Starting phenix.real_space_refine on Tue Mar 19 14:41:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x5b_6705/03_2024/5x5b_6705.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.007 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: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 15678 2.51 5 N 4062 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "C ARG 1073": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24541 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8085 Classifications: {'peptide': 1033} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 47, 'TRANS': 983} Chain breaks: 5 Chain: "B" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8228 Classifications: {'peptide': 1053} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Chain: "C" Number of atoms: 8228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8228 Classifications: {'peptide': 1053} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Time building chain proxies: 12.40, per 1000 atoms: 0.51 Number of scatterers: 24541 At special positions: 0 Unit cell: (149.5, 136.5, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 4670 8.00 N 4062 7.00 C 15678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 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: 8.95 Conformation dependent library (CDL) restraints added in 4.4 seconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 45 sheets defined 22.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.861A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.640A pdb=" N GLY A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.191A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.639A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.560A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 749 through 764 removed outlier: 3.672A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.082A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.555A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 945 removed outlier: 3.546A pdb=" N GLY A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.619A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 975 Processing helix chain 'A' and resid 975 through 1014 removed outlier: 3.610A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 757 removed outlier: 3.837A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 765 Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.136A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 919 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 986 " --> pdb=" O ARG B 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.573A pdb=" N CYS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.536A pdb=" N ASN C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.590A pdb=" N LEU C 355 " --> pdb=" O ASP C 351 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.889A pdb=" N ASN C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 608 removed outlier: 3.793A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.672A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.896A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 removed outlier: 3.836A pdb=" N LEU C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.137A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 919 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 958 through 967 removed outlier: 3.590A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 4.062A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 986 " --> pdb=" O ARG C 982 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.115A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 190 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.659A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.728A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 128 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 5.437A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.681A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 526 removed outlier: 3.671A pdb=" N LEU A 571 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.401A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 700 removed outlier: 3.590A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 716 removed outlier: 4.202A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.436A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AB6, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.440A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.555A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 570 through 572 removed outlier: 7.102A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 684 through 685 Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 697 removed outlier: 3.572A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.283A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1058 through 1059 removed outlier: 4.200A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1071 through 1072 Processing sheet with id=AD4, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.278A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.681A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.567A pdb=" N GLY C 104 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 112 through 116 removed outlier: 4.722A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.485A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE1, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.439A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 344 removed outlier: 3.556A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 384 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 551 through 552 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AE5, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.573A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.282A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1058 through 1059 removed outlier: 4.199A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 746 hydrogen bonds defined for protein. 2082 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: 10.16 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7807 1.34 - 1.46: 5407 1.46 - 1.58: 11736 1.58 - 1.69: 0 1.69 - 1.81: 179 Bond restraints: 25129 Sorted by residual: bond pdb=" C LEU A 222 " pdb=" N PRO A 223 " ideal model delta sigma weight residual 1.334 1.242 0.092 2.34e-02 1.83e+03 1.55e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C ASP C 790 " pdb=" N PRO C 791 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.381 -0.046 1.23e-02 6.61e+03 1.38e+01 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.337 1.379 -0.041 1.24e-02 6.50e+03 1.12e+01 ... (remaining 25124 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.39: 313 103.39 - 111.21: 9654 111.21 - 119.03: 10082 119.03 - 126.84: 13854 126.84 - 134.66: 288 Bond angle restraints: 34191 Sorted by residual: angle pdb=" N SER A 303 " pdb=" CA SER A 303 " pdb=" C SER A 303 " ideal model delta sigma weight residual 111.04 126.16 -15.12 1.55e+00 4.16e-01 9.51e+01 angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.02 -9.11 1.17e+00 7.31e-01 6.06e+01 angle pdb=" N VAL A 969 " pdb=" CA VAL A 969 " pdb=" C VAL A 969 " ideal model delta sigma weight residual 113.71 107.06 6.65 9.50e-01 1.11e+00 4.90e+01 angle pdb=" N PHE B 305 " pdb=" CA PHE B 305 " pdb=" C PHE B 305 " ideal model delta sigma weight residual 108.76 119.74 -10.98 1.58e+00 4.01e-01 4.83e+01 angle pdb=" N PHE C 305 " pdb=" CA PHE C 305 " pdb=" C PHE C 305 " ideal model delta sigma weight residual 