Starting phenix.real_space_refine on Thu Feb 15 22:35:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f5z_28869/02_2024/8f5z_28869_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 101 5.16 5 C 8641 2.51 5 N 2344 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 952": "OD1" <-> "OD2" Residue "B GLU 998": "OE1" <-> "OE2" Residue "B ASP 1099": "OD1" <-> "OD2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A GLU 998": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13598 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6753 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 6759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6759 Classifications: {'peptide': 862} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 829} Chain breaks: 4 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.11, per 1000 atoms: 0.52 Number of scatterers: 13598 At special positions: 0 Unit cell: (113.436, 121.716, 139.104, 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 101 16.00 O 2512 8.00 N 2344 7.00 C 8641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.3 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 14 sheets defined 37.5% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.088A pdb=" N SER B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 105 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 No H-bonds generated for 'chain 'B' and resid 129 through 132' Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.975A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.940A pdb=" N MET B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 381 through 425 removed outlier: 3.858A pdb=" N MET B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 465 through 478 removed outlier: 3.602A pdb=" N GLU B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 493 No H-bonds generated for 'chain 'B' and resid 490 through 493' Processing helix chain 'B' and resid 570 through 586 removed outlier: 3.583A pdb=" N ASP B 574 " --> pdb=" O ASP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 786 Processing helix chain 'B' and resid 791 through 793 No H-bonds generated for 'chain 'B' and resid 791 through 793' Processing helix chain 'B' and resid 815 through 830 removed outlier: 4.730A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 830 " --> pdb=" O ASN B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 888 Processing helix chain 'B' and resid 890 through 895 removed outlier: 3.892A pdb=" N LYS B 895 " --> pdb=" O THR B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 923 Proline residue: B 910 - end of helix removed outlier: 3.610A pdb=" N ILE B 921 " --> pdb=" O THR B 917 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 922 " --> pdb=" O ARG B 918 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 949 removed outlier: 3.652A pdb=" N LYS B 946 " --> pdb=" O GLN B 943 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 947 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 957 No H-bonds generated for 'chain 'B' and resid 954 through 957' Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.625A pdb=" N LEU B 974 " --> pdb=" O LEU B 970 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 980 " --> pdb=" O ALA B 976 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 981 " --> pdb=" O SER B 977 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 983 " --> pdb=" O SER B 979 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 984 " --> pdb=" O GLN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1000 No H-bonds generated for 'chain 'B' and resid 998 through 1000' Processing helix chain 'B' and resid 1010 through 1026 removed outlier: 3.607A pdb=" N ALA B1023 " --> pdb=" O PHE B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 Processing helix chain 'B' and resid 1072 through 1074 No H-bonds generated for 'chain 'B' and resid 1072 through 1074' Processing helix chain 'B' and resid 1083 through 1094 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.464A pdb=" N GLU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 197 through 212 removed outlier: 4.087A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 381 through 425 removed outlier: 3.536A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.578A pdb=" N GLN A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 498 through 504 removed outlier: 4.034A pdb=" N GLY A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 504' Processing helix chain 'A' and resid 570 through 586 removed outlier: 3.600A pdb=" N LEU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 786 Processing helix chain 'A' and resid 815 through 830 removed outlier: 