc_final: 0.5514 (mtp) REVERT: B 580 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6210 (tp30) REVERT: B 591 LYS cc_start: 0.7437 (mtpp) cc_final: 0.7044 (mtpp) REVERT: B 605 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6816 (ttm-80) REVERT: B 633 LYS cc_start: 0.7903 (mttt) cc_final: 0.7279 (mmtt) REVERT: B 647 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7893 (mtmt) REVERT: B 678 MET cc_start: 0.6813 (mmm) cc_final: 0.6313 (mmm) REVERT: B 810 MET cc_start: 0.6585 (mmm) cc_final: 0.6356 (mmm) REVERT: B 832 GLN cc_start: 0.7540 (tp40) cc_final: 0.7258 (tp-100) REVERT: B 877 GLN cc_start: 0.7161 (mt0) cc_final: 0.6949 (tt0) REVERT: B 887 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.7083 (mmm-85) REVERT: B 931 GLU cc_start: 0.7212 (tt0) cc_final: 0.6846 (mt-10) REVERT: B 967 MET cc_start: 0.6815 (mmm) cc_final: 0.6472 (mmm) REVERT: B 983 ASP cc_start: 0.7382 (t0) cc_final: 0.7174 (t0) REVERT: B 1001 ILE cc_start: 0.7756 (mm) cc_final: 0.7477 (mt) REVERT: B 1007 LYS cc_start: 0.7086 (tttt) cc_final: 0.6705 (tttm) REVERT: B 1040 ASN cc_start: 0.7630 (m110) cc_final: 0.7063 (m110) REVERT: B 1057 VAL cc_start: 0.6154 (t) cc_final: 0.5720 (m) REVERT: B 1060 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7391 (tp30) REVERT: B 1110 GLN cc_start: 0.5440 (mp10) cc_final: 0.4949 (mp10) REVERT: B 1115 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6510 (mm-30) REVERT: B 1128 ASP cc_start: 0.6981 (m-30) cc_final: 0.5972 (t0) REVERT: B 1185 ARG cc_start: 0.5971 (mmt180) cc_final: 0.5717 (mmt180) outliers start: 44 outliers final: 37 residues processed: 419 average time/residue: 0.3005 time to fit residues: 187.1145 Evaluate side-chains 422 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 385 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 838 ASP Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 925 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.2980 chunk 128 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 600 HIS A 636 GLN A 832 GLN ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16528 Z= 0.208 Angle : 0.542 11.251 22420 Z= 0.275 Chirality : 0.041 0.268 2696 Planarity : 0.004 0.046 2748 Dihedral : 5.304 93.856 2200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.33 % Allowed : 19.11 % Favored : 78.56 % 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: 1.48 (0.19), residues: 2020 helix: 1.44 (0.14), residues: 1474 sheet: 1.00 (0.58), residues: 72 loop : -0.28 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS B1120 PHE 0.019 0.001 PHE A 268 TYR 0.015 0.001 TYR A 358 ARG 0.009 0.000 ARG A 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 390 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6371 (mt-10) REVERT: A 187 ASN cc_start: 0.7061 (m-40) cc_final: 0.6765 (m110) REVERT: A 199 MET cc_start: 0.7659 (mmm) cc_final: 0.7315 (mmm) REVERT: A 205 MET cc_start: 0.7712 (tpp) cc_final: 0.7476 (tpp) REVERT: A 218 LYS cc_start: 0.8110 (tttt) cc_final: 0.7683 (tttt) REVERT: A 233 GLU cc_start: 0.7729 (tt0) cc_final: 0.7469 (tt0) REVERT: A 269 LEU cc_start: 0.7275 (mt) cc_final: 0.7040 (mm) REVERT: A 300 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 337 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 385 TRP cc_start: 0.7439 (m100) cc_final: 0.7212 (m100) REVERT: A 475 GLN cc_start: 0.7414 (tp40) cc_final: 0.7107 (tp-100) REVERT: A 499 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6864 (ttt180) REVERT: A 503 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 517 PHE cc_start: 0.7281 (m-10) cc_final: 0.6787 (m-10) REVERT: A 579 MET cc_start: 0.5877 (mpp) cc_final: 0.5628 (mpp) REVERT: A 633 LYS cc_start: 0.7883 (mttt) cc_final: 0.7059 (mmtm) REVERT: A 647 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7815 (mmtm) REVERT: A 678 MET cc_start: 0.6921 (mmm) cc_final: 0.6458 (mmm) REVERT: A 688 ILE cc_start: 0.8185 (mt) cc_final: 0.7921 (tp) REVERT: A 822 ILE cc_start: 0.7221 (tp) cc_final: 0.6914 (pt) REVERT: A 832 GLN cc_start: 0.7441 (tp40) cc_final: 0.7005 (tm-30) REVERT: A 841 LYS cc_start: 0.7140 (tttt) cc_final: 0.6686 (mmmt) REVERT: A 849 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6639 (mt-10) REVERT: A 881 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6938 (mm-30) REVERT: A 931 GLU cc_start: 0.7278 (tt0) cc_final: 0.7013 (tt0) REVERT: A 955 ASN cc_start: 0.7654 (t0) cc_final: 0.7431 (t0) REVERT: A 958 LYS cc_start: 0.7470 (ttpp) cc_final: 0.7070 (ttpp) REVERT: A 967 MET cc_start: 0.6616 (mtp) cc_final: 0.6173 (mtp) REVERT: A 971 ASP cc_start: 0.7214 (m-30) cc_final: 0.6797 (m-30) REVERT: A 972 PHE cc_start: 0.7420 (t80) cc_final: 0.6955 (t80) REVERT: A 986 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 1033 GLU cc_start: 0.6329 (mp0) cc_final: 0.6043 (mp0) REVERT: A 1034 ASP cc_start: 0.6866 (t0) cc_final: 0.6648 (t0) REVERT: A 1040 ASN cc_start: 0.7346 (m110) cc_final: 0.6731 (m110) REVERT: A 1122 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6979 (pp20) REVERT: B 76 LYS cc_start: 0.7588 (mttm) cc_final: 0.7115 (mmtm) REVERT: B 125 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7047 (mp0) REVERT: B 128 ARG cc_start: 0.7174 (ttp-170) cc_final: 0.6843 (ptp-110) REVERT: B 154 MET cc_start: 0.8088 (mtp) cc_final: 0.7789 (mtp) REVERT: B 205 MET cc_start: 0.7624 (tpp) cc_final: 0.7032 (mmp) REVERT: B 236 LEU cc_start: 0.7531 (mm) cc_final: 0.7261 (mp) REVERT: B 256 GLN cc_start: 0.7658 (mt0) cc_final: 0.7284 (mt0) REVERT: B 269 LEU cc_start: 0.7344 (mt) cc_final: 0.7082 (mm) REVERT: B 337 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 346 GLU cc_start: 0.7518 (tt0) cc_final: 0.7011 (tt0) REVERT: B 366 MET cc_start: 0.7716 (mtp) cc_final: 0.7488 (mmm) REVERT: B 475 GLN cc_start: 0.7268 (tp40) cc_final: 0.6949 (tp-100) REVERT: B 503 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6831 (mt-10) REVERT: B 579 MET cc_start: 0.5858 (mtp) cc_final: 0.5472 (mtp) REVERT: B 580 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6108 (tp30) REVERT: B 591 LYS cc_start: 0.7441 (mtpp) cc_final: 0.7042 (mtpp) REVERT: B 605 ARG cc_start: 0.7130 (ttm-80) cc_final: 0.6840 (ttm-80) REVERT: B 633 LYS cc_start: 0.7954 (mttt) cc_final: 0.7332 (mmtt) REVERT: B 647 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7892 (mtmt) REVERT: B 678 MET cc_start: 0.6796 (mmm) cc_final: 0.6286 (mmm) REVERT: B 810 MET cc_start: 0.6673 (mmm) cc_final: 0.6366 (mmm) REVERT: B 832 GLN cc_start: 0.7540 (tp40) cc_final: 0.7261 (tp-100) REVERT: B 841 LYS cc_start: 0.7088 (tttt) cc_final: 0.6328 (mmmt) REVERT: B 877 GLN cc_start: 0.7178 (mt0) cc_final: 0.6939 (tt0) REVERT: B 887 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.7047 (mmm-85) REVERT: B 931 GLU cc_start: 0.7220 (tt0) cc_final: 0.6846 (mt-10) REVERT: B 983 ASP cc_start: 0.7370 (t0) cc_final: 0.7158 (t0) REVERT: B 1001 ILE cc_start: 0.7759 (mm) cc_final: 0.7476 (mt) REVERT: B 1007 LYS cc_start: 0.7107 (tttt) cc_final: 0.6442 (tttp) REVERT: B 1040 ASN cc_start: 0.7584 (m110) cc_final: 0.7018 (m110) REVERT: B 1060 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6959 (mp0) REVERT: B 1110 GLN cc_start: 0.5376 (mp10) cc_final: 0.5035 (mp10) REVERT: B 1115 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6523 (mm-30) REVERT: B 1128 ASP cc_start: 0.6946 (m-30) cc_final: 0.5951 (t0) outliers start: 41 outliers final: 35 residues processed: 414 average time/residue: 0.3207 time to fit residues: 195.6864 Evaluate side-chains 426 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 391 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1128 ASP Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 838 ASP Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1141 THR Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 67 optimal weight: 0.0010 chunk 166 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 0.0980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 600 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 600 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.173424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144895 restraints weight = 22980.771| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.90 r_work: 0.3624 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16528 Z= 0.166 Angle : 0.530 11.131 22420 Z= 0.266 Chirality : 0.040 0.257 2696 Planarity : 0.004 0.044 2748 Dihedral : 5.254 92.783 2200 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 19.45 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 2020 helix: 1.49 (0.14), residues: 1472 sheet: 0.94 (0.58), residues: 72 loop : -0.25 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.003 0.001 HIS A 292 PHE 0.016 0.001 PHE A 982 TYR 0.014 0.001 TYR B 267 ARG 0.009 0.000 ARG B 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4452.50 seconds wall clock time: 81 minutes 35.16 seconds (4895.16 seconds total)