108.76 119.67 -10.91 1.58e+00 4.01e-01 4.77e+01 ... (remaining 34186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 14158 16.46 - 32.91: 566 32.91 - 49.37: 119 49.37 - 65.82: 15 65.82 - 82.28: 25 Dihedral angle restraints: 14883 sinusoidal: 5721 harmonic: 9162 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -165.24 79.24 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.32 73.32 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CB CYS C 524 " pdb=" SG CYS C 524 " pdb=" SG CYS C 576 " pdb=" CB CYS C 576 " ideal model delta sinusoidal sigma weight residual -86.00 -159.29 73.29 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 14880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3454 0.095 - 0.190: 366 0.190 - 0.285: 26 0.285 - 0.380: 10 0.380 - 0.475: 2 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB ILE A1097 " pdb=" CA ILE A1097 " pdb=" CG1 ILE A1097 " pdb=" CG2 ILE A1097 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 3855 not shown) Planarity restraints: 4427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.058 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 617 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO C 617 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 469 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 470 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " -0.034 5.00e-02 4.00e+02 ... (remaining 4424 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5162 2.77 - 3.30: 22639 3.30 - 3.84: 41136 3.84 - 4.37: 48496 4.37 - 4.90: 81134 Nonbonded interactions: 198567 Sorted by model distance: nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.242 2.440 nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.247 2.440 nonbonded pdb=" O ASP A 564 " pdb=" N SER A 568 " model vdw 2.255 2.520 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.261 2.440 ... (remaining 198562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 809 or resid 831 through 1104)) selection = (chain 'B' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) selection = (chain 'C' and (resid 18 through 315 or resid 322 through 502 or resid 518 throu \ gh 1104)) } 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 group one per residue 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.150 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 63.730 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.006 0.092 25129 Z= 0.407 Angle : 1.133 15.798 34191 Z= 0.646 Chirality : 0.060 0.475 3858 Planarity : 0.007 0.087 4427 Dihedral : 10.423 82.277 8933 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.96 % Favored : 88.01 % Rotamer: Outliers : 0.66 % Allowed : 5.06 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.67 % Twisted General : 0.50 % 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: -4.94 (0.12), residues: 3111 helix: -3.82 (0.10), residues: 630 sheet: -2.74 (0.20), residues: 493 loop : -3.42 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 423 HIS 0.014 0.003 HIS A1030 PHE 0.044 0.003 PHE B1077 TYR 0.034 0.003 TYR A 481 ARG 0.017 0.001 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 680 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9193 (mm) cc_final: 0.8620 (tt) REVERT: A 74 HIS cc_start: 0.7040 (m-70) cc_final: 0.6621 (t-90) REVERT: A 190 LYS cc_start: 0.8516 (tttp) cc_final: 0.8159 (tptp) REVERT: A 232 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.6951 (ttt180) REVERT: A 294 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8597 (tm-30) REVERT: A 524 CYS cc_start: 0.8600 (m) cc_final: 0.7339 (m) REVERT: A 554 ASP cc_start: 0.8953 (t70) cc_final: 0.8686 (t70) REVERT: A 563 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6413 (tpp80) REVERT: A 582 SER cc_start: 0.9085 (m) cc_final: 0.8848 (t) REVERT: A 730 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9003 (mp0) REVERT: A 733 ASN cc_start: 0.9245 (t160) cc_final: 0.8935 (p0) REVERT: A 742 CYS cc_start: 0.8559 (t) cc_final: 0.8271 (p) REVERT: A 747 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8513 (ttp-170) REVERT: A 755 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 768 LYS cc_start: 0.9077 (tttp) cc_final: 0.8598 (tppt) REVERT: A 849 ASP cc_start: 0.9372 (m-30) cc_final: 0.9145 (p0) REVERT: A 850 ASP cc_start: 0.9383 (m-30) cc_final: 0.9068 (t0) REVERT: A 936 GLN cc_start: 0.8991 (tt0) cc_final: 0.8704 (pt0) REVERT: A 939 GLN cc_start: 0.8909 (tm130) cc_final: 0.8663 (tm-30) REVERT: A 955 ILE cc_start: 0.9091 (mm) cc_final: 0.8890 (mm) REVERT: A 963 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (mm) REVERT: A 967 ASP cc_start: 0.8839 (m-30) cc_final: 0.8563 (t0) REVERT: A 972 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8974 (pp20) REVERT: A 1049 TYR cc_start: 0.8495 (t80) cc_final: 0.8271 (t80) REVERT: B 89 PHE cc_start: 0.8659 (t80) cc_final: 0.8443 (t80) REVERT: B 179 PHE cc_start: 0.6022 (m-10) cc_final: 0.5543 (m-80) REVERT: B 197 TYR cc_start: 0.6285 (m-10) cc_final: 0.6070 (m-10) REVERT: B 214 ASN cc_start: 0.6662 (t0) cc_final: 0.6069 (p0) REVERT: B 231 PHE cc_start: 0.7739 (p90) cc_final: 0.7503 (p90) REVERT: B 256 TYR cc_start: 0.7432 (m-80) cc_final: 0.6915 (m-10) REVERT: B 261 THR cc_start: 0.8680 (m) cc_final: 0.8087 (p) REVERT: B 289 SER cc_start: 0.9209 (m) cc_final: 0.8999 (p) REVERT: B 305 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: B 322 LEU cc_start: 0.7926 (pt) cc_final: 0.7191 (tt) REVERT: B 389 VAL cc_start: 0.8487 (m) cc_final: 0.8272 (p) REVERT: B 394 VAL cc_start: 0.8604 (t) cc_final: 0.8353 (p) REVERT: B 407 ASP cc_start: 0.6948 (t70) cc_final: 0.6600 (t70) REVERT: B 447 LYS cc_start: 0.8691 (mttt) cc_final: 0.8039 (mmmt) REVERT: B 522 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8403 (t0) REVERT: B 675 VAL cc_start: 0.8982 (t) cc_final: 0.8706 (p) REVERT: B 721 ASN cc_start: 0.9380 (t160) cc_final: 0.8908 (m-40) REVERT: B 722 MET cc_start: 0.9409 (tpt) cc_final: 0.9207 (tpp) REVERT: B 758 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8697 (tmt170) REVERT: B 768 LYS cc_start: 0.8861 (tptt) cc_final: 0.8381 (mtmm) REVERT: B 770 MET cc_start: 0.8568 (mmp) cc_final: 0.8054 (mpp) REVERT: B 787 ILE cc_start: 0.9172 (tt) cc_final: 0.8854 (tt) REVERT: B 882 MET cc_start: 0.8896 (mmm) cc_final: 0.8357 (mmt) REVERT: B 925 THR cc_start: 0.8019 (m) cc_final: 0.7716 (p) REVERT: B 942 ASN cc_start: 0.9175 (t0) cc_final: 0.8963 (m-40) REVERT: B 951 ASN cc_start: 0.8077 (t0) cc_final: 0.7753 (t0) REVERT: B 987 GLN cc_start: 0.8640 (tp40) cc_final: 0.8328 (tp40) REVERT: B 999 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9029 (tt0) REVERT: B 1022 VAL cc_start: 0.8990 (m) cc_final: 0.8766 (m) REVERT: B 1027 LYS cc_start: 0.8379 (mmmt) cc_final: 0.7468 (tptp) REVERT: B 1029 TYR cc_start: 0.8834 (m-80) cc_final: 0.8164 (m-80) REVERT: B 1055 ARG cc_start: 0.9008 (mmm160) cc_final: 0.8674 (mmm-85) REVERT: B 1066 GLU cc_start: 0.9011 (tt0) cc_final: 0.8767 (pm20) REVERT: B 1090 ASN cc_start: 0.9070 (m-40) cc_final: 0.8684 (m-40) REVERT: C 56 GLN cc_start: 0.9068 (tt0) cc_final: 0.8614 (pp30) REVERT: C 191 ASP cc_start: 0.8760 (m-30) cc_final: 0.8543 (p0) REVERT: C 214 ASN cc_start: 0.7781 (t0) cc_final: 0.7527 (m-40) REVERT: C 268 GLU cc_start: 0.9296 (tt0) cc_final: 0.9046 (pp20) REVERT: C 278 CYS cc_start: 0.8677 (t) cc_final: 0.8036 (m) REVERT: C 387 PHE cc_start: 0.8294 (p90) cc_final: 0.7910 (p90) REVERT: C 457 ASN cc_start: 0.8166 (t0) cc_final: 0.7741 (m-40) REVERT: C 647 GLU cc_start: 0.7552 (tt0) cc_final: 0.7329 (pm20) REVERT: C 745 LEU