4.576A pdb=" N VAL A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 893 through 921 removed outlier: 3.612A pdb=" N ASN A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.956A pdb=" N ARG A 932 " --> pdb=" O PRO A 928 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 944 " --> pdb=" O CYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.815A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS A 984 " --> pdb=" O GLN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1009 through 1026 removed outlier: 3.790A pdb=" N PHE A1026 " --> pdb=" O MET A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1048 No H-bonds generated for 'chain 'A' and resid 1046 through 1048' Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 4.315A pdb=" N GLN A1071 " --> pdb=" O PHE A1067 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A1072 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1096 removed outlier: 3.709A pdb=" N LEU A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1092 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 156 through 159 Processing sheet with id= B, first strand: chain 'B' and resid 287 through 290 removed outlier: 3.989A pdb=" N VAL B 369 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 254 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 243 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 252 " --> pdb=" O LYS B 243 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 447 through 451 removed outlier: 3.660A pdb=" N ALA B 449 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 514 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE B 519 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG B 512 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TRP B 521 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA B 510 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 484 " --> pdb=" O LYS B 744 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 755 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.945A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.165A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 870 " --> pdb=" O PHE B 767 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS B 858 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL B 868 " --> pdb=" O SER B 856 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER B 856 " --> pdb=" O VAL B 868 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 870 " --> pdb=" O CYS B 854 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 854 " --> pdb=" O CYS B 870 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 872 " --> pdb=" O LEU B 852 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 852 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 993 through 995 removed outlier: 3.545A pdb=" N THR B1058 " --> pdb=" O THR B1034 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1053 through 1055 removed outlier: 3.569A pdb=" N ALA B1115 " --> pdb=" O LEU B1053 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 156 through 159 Processing sheet with id= I, first strand: chain 'A' and resid 250 through 257 removed outlier: 6.622A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.640A pdb=" N PHE A 745 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 529 through 532 removed outlier: 4.219A pdb=" N VAL A 530 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 559 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 835 through 842 removed outlier: 3.532A pdb=" N VAL A 855 " --> pdb=" O GLU A 835 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 769 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 991 through 994 removed outlier: 3.761A pdb=" N VAL A1035 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1036 through 1040 removed outlier: 3.649A pdb=" N ARG A1056 " --> pdb=" O SER A1036 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1053 " --> pdb=" O ALA A1115 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1488 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: 4.15 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2818 1.33 - 1.45: 3000 1.45 - 1.57: 7869 1.57 - 1.69: 1 1.69 - 1.81: 162 Bond restraints: 13850 Sorted by residual: bond pdb=" CAL O6E A1201 " pdb=" OAZ O6E A1201 " ideal model delta sigma weight residual 1.247 1.341 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CAL O6E B1201 " pdb=" OAZ O6E B1201 " ideal model delta sigma weight residual 1.247 1.340 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAM O6E A1201 " pdb=" OBG O6E A1201 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CAM O6E B1201 " pdb=" OBG O6E B1201 " ideal model delta sigma weight residual 1.248 1.340 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CAW O6E A1201 " pdb=" CBC O6E A1201 " ideal model delta sigma weight residual 1.460 1.408 0.052 2.00e-02 2.50e+03 6.75e+00 ... (remaining 13845 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.98: 289 105.98 - 112.98: 7634 112.98 - 119.99: 4549 119.99 - 127.00: 6089 127.00 - 134.00: 146 Bond angle restraints: 18707 Sorted by residual: angle pdb=" N GLY B 250 " pdb=" CA GLY B 250 " pdb=" C GLY B 250 " ideal model delta sigma weight residual 111.18 115.59 -4.41 1.54e+00 4.22e-01 8.19e+00 angle pdb=" CB GLU A 262 " pdb=" CG GLU A 262 " pdb=" CD GLU A 262 " ideal model delta sigma weight residual 112.60 117.35 -4.75 1.70e+00 3.46e-01 7.81e+00 angle pdb=" CA LEU A 953 " pdb=" CB LEU A 953 " pdb=" CG LEU A 953 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.73e+00 angle pdb=" C GLN A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 120.09 123.51 -3.42 1.25e+00 6.40e-01 7.49e+00 angle pdb=" CA PRO B 759 " pdb=" N PRO B 759 " pdb=" CD PRO B 759 " ideal model delta sigma weight residual 112.00 108.17 3.83 1.40e+00 5.10e-01 7.47e+00 ... (remaining 18702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7189 17.93 - 35.86: 958 35.86 - 53.79: 262 53.79 - 71.72: 41 71.72 - 89.65: 13 Dihedral angle restraints: 8463 sinusoidal: 3473 harmonic: 4990 Sorted by residual: dihedral pdb=" CG ARG A 299 " pdb=" CD ARG A 299 " pdb=" NE ARG A 299 " pdb=" CZ ARG A 299 " ideal model delta sinusoidal sigma weight residual 90.00 133.85 -43.85 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B1090 " pdb=" CD ARG B1090 " pdb=" NE ARG B1090 " pdb=" CZ ARG B1090 " ideal model delta sinusoidal sigma weight residual -90.00 -133.85 43.85 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP A1078 " pdb=" CB ASP A1078 " pdb=" CG ASP A1078 " pdb=" OD1 ASP A1078 " ideal model delta sinusoidal sigma weight residual -30.00 -84.48 54.48 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 8460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1498 0.035 - 0.069: 456 0.069 - 0.104: 125 0.104 - 0.138: 51 0.138 - 0.173: 4 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CBJ O6E A1201 " pdb=" CAC O6E A1201 " pdb=" CBD O6E A1201 " pdb=" CBN O6E A1201 " both_signs ideal model delta sigma weight residual False 2.70 2.88 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.85 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.85 0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2131 not shown) Planarity restraints: 2385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.202 2.00e-02 2.50e+03 2.06e-01 1.06e+03 pdb=" CAP O6E B1201 " -0.308 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.027 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.181 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.054 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.052 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.471 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.023 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.162 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.197 2.00e-02 2.50e+03 1.99e-01 9.92e+02 pdb=" CAP O6E A1201 " 0.295 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.020 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.177 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.050 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.050 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.456 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.026 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.159 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.003 2.00e-02 2.50e+03 3.52e-02 3.09e+01 pdb=" CAO O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.005 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.038 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.032 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.006 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.008 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.011 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.079 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.027 2.00e-02 2.50e+03 ... (remaining 2382 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2427 2.77 - 3.30: 12715 3.30 - 3.83: 21946 3.83 - 4.37: 25751 4.37 - 4.90: 44275 Nonbonded interactions: 107114 Sorted by model distance: nonbonded pdb=" OG SER A 434 " pdb=" OE1 GLN A 435 " model vdw 2.234 2.440 nonbonded pdb=" OD2 ASP B 273 " pdb=" OH TYR B 327 " model vdw 2.245 2.440 nonbonded pdb=" OD2 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.249 2.440 nonbonded pdb=" O ASP