cc_start: 0.9308 (tm) cc_final: 0.9066 (mt) REVERT: C 776 LEU cc_start: 0.9188 (mt) cc_final: 0.8975 (tp) REVERT: C 796 LYS cc_start: 0.8933 (mtmm) cc_final: 0.8476 (ttpp) REVERT: C 840 LEU cc_start: 0.9476 (mm) cc_final: 0.9023 (mm) REVERT: C 868 TRP cc_start: 0.8285 (m100) cc_final: 0.7120 (t60) REVERT: C 956 SER cc_start: 0.9266 (t) cc_final: 0.8875 (m) REVERT: C 987 GLN cc_start: 0.8916 (tp40) cc_final: 0.8511 (tt0) REVERT: C 999 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8820 (tm-30) outliers start: 18 outliers final: 5 residues processed: 695 average time/residue: 0.3854 time to fit residues: 405.1849 Evaluate side-chains 382 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 374 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 920 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 0.0470 chunk 237 optimal weight: 0.8980 chunk 131 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 284 optimal weight: 0.0060 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 201 GLN A 301 GLN A 409 ASN A 522 ASN A 528 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 733 ASN A 746 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 889 ASN A 915 GLN A 942 ASN A1101 ASN B 96 ASN B 129 ASN B 201 GLN B 522 ASN B 528 ASN B 549 GLN B 550 GLN B 599 GLN B 611 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS B 721 ASN B 766 GLN B 783 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B 947 GLN B1036 GLN B1065 HIS C 96 ASN C 201 GLN C 227 ASN C 381 ASN C 526 ASN C 550 GLN C 599 GLN C 611 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS C 721 ASN C 783 ASN C 806 ASN ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 ASN C 917 GLN C 935 ASN C1065 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 25129 Z= 0.183 Angle : 0.691 10.951 34191 Z= 0.357 Chirality : 0.045 0.227 3858 Planarity : 0.005 0.078 4427 Dihedral : 6.957 53.859 3388 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.75 % Allowed : 10.72 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.67 % Twisted General : 0.24 % 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: -3.58 (0.13), residues: 3111 helix: -1.30 (0.18), residues: 660 sheet: -1.95 (0.21), residues: 521 loop : -3.07 (0.12), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 423 HIS 0.003 0.001 HIS A1046 PHE 0.037 0.002 PHE A 909 TYR 0.029 0.002 TYR C 598 ARG 0.009 0.001 ARG C 620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 465 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8123 (mmp) cc_final: 0.7465 (tpp) REVERT: A 54 LEU cc_start: 0.9176 (mm) cc_final: 0.8944 (tt) REVERT: A 74 HIS cc_start: 0.6903 (m-70) cc_final: 0.6422 (t-90) REVERT: A 87 ILE cc_start: 0.8915 (pt) cc_final: 0.8672 (mm) REVERT: A 135 ASN cc_start: 0.2363 (t160) cc_final: 0.1549 (t0) REVERT: A 151 MET cc_start: 0.5781 (mpp) cc_final: 0.4815 (ptm) REVERT: A 200 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (t80) REVERT: A 268 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8681 (pm20) REVERT: A 294 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8661 (tm-30) REVERT: A 551 PHE cc_start: 0.7792 (m-10) cc_final: 0.7581 (m-80) REVERT: A 563 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6967 (tpp80) REVERT: A 605 ASP cc_start: 0.9135 (m-30) cc_final: 0.8890 (t0) REVERT: A 762 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8814 (mt-10) REVERT: A 768 LYS cc_start: 0.9053 (tttp) cc_final: 0.8543 (tppt) REVERT: A 770 MET cc_start: 0.8517 (ttm) cc_final: 0.8298 (mtp) REVERT: A 936 GLN cc_start: 0.9024 (tt0) cc_final: 0.8642 (pt0) REVERT: A 939 GLN cc_start: 0.8673 (tm130) cc_final: 0.8467 (tm-30) REVERT: A 963 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8728 (mt) REVERT: A 1021 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8112 (ptm-80) REVERT: A 1022 VAL cc_start: 0.9036 (m) cc_final: 0.8813 (p) REVERT: B 89 PHE cc_start: 0.8882 (t80) cc_final: 0.8503 (t80) REVERT: B 185 PHE cc_start: 0.7255 (m-10) cc_final: 0.6762 (m-10) REVERT: B 305 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.6011 (m-80) REVERT: B 322 LEU cc_start: 0.7786 (pt) cc_final: 0.7005 (tt) REVERT: B 492 GLN cc_start: 0.7114 (mt0) cc_final: 0.6281 (tp40) REVERT: B 519 LEU cc_start: 0.7711 (pp) cc_final: 0.7466 (pp) REVERT: B 598 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: B 675 VAL cc_start: 0.8843 (t) cc_final: 0.8567 (p) REVERT: B 721 ASN cc_start: 0.8877 (t0) cc_final: 0.8662 (m-40) REVERT: B 733 ASN cc_start: 0.8919 (t0) cc_final: 0.8612 (m110) REVERT: B 738 TYR cc_start: 0.8204 (m-80) cc_final: 0.7885 (m-80) REVERT: B 758 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8463 (tmt170) REVERT: B 768 LYS cc_start: 0.8812 (tptt) cc_final: 0.8385 (mtmm) REVERT: B 770 MET cc_start: 0.8499 (mmp) cc_final: 0.8005 (mpp) REVERT: B 804 LEU cc_start: 0.9257 (mt) cc_final: 0.9025 (mt) REVERT: B 833 CYS cc_start: 0.7160 (m) cc_final: 0.6298 (t) REVERT: B 884 MET cc_start: 0.9575 (tpp) cc_final: 0.9293 (mmt) REVERT: B 972 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8266 (mt-10) REVERT: B 973 VAL cc_start: 0.8820 (t) cc_final: 0.8596 (p) REVERT: B 999 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9146 (tt0) REVERT: B 1016 LEU cc_start: 0.9083 (mt) cc_final: 0.8866 (mt) REVERT: B 1027 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7393 (tptp) REVERT: B 1055 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8579 (mmm-85) REVERT: C 56 GLN cc_start: 0.9059 (tt0) cc_final: 0.8816 (pp30) REVERT: C 214 ASN cc_start: 0.7919 (t0) cc_final: 0.7646 (m-40) REVERT: C 268 GLU cc_start: 0.9189 (tt0) cc_final: 0.8868 (pp20) REVERT: C 278 CYS cc_start: 0.8785 (t) cc_final: 0.8046 (m) REVERT: C 323 CYS cc_start: 0.5637 (OUTLIER) cc_final: 0.5352 (t) REVERT: C 417 MET cc_start: 0.6819 (ptt) cc_final: 0.5833 (ppp) REVERT: C 448 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6443 (tt) REVERT: C 449 ARG cc_start: 0.5241 (mtm180) cc_final: 0.5035 (mtm180) REVERT: C 457 ASN cc_start: 0.8137 (t0) cc_final: 0.7614 (m-40) REVERT: C 514 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8175 (mmtt) REVERT: C 551 PHE cc_start: 0.7220 (m-80) cc_final: 0.6995 (m-80) REVERT: C 635 CYS cc_start: 0.9071 (p) cc_final: 0.8187 (t) REVERT: C 707 GLU cc_start: 0.8747 (tt0) cc_final: 0.8419 (tt0) REVERT: C 743 THR cc_start: 0.9168 (m) cc_final: 0.8913 (p) REVERT: C 796 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8318 (ttpt) REVERT: C 868 TRP cc_start: 0.8269 (m100) cc_final: 0.7555 (m100) REVERT: C 942 ASN cc_start: 0.8590 (t0) cc_final: 0.8242 (t0) REVERT: C 956 SER cc_start: 0.9336 (t) cc_final: 0.8830 (m) REVERT: C 972 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7647 (pt0) REVERT: C 976 ASP cc_start: 0.8927 (t70) cc_final: 0.8511 (p0) REVERT: C 987 GLN cc_start: 0.8868 (tp40) cc_final: 0.8476 (tt0) REVERT: C 999 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8915 (tm-30) REVERT: C 1001 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8712 (ttp80) REVERT: C 1102 THR cc_start: 0.9147 (p) cc_final: 0.8785 (t) outliers start: 75 outliers final: 37 residues processed: 518 average time/residue: 0.3696 time to fit residues: 304.7157 Evaluate side-chains 384 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 340 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 387 PHE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 904 GLN Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 157 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 282 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 108 