A 446 " pdb=" OG1 THR A 461 " model vdw 2.269 2.440 nonbonded pdb=" OG1 THR B 924 " pdb=" OE1 GLN A 930 " model vdw 2.273 2.440 ... (remaining 107109 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 69 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 587 or resid 743 through 1119 o \ r resid 1201)) selection = (chain 'B' and (resid 69 through 1119 or resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.010 Extract box with map and model: 7.190 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.620 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13850 Z= 0.226 Angle : 0.588 9.734 18707 Z= 0.282 Chirality : 0.039 0.173 2134 Planarity : 0.008 0.206 2385 Dihedral : 17.242 89.652 5223 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.47 % Allowed : 31.28 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1704 helix: 0.62 (0.22), residues: 596 sheet: 0.14 (0.29), residues: 353 loop : -0.36 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.004 0.001 HIS A1059 PHE 0.031 0.001 PHE A 83 TYR 0.012 0.001 TYR B 168 ARG 0.016 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 398 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 MET cc_start: 0.7380 (mmm) cc_final: 0.7136 (mmm) REVERT: B 554 PHE cc_start: 0.8402 (m-80) cc_final: 0.8117 (m-80) REVERT: B 967 GLU cc_start: 0.8021 (mp0) cc_final: 0.7596 (mm-30) outliers start: 7 outliers final: 6 residues processed: 401 average time/residue: 0.2926 time to fit residues: 163.0106 Evaluate side-chains 386 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 380 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain A residue 495 PHE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 1101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN B 827 ASN B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13850 Z= 0.405 Angle : 0.634 11.772 18707 Z= 0.323 Chirality : 0.044 0.175 2134 Planarity : 0.005 0.083 2385 Dihedral : 6.071 80.825 1938 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.36 % Allowed : 27.79 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1704 helix: 0.61 (0.20), residues: 606 sheet: 0.13 (0.29), residues: 351 loop : -0.63 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 521 HIS 0.005 0.001 HIS B 245 PHE 0.033 0.002 PHE A1111 TYR 0.023 0.002 TYR A 242 ARG 0.009 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 1.535 Fit side-chains REVERT: B 373 ASN cc_start: 0.8099 (t0) cc_final: 0.7875 (t0) REVERT: B 408 MET cc_start: 0.7537 (mmm) cc_final: 0.7254 (mmm) REVERT: B 421 CYS cc_start: 0.8223 (m) cc_final: 0.7923 (m) REVERT: B 422 ASP cc_start: 0.8177 (t0) cc_final: 0.7663 (t0) REVERT: B 518 MET cc_start: 0.7958 (ptp) cc_final: 0.7745 (mtm) REVERT: B 784 LYS cc_start: 0.8129 (pptt) cc_final: 0.7762 (pptt) REVERT: B 883 LEU cc_start: 0.8598 (mm) cc_final: 0.8337 (mm) REVERT: B 905 ARG cc_start: 0.7225 (ttm170) cc_final: 0.6982 (mtp180) REVERT: B 973 VAL cc_start: 0.8077 (p) cc_final: 0.7841 (t) REVERT: B 1091 LYS cc_start: 0.7505 (tttm) cc_final: 0.7133 (tttm) REVERT: A 99 TYR cc_start: 0.8098 (p90) cc_final: 0.7596 (p90) REVERT: A 206 LYS cc_start: 0.7928 (tmtt) cc_final: 0.7707 (tmtt) REVERT: A 229 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 264 TYR cc_start: 0.8022 (m-10) cc_final: 0.7753 (m-10) REVERT: A 303 ASP cc_start: 0.6931 (t0) cc_final: 0.6719 (t70) REVERT: A 422 ASP cc_start: 0.7860 (t0) cc_final: 0.7410 (t0) REVERT: A 440 MET cc_start: 0.8355 (mtp) cc_final: 0.8143 (ttt) REVERT: A 446 ASP cc_start: 0.7267 (m-30) cc_final: 0.7063 (m-30) REVERT: A 471 ILE cc_start: 0.7626 (mm) cc_final: 0.7423 (mt) REVERT: A 495 PHE cc_start: 0.8780 (t80) cc_final: 0.8457 (t80) REVERT: A 573 MET cc_start: 0.7861 (tpp) cc_final: 0.7330 (mpp) REVERT: A 816 GLU cc_start: 0.7444 (tp30) cc_final: 0.7214 (tp30) REVERT: A 878 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 881 GLN cc_start: 0.7858 (mp10) cc_final: 0.7377 (mp10) REVERT: A 949 ASP cc_start: 0.6734 (m-30) cc_final: 0.6413 (m-30) REVERT: A 965 MET cc_start: 0.4282 (tpt) cc_final: 0.2375 (tpt) REVERT: A 1091 LYS cc_start: 0.7649 (mttm) cc_final: 0.7410 (mttp) outliers start: 65 outliers final: 48 residues processed: 434 average time/residue: 0.2903 time to fit residues: 175.3720 Evaluate side-chains 446 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 398 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.0000 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 ASN B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13850 Z= 0.229 Angle : 0.542 10.046 18707 Z= 0.272 Chirality : 0.040 0.148 2134 Planarity : 0.004 0.056 2385 Dihedral : 5.388 75.262 1928 