ASN C 381 ASN ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25129 Z= 0.292 Angle : 0.696 12.470 34191 Z= 0.362 Chirality : 0.046 0.234 3858 Planarity : 0.005 0.075 4427 Dihedral : 6.627 57.983 3381 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 3.78 % Allowed : 12.95 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.17 % 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: -3.08 (0.14), residues: 3111 helix: -0.31 (0.19), residues: 661 sheet: -1.85 (0.21), residues: 563 loop : -2.92 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 423 HIS 0.007 0.001 HIS B 641 PHE 0.027 0.002 PHE A 909 TYR 0.027 0.002 TYR B 408 ARG 0.008 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 355 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9242 (mm) cc_final: 0.8949 (tt) REVERT: A 74 HIS cc_start: 0.7217 (m-70) cc_final: 0.6731 (t-90) REVERT: A 87 ILE cc_start: 0.9008 (pt) cc_final: 0.8689 (mm) REVERT: A 232 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7274 (mtp180) REVERT: A 268 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8967 (mp0) REVERT: A 294 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8647 (tm-30) REVERT: A 558 PHE cc_start: 0.8334 (m-10) cc_final: 0.8000 (m-10) REVERT: A 560 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8342 (p0) REVERT: A 598 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 741 PHE cc_start: 0.8829 (m-10) cc_final: 0.8571 (m-10) REVERT: A 768 LYS cc_start: 0.9074 (tttp) cc_final: 0.8709 (tppt) REVERT: A 835 GLN cc_start: 0.8024 (tt0) cc_final: 0.7662 (tt0) REVERT: A 1021 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7277 (ptp90) REVERT: B 185 PHE cc_start: 0.7394 (m-10) cc_final: 0.7168 (m-10) REVERT: B 305 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: B 401 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7611 (mt0) REVERT: B 558 PHE cc_start: 0.6333 (m-80) cc_final: 0.6133 (m-80) REVERT: B 582 SER cc_start: 0.9091 (m) cc_final: 0.8086 (p) REVERT: B 598 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: B 675 VAL cc_start: 0.9329 (t) cc_final: 0.9079 (p) REVERT: B 722 MET cc_start: 0.9220 (tpp) cc_final: 0.8938 (tpp) REVERT: B 758 ARG cc_start: 0.8748 (ttm-80) cc_final: 0.8460 (tmt170) REVERT: B 768 LYS cc_start: 0.8842 (tptt) cc_final: 0.8350 (mtmm) REVERT: B 770 MET cc_start: 0.8749 (mmp) cc_final: 0.8279 (mpp) REVERT: B 801 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8827 (mt-10) REVERT: B 804 LEU cc_start: 0.9284 (mt) cc_final: 0.9040 (mt) REVERT: B 833 CYS cc_start: 0.6605 (m) cc_final: 0.5536 (t) REVERT: B 972 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8345 (mt-10) REVERT: B 1027 LYS cc_start: 0.8463 (mmmt) cc_final: 0.7568 (tptp) REVERT: B 1055 ARG cc_start: 0.8768 (mmm160) cc_final: 0.8363 (mmm-85) REVERT: C 37 MET cc_start: 0.8527 (mmm) cc_final: 0.7962 (mmm) REVERT: C 56 GLN cc_start: 0.9222 (tt0) cc_final: 0.8792 (pp30) REVERT: C 268 GLU cc_start: 0.9259 (tt0) cc_final: 0.8949 (pp20) REVERT: C 306 ARG cc_start: 0.7108 (tpp-160) cc_final: 0.6763 (tpp80) REVERT: C 396 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7189 (mp10) REVERT: C 417 MET cc_start: 0.6507 (ptt) cc_final: 0.5904 (ppp) REVERT: C 448 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6754 (tt) REVERT: C 457 ASN cc_start: 0.8118 (t0) cc_final: 0.7597 (m-40) REVERT: C 514 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8177 (mmtt) REVERT: C 707 GLU cc_start: 0.8843 (tt0) cc_final: 0.8419 (tt0) REVERT: C 743 THR cc_start: 0.9209 (m) cc_final: 0.8874 (p) REVERT: C 796 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8457 (ttpt) REVERT: C 905 ILE cc_start: 0.9456 (tt) cc_final: 0.9147 (mt) REVERT: C 942 ASN cc_start: 0.8825 (t0) cc_final: 0.8520 (t0) REVERT: C 956 SER cc_start: 0.9425 (t) cc_final: 0.9000 (m) REVERT: C 972 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8087 (pt0) REVERT: C 987 GLN cc_start: 0.8922 (tp40) cc_final: 0.8535 (tt0) REVERT: C 999 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8929 (tm-30) outliers start: 103 outliers final: 63 residues processed: 431 average time/residue: 0.3496 time to fit residues: 237.7639 Evaluate side-chains 361 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 281 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 641 HIS A 661 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN C 614 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25129 Z= 0.244 Angle : 0.650 11.673 34191 Z= 0.336 Chirality : 0.045 0.221 3858 Planarity : 0.004 0.068 4427 Dihedral : 6.358 58.312 3381 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 4.04 % Allowed : 13.91 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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: -2.77 (0.14), residues: 3111 helix: 0.22 (0.20), residues: 655 sheet: -1.80 (0.21), residues: 552 loop : -2.76 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 868 HIS 0.003 0.001 HIS B 445 PHE 0.028 0.002 PHE B 89 TYR 0.022 0.002 TYR B 408 ARG 0.006 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 334 time to evaluate : 2.888 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 37 MET cc_start: 0.7873 (mmt) cc_final: 0.7305 (tpp) REVERT: A 54 LEU cc_start: 0.9295 (mm) cc_final: 0.8997 (tp) REVERT: A 74 HIS cc_start: 0.7247 (m-70) cc_final: 0.6749 (t-90) REVERT: A 87 ILE cc_start: 0.9019 (pt) cc_final: 0.8631 (mm) REVERT: A 232 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7386 (mtp180) REVERT: A 294 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8656 (tm-30) REVERT: A 560 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8354 (p0) REVERT: A 598 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 722 MET cc_start: 0.8816 (tpt) cc_final: 0.8388 (tpp) REVERT: A 735 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8911 (tp) REVERT: A 768 LYS cc_start: 0.9053 (tttp) cc_final: 0.8713 (tppt) REVERT: A 835 GLN cc_start: 0.8138 (tt0) cc_final: 0.7767 (tt0) REVERT: A 966 LEU cc_start: 0.7692 (mt) cc_final: 0.6616 (tp) REVERT: A 1021 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7275 (ptp90) REVERT: A 1027 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8516 (tptt) REVERT: B 305 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: B 558 PHE cc_start: 0.6523 (m-80) cc_final: 0.6283 (m-80) REVERT: B 582 SER cc_start: 0.9097 (m) cc_final: 0.8015 (p) REVERT: B 598 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7312 (m-10) REVERT: B 675 VAL cc_start: 0.9388 (t) cc_final: 0.9116 (p) REVERT: B 722 MET cc_start: 0.9162 (tpp) cc_final: 0.8891 (tpp) REVERT: B 758 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8545 (tmt170) REVERT: B 768 LYS cc_start: 0.8776 (tptt) cc_final: 0.8253 (mtmm) REVERT: B 770 MET cc_start: 0.8859 (mmp) cc_final: 0.8509 (mpp) REVERT: B 801 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8792 (mt-10) REVERT: B 804 LEU cc_start: 0.9262 (mt) cc_final: 0.8989 (mt) REVERT: B 833 CYS cc_start: 0.6731 (m) cc_final: 0.5752 (t) REVERT: B 963 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8121 (mt) REVERT: B 972 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8282 (mt-10) REVERT: B 1027 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7541 (tptp) REVERT: B 1055 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8608 (mmm-85) REVERT: C 37 MET cc_start: 0.8563 (mmm) cc_final: 0.7934 (mmm) REVERT: C 56 GLN cc_start: 0.9189 (tt0) cc_final: 0.8684 (tm-30) REVERT: C 268 GLU cc_start: 0.9300 (tt0) cc_final: 0.9014 (pp20) REVERT: C 396 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7581 (mm-40) REVERT: C 411 LYS cc_start: 0.8311 (tppt) cc_final: 0.8008 (tptt) REVERT: C 417 MET cc_start: 0.6674 (ptt) cc_final: 0.5895 (ppp) REVERT: C 448 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6657 (tt) REVERT: C 457 ASN cc_start: 0.8155 (t0) cc_final: 0.7664 (m-40) REVERT: C 514 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8234 (mptt) REVERT: C 707 GLU cc_start: 0.8785 (tt0) cc_final: 0.8391 (tt0) REVERT: C 743 THR cc_start: 0.9220 (m) cc_final: 0.8891 (p) REVERT: C 745 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8908 (mt) REVERT: C 796 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8440 (ttpp) REVERT: C 942 ASN cc_start: 0.8726 (t0) cc_final: 0.8462 (t0) REVERT: C 956 SER cc_start: 0.9500 (t) cc_final: 0.9054 (m) REVERT: C 972 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8072 (pt0) REVERT: C 977 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8295 (ptm160) REVERT: C 987 GLN cc_start: 0.8895 (tp40) cc_final: 0.8547 (tt0) REVERT: C 999 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8900 (tm-30) outliers start: 110 outliers final: 72 residues processed: 416 average time/residue: 0.3291 time to fit residues: 217.8315 Evaluate side-chains 375 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 294 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 932 ASP Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 251 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1036 GLN B 70 HIS ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 473 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 935 ASN ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN ** C 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25129 Z= 0.430 Angle : 0.749 13.410 34191 Z= 0.392 Chirality : 0.048 0.235 3858 Planarity : 0.005 0.078 4427 Dihedral : 6.678 59.901 3379 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.05 % Favored : 86.92 % Rotamer: Outliers : 5.32 % Allowed : 14.46 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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: -2.80 (0.14), residues: 3111 helix: 0.12 (0.20), residues: 650 sheet: -1.78 (0.22), residues: 533 loop : -2.76 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 868 HIS 0.006 0.001 HIS C 181 PHE 0.031 0.002 PHE B 89 TYR 0.025 0.002 TYR A1049 ARG 0.009 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 306 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8104 (mmt) cc_final: 0.7444 (tpp) REVERT: A 54 LEU cc_start: 0.9339 (mm) cc_final: 0.9012 (tt) REVERT: A 74 HIS cc_start: 0.7290 (m-70) cc_final: 0.6780 (t-90) REVERT: A 87 ILE cc_start: 0.8990 (pt) cc_final: 0.8632 (mm) REVERT: A 102 VAL cc_start: 0.9461 (t) cc_final: 0.9246 (p) REVERT: A 294 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8485 (tm-30) REVERT: A 598 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: A 681 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7492 (mm) REVERT: A 722 MET cc_start: 0.8935 (tpt) cc_final: 0.8450 (tpp) REVERT: A 768 LYS cc_start: 0.9155 (tttp) cc_final: 0.8734 (tppt) REVERT: A 1021 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7300 (ptp90) REVERT: A 1027 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8416 (tptt) REVERT: B 305 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: B 437 ASN cc_start: 0.8062 (m-40) cc_final: 0.7699 (p0) REVERT: B 582 SER cc_start: 0.9302 (m) cc_final: 0.8797 (p) REVERT: B 627 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7331 (p0) REVERT: B 675 VAL cc_start: 0.9539 (t) cc_final: 0.9307 (p) REVERT: B 722 MET cc_start: 0.9247 (tpp) cc_final: 0.8963 (tpp) REVERT: B 758 ARG cc_start: 0.8916 (ttm-80) cc_final: 0.8566 (tmt170) REVERT: B 768 LYS cc_start: 0.8776 (tptt) cc_final: 0.8206 (mtmm) REVERT: B 804 LEU cc_start: 0.9379 (mt) cc_final: 0.9047 (mt) REVERT: B 947 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8607 (pp30) REVERT: B 963 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 972 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8399 (mt-10) REVERT: B 1027 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7576 (tptp) REVERT: C 37 MET cc_start: 0.8583 (mmm) cc_final: 0.8247 (mmm) REVERT: C 268 GLU cc_start: 0.9294 (tt0) cc_final: 0.9033 (pp20) REVERT: C 278 CYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8215 (m) REVERT: C 329 PHE cc_start: 0.8790 (m-80) cc_final: 0.8548 (m-80) REVERT: C 396 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7611 (mm-40) REVERT: C 411 LYS cc_start: 0.8436 (tppt) cc_final: 0.8211 (tptt) REVERT: C 514 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8188 (mptt) REVERT: C 551 PHE cc_start: 0.7466 (m-80) cc_final: 0.7215 (m-80) REVERT: C 707 GLU cc_start: 0.8805 (tt0) cc_final: 0.8354 (tt0) REVERT: C 709 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8461 (mtp) REVERT: C 745 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8875 (mt) REVERT: C 796 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8645 (ttpt) REVERT: C 956 SER cc_start: 0.9585 (t) cc_final: 0.9103 (m) REVERT: C 972 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8167 (pt0) REVERT: C 987 GLN cc_start: 0.8986 (tp40) cc_final: 0.8650 (tt0) REVERT: C 999 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8888 (tm-30) outliers start: 145 outliers final: 92 residues processed: 415 average time/residue: 0.3381 time to fit residues: 222.4809 Evaluate side-chains 379 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 277 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 627 ASN Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 LEU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25129 Z= 0.293 Angle : 0.672 12.484 34191 Z= 0.348 Chirality : 0.046 0.178 3858 Planarity : 0.005 0.073 4427 Dihedral : 6.404 58.793 3379 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 5.28 % Allowed : 15.27 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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: -2.63 (0.14), residues: 3111 helix: 0.43 (0.20), residues: 644 sheet: -1.66 (0.22), residues: 550 loop : -2.72 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 868 HIS 0.004 0.001 HIS B 445 PHE 0.029 0.002 PHE B 185 TYR 0.033 0.002 TYR B 53 ARG 0.009 0.001 ARG B1055 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 320 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8151 (mmt) cc_final: 0.7581 (tpp) REVERT: A 54 LEU cc_start: 0.9347 (mm) cc_final: 0.8897 (tp) REVERT: A 74 HIS cc_start: 0.7267 (m-70) cc_final: 0.6777 (t-90) REVERT: A 87 ILE cc_start: 0.9011 (pt) cc_final: 0.8631 (mm) REVERT: A 102 VAL cc_start: 0.9453 (t) cc_final: 0.9238 (p) REVERT: A 294 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8395 (tm-30) REVERT: A 598 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: A 629 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 707 GLU cc_start: 0.9152 (tt0) cc_final: 0.8946 (tt0) REVERT: A 722 MET cc_start: 0.8868 (tpt) cc_final: 0.8575 (tpp) REVERT: A 768 LYS cc_start: 0.9130 (tttp) cc_final: 0.8762 (tppt) REVERT: A 786 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8099 (pp30) REVERT: A 884 MET cc_start: 0.9559 (mmm) cc_final: 0.9264 (tpp) REVERT: A 1021 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7346 (ptp90) REVERT: A 1027 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8406 (tptt) REVERT: A 1074 GLU cc_start: 0.8543 (tp30) cc_final: 0.8285 (tp30) REVERT: B 85 ASP cc_start: 0.8161 (m-30) cc_final: 0.7837 (t0) REVERT: B 254 VAL cc_start: 0.9150 (t) cc_final: 0.8882 (p) REVERT: B 305 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: B 437 ASN cc_start: 0.7881 (m-40) cc_final: 0.7560 (p0) REVERT: B 582 SER cc_start: 0.9076 (m) cc_final: 0.8263 (p) REVERT: B 598 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: B 675 VAL cc_start: 0.9545 (t) cc_final: 0.9296 (p) REVERT: B 722 MET cc_start: 0.9101 (tpp) cc_final: 0.8825 (tpp) REVERT: B 758 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8570 (tmt170) REVERT: B 768 LYS cc_start: 0.8806 (tptt) cc_final: 0.8244 (mtmm) REVERT: B 804 LEU cc_start: 0.9383 (mt) cc_final: 0.9137 (mt) REVERT: B 855 TYR cc_start: 0.9364 (m-80) cc_final: 0.9016 (m-80) REVERT: B 882 MET cc_start: 0.9280 (mmm) cc_final: 0.9059 (mmm) REVERT: B 947 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8469 (pp30) REVERT: B 972 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8367 (mt-10) REVERT: B 1027 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7582 (tptp) REVERT: C 37 MET cc_start: 0.8582 (mmm) cc_final: 0.7841 (mmm) REVERT: C 268 GLU cc_start: 0.9295 (tt0) cc_final: 0.9038 (pp20) REVERT: C 278 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8153 (m) REVERT: C 329 PHE cc_start: 0.8748 (m-80) cc_final: 0.8481 (m-80) REVERT: C 417 MET cc_start: 0.7360 (ptt) cc_final: 0.6294 (ppp) REVERT: C 481 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5557 (t80) REVERT: C 514 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8231 (mptt) REVERT: C 545 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5225 (m-10) REVERT: C 707 GLU cc_start: 0.8863 (tt0) cc_final: 0.8420 (tt0) REVERT: C 709 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8517 (mtp) REVERT: C 745 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8904 (mt) REVERT: C 796 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8592 (ttpp) REVERT: C 837 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: C 905 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9192 (mt) REVERT: C 956 SER cc_start: 0.9601 (t) cc_final: 0.9132 (m) REVERT: C 972 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8100 (pt0) REVERT: C 987 GLN cc_start: 0.8900 (tp40) cc_final: 0.8570 (tt0) REVERT: C 999 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8894 (tm-30) outliers start: 144 outliers final: 107 residues processed: 426 average time/residue: 0.3537 time to fit residues: 240.0637 Evaluate side-chains 404 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 283 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1021 ARG Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 932 ASP Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 291 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25129 Z= 0.190 Angle : 0.624 11.332 34191 Z= 0.321 Chirality : 0.044 0.210 3858 Planarity : 0.004 0.077 4427 Dihedral : 5.996 56.064 3379 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.22 % Allowed : 16.81 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.07 % 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: -2.35 (0.15), residues: 3111 helix: 0.80 (0.21), residues: 648 sheet: -1.42 (0.22), residues: 570 loop : -2.63 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 868 HIS 0.002 0.001 HIS B 445 PHE 0.019 0.001 PHE A 89 TYR 0.035 0.001 TYR A 53 ARG 0.004 0.000 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 346 time to evaluate : 2.536 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 54 LEU cc_start: 0.9395 (mm) cc_final: 0.9065 (tt) REVERT: A 74 HIS cc_start: 0.7153 (m-70) cc_final: 0.6631 (t-170) REVERT: A 102 VAL cc_start: 0.9444 (t) cc_final: 0.9239 (p) REVERT: A 151 MET cc_start: 0.5798 (mpp) cc_final: 0.4770 (ptm) REVERT: A 294 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8591 (tp30) REVERT: A 598 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8236 (m-80) REVERT: A 629 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: A 707 GLU cc_start: 0.9075 (tt0) cc_final: 0.8799 (tt0) REVERT: A 722 MET cc_start: 0.8817 (tpt) cc_final: 0.8540 (tpp) REVERT: A 768 LYS cc_start: 0.9073 (tttp) cc_final: 0.8721 (tppt) REVERT: A 786 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8082 (pp30) REVERT: A 968 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7976 (tmtt) REVERT: A 1074 GLU cc_start: 0.8640 (tp30) cc_final: 0.8321 (tp30) REVERT: B 85 ASP cc_start: 0.8187 (m-30) cc_final: 0.7768 (t0) REVERT: B 89 PHE cc_start: 0.9015 (t80) cc_final: 0.8699 (t80) REVERT: B 254 VAL cc_start: 0.9073 (t) cc_final: 0.8754 (p) REVERT: B 437 ASN cc_start: 0.7667 (m-40) cc_final: 0.7343 (p0) REVERT: B 582 SER cc_start: 0.9169 (m) cc_final: 0.8325 (p) REVERT: B 598 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 675 VAL cc_start: 0.9536 (t) cc_final: 0.9261 (p) REVERT: B 722 MET cc_start: 0.9001 (tpp) cc_final: 0.8734 (tpp) REVERT: B 758 ARG cc_start: 0.8877 (ttm-80) cc_final: 0.8571 (tmt170) REVERT: B 768 LYS cc_start: 0.8822 (tptt) cc_final: 0.8367 (mtmm) REVERT: B 833 CYS cc_start: 0.7083 (m) cc_final: 0.5724 (t) REVERT: B 855 TYR cc_start: 0.9361 (m-80) cc_final: 0.8817 (m-80) REVERT: B 882 MET cc_start: 0.9218 (mmm) cc_final: 0.8869 (mmt) REVERT: B 1027 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7568 (tptp) REVERT: C 37 MET cc_start: 0.8601 (mmm) cc_final: 0.7910 (mmm) REVERT: C 268 GLU cc_start: 0.9298 (tt0) cc_final: 0.9035 (pp20) REVERT: C 278 CYS cc_start: 0.9004 (t) cc_final: 0.8151 (m) REVERT: C 301 GLN cc_start: 0.8954 (mt0) cc_final: 0.8525 (mm110) REVERT: C 329 PHE cc_start: 0.8627 (m-80) cc_final: 0.8293 (m-80) REVERT: C 379 PHE cc_start: 0.7640 (m-80) cc_final: 0.7350 (m-80) REVERT: C 417 MET cc_start: 0.7316 (ptt) cc_final: 0.6283 (ppp) REVERT: C 457 ASN cc_start: 0.8102 (t0) cc_final: 0.7542 (m-40) REVERT: C 481 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5947 (t80) REVERT: C 494 TYR cc_start: 0.7188 (m-80) cc_final: 0.6675 (m-80) REVERT: C 502 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8013 (mm-30) REVERT: C 514 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8216 (mptt) REVERT: C 545 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.5432 (m-10) REVERT: C 598 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: C 707 GLU cc_start: 0.8855 (tt0) cc_final: 0.8433 (tt0) REVERT: C 745 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8876 (mt) REVERT: C 770 MET cc_start: 0.8532 (mmm) cc_final: 0.8177 (mtp) REVERT: C 796 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8610 (ttpt) REVERT: C 837 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: C 905 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9270 (mt) REVERT: C 918 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8450 (pp20) REVERT: C 956 SER cc_start: 0.9601 (t) cc_final: 0.9144 (m) REVERT: C 972 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8153 (pt0) REVERT: C 987 GLN cc_start: 0.8800 (tp40) cc_final: 0.8490 (tt0) REVERT: C 999 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8899 (tm-30) REVERT: C 1001 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8837 (ttp80) REVERT: C 1032 MET cc_start: 0.8320 (ptm) cc_final: 0.8076 (ptt) outliers start: 115 outliers final: 80 residues processed: 429 average time/residue: 0.3361 time to fit residues: 230.6905 Evaluate side-chains 402 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 311 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 932 ASP Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 186 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 237 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25129 Z= 0.277 Angle : 0.665 12.328 34191 Z= 0.342 Chirality : 0.045 0.247 3858 Planarity : 0.005 0.077 4427 Dihedral : 6.061 56.739 3379 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 4.48 % Allowed : 17.36 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 2.00 % Twisted General : 0.03 % 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: -2.33 (0.15), residues: 3111 helix: 0.70 (0.21), residues: 650 sheet: -1.32 (0.22), residues: 542 loop : -2.58 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 868 HIS 0.011 0.001 HIS A 611 PHE 0.016 0.002 PHE B 231 TYR 0.024 0.002 TYR B 598 ARG 0.005 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 328 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9396 (mm) cc_final: 0.9044 (tt) REVERT: A 74 HIS cc_start: 0.7149 (m-70) cc_final: 0.6617 (t-170) REVERT: A 151 MET cc_start: 0.5860 (mpp) cc_final: 0.4817 (ptm) REVERT: A 294 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8572 (tp30) REVERT: A 598 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: A 629 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: A 707 GLU cc_start: 0.9164 (tt0) cc_final: 0.8912 (tt0) REVERT: A 722 MET cc_start: 0.8927 (tpt) cc_final: 0.8631 (tpp) REVERT: A 768 LYS cc_start: 0.9080 (tttp) cc_final: 0.8737 (tppt) REVERT: A 786 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: A 884 MET cc_start: 0.9364 (mmm) cc_final: 0.9157 (tpp) REVERT: A 1074 GLU cc_start: 0.8631 (tp30) cc_final: 0.8359 (tp30) REVERT: B 54 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8265 (tt) REVERT: B 85 ASP cc_start: 0.8098 (m-30) cc_final: 0.7847 (t0) REVERT: B 254 VAL cc_start: 0.9143 (t) cc_final: 0.8891 (p) REVERT: B 437 ASN cc_start: 0.7662 (m-40) cc_final: 0.7328 (p0) REVERT: B 582 SER cc_start: 0.9136 (m) cc_final: 0.8545 (p) REVERT: B 675 VAL cc_start: 0.9585 (t) cc_final: 0.9350 (p) REVERT: B 722 MET cc_start: 0.9028 (tpp) cc_final: 0.8776 (tpp) REVERT: B 758 ARG cc_start: 0.8918 (ttm-80) cc_final: 0.8598 (tmt170) REVERT: B 768 LYS cc_start: 0.8800 (tptt) cc_final: 0.8335 (mtmm) REVERT: B 833 CYS cc_start: 0.7091 (m) cc_final: 0.5712 (t) REVERT: B 1027 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7522 (tptp) REVERT: C 37 MET cc_start: 0.8547 (mmm) cc_final: 0.7942 (mmm) REVERT: C 268 GLU cc_start: 0.9306 (tt0) cc_final: 0.9056 (pp20) REVERT: C 278 CYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8256 (m) REVERT: C 329 PHE cc_start: 0.8644 (m-80) cc_final: 0.8375 (m-80) REVERT: C 379 PHE cc_start: 0.7726 (m-80) cc_final: 0.7391 (m-80) REVERT: C 451 PHE cc_start: 0.8011 (m-80) cc_final: 0.7750 (m-80) REVERT: C 457 ASN cc_start: 0.7944 (t0) cc_final: 0.7359 (m-40) REVERT: C 481 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6000 (t80) REVERT: C 502 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7990 (mm-30) REVERT: C 514 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8292 (mptt) REVERT: C 545 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.5267 (m-10) REVERT: C 707 GLU cc_start: 0.8862 (tt0) cc_final: 0.8420 (tt0) REVERT: C 745 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8929 (mt) REVERT: C 770 MET cc_start: 0.8407 (mmm) cc_final: 0.8118 (mtp) REVERT: C 796 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8664 (ttpt) REVERT: C 837 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: C 905 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9256 (mt) REVERT: C 918 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8501 (pp20) REVERT: C 956 SER cc_start: 0.9608 (t) cc_final: 0.9147 (m) REVERT: C 972 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8121 (pt0) REVERT: C 987 GLN cc_start: 0.8835 (tp40) cc_final: 0.8535 (tt0) REVERT: C 999 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8886 (tm-30) REVERT: C 1001 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8899 (ttp80) REVERT: C 1032 MET cc_start: 0.8413 (ptm) cc_final: 0.8187 (ptt) outliers start: 122 outliers final: 96 residues processed: 418 average time/residue: 0.3608 time to fit residues: 246.1132 Evaluate side-chains 409 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 303 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 611 HIS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 950 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 427 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1031 LEU Chi-restraints excluded: chain C residue 1043 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 0.9990 chunk 289 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 254 optimal weight: 0.2980 chunk 265 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 GLN B 883 GLN ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25129 Z= 0.173 Angle : 0.641 11.484 34191 Z= 0.327 Chirality : 0.044 0.308 3858 Planarity : 0.004 0.076 4427 Dihedral : 5.792 54.043 3379 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.56 % Allowed : 18.79 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 1.33 % Twisted General : 0.07 % 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: -2.13 (0.15), residues: 3111 helix: 0.95 (0.21), residues: 647 sheet: -1.26 (0.22), residues: 576 loop : -2.47 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 619 HIS 0.015 0.001 HIS A 611 PHE 0.043 0.001 PHE B 89 TYR 0.025 0.001 TYR B 408 ARG 0.005 0.000 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 345 time to evaluate : 2.762 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 54 LEU cc_start: 0.9380 (mm) cc_final: 0.8996 (tt) REVERT: A 74 HIS cc_start: 0.7225 (m-70) cc_final: 0.6706 (t-170) REVERT: A 294 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8779 (tp30) REVERT: A 598 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: A 629 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: A 707 GLU cc_start: 0.9110 (tt0) cc_final: 0.8903 (tt0) REVERT: A 722 MET cc_start: 0.8816 (tpt) cc_final: 0.8533 (tpp) REVERT: A 768 LYS cc_start: 0.9116 (tttp) cc_final: 0.8776 (tppt) REVERT: A 786 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8150 (pp30) REVERT: A 966 LEU cc_start: 0.7655 (mt) cc_final: 0.6457 (tp) REVERT: A 1074 GLU cc_start: 0.8598 (tp30) cc_final: 0.8264 (tp30) REVERT: B 54 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 85 ASP cc_start: 0.8022 (m-30) cc_final: 0.7616 (t0) REVERT: B 163 TYR cc_start: 0.6219 (t80) cc_final: 0.5938 (t80) REVERT: B 254 VAL cc_start: 0.9092 (t) cc_final: 0.8811 (p) REVERT: B 437 ASN cc_start: 0.7900 (m-40) cc_final: 0.7668 (p0) REVERT: B 582 SER cc_start: 0.9126 (m) cc_final: 0.8379 (p) REVERT: B 675 VAL cc_start: 0.9538 (t) cc_final: 0.9268 (p) REVERT: B 722 MET cc_start: 0.8937 (tpp) cc_final: 0.8693 (tpp) REVERT: B 755 GLU cc_start: 0.9061 (pt0) cc_final: 0.8765 (tt0) REVERT: B 758 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8524 (tmt170) REVERT: B 768 LYS cc_start: 0.8768 (tptt) cc_final: 0.8296 (mtmm) REVERT: B 833 CYS cc_start: 0.7725 (m) cc_final: 0.6441 (t) REVERT: B 859 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8809 (mm) REVERT: B 959 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6714 (pp) REVERT: B 1027 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7582 (tptp) REVERT: C 37 MET cc_start: 0.8520 (mmm) cc_final: 0.7867 (mmm) REVERT: C 268 GLU cc_start: 0.9307 (tt0) cc_final: 0.9063 (pp20) REVERT: C 278 CYS cc_start: 0.9006 (t) cc_final: 0.8233 (m) REVERT: C 329 PHE cc_start: 0.8607 (m-80) cc_final: 0.8340 (m-80) REVERT: C 411 LYS cc_start: 0.8198 (tptt) cc_final: 0.7944 (tptt) REVERT: C 451 PHE cc_start: 0.8008 (m-80) cc_final: 0.7611 (m-80) REVERT: C 457 ASN cc_start: 0.8105 (t0) cc_final: 0.7546 (m-40) REVERT: C 494 TYR cc_start: 0.7215 (m-80) cc_final: 0.6660 (m-80) REVERT: C 502 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7975 (mm-30) REVERT: C 514 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8338 (mptt) REVERT: C 545 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.5294 (m-10) REVERT: C 598 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 707 GLU cc_start: 0.8948 (tt0) cc_final: 0.8698 (tt0) REVERT: C 745 LEU cc_start: 0.9269 (tp) cc_final: 0.8889 (mt) REVERT: C 760 THR cc_start: 0.9441 (m) cc_final: 0.9206 (p) REVERT: C 770 MET cc_start: 0.8483 (mmm) cc_final: 0.8185 (mtp) REVERT: C 796 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8642 (ttpt) REVERT: C 837 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: C 905 ILE cc_start: 0.9552 (tt) cc_final: 0.9315 (mt) REVERT: C 918 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8351 (pp20) REVERT: C 956 SER cc_start: 0.9573 (t) cc_final: 0.9138 (m) REVERT: C 972 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8139 (pt0) REVERT: C 987 GLN cc_start: 0.8689 (tp40) cc_final: 0.8432 (tt0) REVERT: C 999 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8829 (tm-30) REVERT: C 1001 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8773 (ttp80) REVERT: C 1032 MET cc_start: 0.8354 (ptm) cc_final: 0.8090 (ptt) outliers start: 97 outliers final: 72 residues processed: 415 average time/residue: 0.3278 time to fit residues: 218.7264 Evaluate side-chains 393 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 312 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 1031 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 280 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B 908 GLN ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25129 Z= 0.306 Angle : 0.689 13.233 34191 Z= 0.354 Chirality : 0.046 0.316 3858 Planarity : 0.005 0.079 4427 Dihedral : 5.996 55.414 3379 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 3.41 % Allowed : 19.19 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 1.33 % Twisted General : 0.07 % 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: -2.25 (0.15), residues: 3111 helix: 0.71 (0.21), residues: 650 sheet: -1.29 (0.22), residues: 548 loop : -2.50 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 619 HIS 0.004 0.001 HIS C 181 PHE 0.042 0.002 PHE B 89 TYR 0.026 0.002 TYR A1049 ARG 0.006 0.001 ARG A1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 300 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9390 (mm) cc_final: 0.9004 (tt) REVERT: A 74 HIS cc_start: 0.7183 (m-70) cc_final: 0.6681 (t-170) REVERT: A 151 MET cc_start: 0.5810 (mpp) cc_final: 0.4884 (ptm) REVERT: A 232 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7236 (mtp180) REVERT: A 294 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8494 (tp30) REVERT: A 598 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: A 629 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: A 707 GLU cc_start: 0.9170 (tt0) cc_final: 0.8920 (tt0) REVERT: A 722 MET cc_start: 0.8943 (tpt) cc_final: 0.8662 (tpp) REVERT: A 768 LYS cc_start: 0.9077 (tttp) cc_final: 0.8774 (tppt) REVERT: A 786 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8235 (pp30) REVERT: A 1032 MET cc_start: 0.8420 (ptp) cc_final: 0.8095 (ptm) REVERT: A 1074 GLU cc_start: 0.8644 (tp30) cc_final: 0.8367 (tp30) REVERT: B 54 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 85 ASP cc_start: 0.8178 (m-30) cc_final: 0.7882 (t0) REVERT: B 163 TYR cc_start: 0.6152 (t80) cc_final: 0.5891 (t80) REVERT: B 437 ASN cc_start: 0.8011 (m-40) cc_final: 0.7718 (p0) REVERT: B 582 SER cc_start: 0.9155 (m) cc_final: 0.8535 (p) REVERT: B 675 VAL cc_start: 0.9610 (t) cc_final: 0.9377 (p) REVERT: B 722 MET cc_start: 0.9014 (tpp) cc_final: 0.8786 (tpp) REVERT: B 758 ARG cc_start: 0.8912 (ttm-80) cc_final: 0.8587 (tmt170) REVERT: B 768 LYS cc_start: 0.8826 (tptt) cc_final: 0.8354 (mtmm) REVERT: B 833 CYS cc_start: 0.7563 (m) cc_final: 0.6074 (t) REVERT: B 859 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 1027 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7578 (tptp) REVERT: C 37 MET cc_start: 0.8549 (mmm) cc_final: 0.8337 (mmm) REVERT: C 268 GLU cc_start: 0.9311 (tt0) cc_final: 0.9066 (pp20) REVERT: C 278 CYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8239 (m) REVERT: C 329 PHE cc_start: 0.8626 (m-80) cc_final: 0.8393 (m-80) REVERT: C 451 PHE cc_start: 0.8121 (m-80) cc_final: 0.7803 (m-80) REVERT: C 457 ASN cc_start: 0.8013 (t0) cc_final: 0.7431 (m-40) REVERT: C 502 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7678 (mm-30) REVERT: C 514 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8191 (mptt) REVERT: C 545 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.5177 (m-10) REVERT: C 707 GLU cc_start: 0.8935 (tt0) cc_final: 0.8515 (tt0) REVERT: C 745 LEU cc_start: 0.9278 (tp) cc_final: 0.8907 (mt) REVERT: C 770 MET cc_start: 0.8409 (mmm) cc_final: 0.8144 (mtp) REVERT: C 796 LYS cc_start: 0.9041 (mtmm) cc_final: 0.8708 (ttpt) REVERT: C 837 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: C 905 ILE cc_start: 0.9514 (tt) cc_final: 0.9242 (mt) REVERT: C 918 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8348 (pp20) REVERT: C 956 SER cc_start: 0.9647 (t) cc_final: 0.9232 (m) REVERT: C 972 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8090 (pt0) REVERT: C 987 GLN cc_start: 0.8758 (tp40) cc_final: 0.8549 (tt0) REVERT: C 999 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8900 (tm-30) REVERT: C 1001 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8939 (ttp80) outliers start: 93 outliers final: 74 residues processed: 372 average time/residue: 0.3278 time to fit residues: 197.0300 Evaluate side-chains 372 residues out of total 2725 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 290 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 598 TYR Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 980 THR Chi-restraints excluded: chain B residue 1016 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 423 TRP Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 598 TYR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 802 ASP Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 1031 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 152 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 228 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105649 restraints weight = 59285.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106200 restraints weight = 40009.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.106930 restraints weight = 26733.017| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25129 Z= 0.237 Angle : 0.662 12.215 34191 Z= 0.339 Chirality : 0.045 0.289 3858 Planarity : 0.005 0.082 4427 Dihedral : 5.911 54.027 3379 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.74 % Allowed : 19.23 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.10 % Twisted Proline : 1.33 % Twisted General : 0.07 % 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: -2.17 (0.15), residues: 3111 helix: 0.82 (0.21), residues: 650 sheet: -1.15 (0.23), residues: 537 loop : -2.50 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 619 HIS 0.004 0.001 HIS A 611 PHE 0.038 0.002 PHE B 89 TYR 0.023 0.002 TYR A1049 ARG 0.005 0.000 ARG A1001 =============================================================================== Job complete usr+sys time: 5149.54 seconds wall clock time: 94 minutes 16.65 seconds (5656.65 seconds total)