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.04 % Allowed : 26.31 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1704 helix: 0.90 (0.21), residues: 608 sheet: -0.01 (0.29), residues: 357 loop : -0.60 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 PHE 0.022 0.001 PHE A1111 TYR 0.015 0.001 TYR A 242 ARG 0.005 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 412 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8480 (tt) REVERT: B 202 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8176 (mttp) REVERT: B 206 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7779 (mtpp) REVERT: B 373 ASN cc_start: 0.8105 (t0) cc_final: 0.7870 (t0) REVERT: B 408 MET cc_start: 0.7579 (mmm) cc_final: 0.7337 (tpp) REVERT: B 421 CYS cc_start: 0.8207 (m) cc_final: 0.7907 (m) REVERT: B 422 ASP cc_start: 0.8107 (t0) cc_final: 0.7723 (t0) REVERT: B 489 SER cc_start: 0.8685 (t) cc_final: 0.8193 (p) REVERT: B 497 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: B 518 MET cc_start: 0.7884 (ptp) cc_final: 0.7655 (mtm) REVERT: B 573 MET cc_start: 0.8004 (mmm) cc_final: 0.7673 (mmp) REVERT: B 784 LYS cc_start: 0.8159 (pptt) cc_final: 0.7772 (pptt) REVERT: B 811 ARG cc_start: 0.7759 (ttp-110) cc_final: 0.7431 (ttp-110) REVERT: B 842 PHE cc_start: 0.8115 (m-10) cc_final: 0.7616 (m-10) REVERT: B 883 LEU cc_start: 0.8584 (mm) cc_final: 0.8212 (mm) REVERT: B 973 VAL cc_start: 0.8000 (p) cc_final: 0.7759 (t) REVERT: B 1091 LYS cc_start: 0.7358 (tttm) cc_final: 0.6969 (tttm) REVERT: B 1108 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6759 (mmmm) REVERT: A 99 TYR cc_start: 0.8083 (p90) cc_final: 0.7500 (p90) REVERT: A 229 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 422 ASP cc_start: 0.7873 (t0) cc_final: 0.7412 (t0) REVERT: A 571 TYR cc_start: 0.8191 (p90) cc_final: 0.7964 (p90) REVERT: A 573 MET cc_start: 0.7861 (tpp) cc_final: 0.7522 (mmp) REVERT: A 816 GLU cc_start: 0.7414 (tp30) cc_final: 0.7148 (tp30) REVERT: A 881 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: A 940 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6505 (t) REVERT: A 949 ASP cc_start: 0.6545 (m-30) cc_final: 0.6238 (m-30) REVERT: A 1001 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5121 (mtt) outliers start: 90 outliers final: 59 residues processed: 456 average time/residue: 0.2901 time to fit residues: 184.6196 Evaluate side-chains 471 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 408 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 ASN B 877 HIS ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13850 Z= 0.215 Angle : 0.541 10.383 18707 Z= 0.269 Chirality : 0.040 0.191 2134 Planarity : 0.004 0.044 2385 Dihedral : 5.198 68.667 1928 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 6.17 % Allowed : 26.78 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1704 helix: 1.09 (0.21), residues: 603 sheet: -0.01 (0.29), residues: 356 loop : -0.59 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 521 HIS 0.005 0.001 HIS B 877 PHE 0.018 0.001 PHE A1111 TYR 0.015 0.001 TYR A 242 ARG 0.006 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 409 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 202 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8230 (mttp) REVERT: B 206 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7769 (mtpp) REVERT: B 373 ASN cc_start: 0.8094 (t0) cc_final: 0.7822 (t0) REVERT: B 408 MET cc_start: 0.7589 (mmm) cc_final: 0.7335 (tpp) REVERT: B 421 CYS cc_start: 0.8228 (m) cc_final: 0.7890 (m) REVERT: B 422 ASP cc_start: 0.8068 (t0) cc_final: 0.7526 (t0) REVERT: B 489 SER cc_start: 0.8647 (t) cc_final: 0.8170 (p) REVERT: B 497 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7517 (mtm-85) REVERT: B 518 MET cc_start: 0.7851 (ptp) cc_final: 0.7628 (mtm) REVERT: B 559 GLU cc_start: 0.6951 (tp30) cc_final: 0.6622 (tp30) REVERT: B 784 LYS cc_start: 0.8139 (pptt) cc_final: 0.7751 (pptt) REVERT: B 811 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7415 (ttp-110) REVERT: B 842 PHE cc_start: 0.8014 (m-10) cc_final: 0.7514 (m-10) REVERT: B 883 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8234 (mm) REVERT: B 973 VAL cc_start: 0.7994 (p) cc_final: 0.7757 (t) REVERT: B 1054 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: B 1091 LYS cc_start: 0.7224 (tttm) cc_final: 0.6594 (tttt) REVERT: B 1108 LYS cc_start: 0.6991 (mmmt) cc_final: 0.6706 (mmmt) REVERT: A 99 TYR cc_start: 0.8091 (p90) cc_final: 0.7505 (p90) REVERT: A 273 ASP cc_start: 0.7932 (m-30) cc_final: 0.7396 (m-30) REVERT: A 422 ASP cc_start: 0.7872 (t0) cc_final: 0.7412 (t0) REVERT: A 423 MET cc_start: 0.7928 (mmm) cc_final: 0.7710 (mmm) REVERT: A 571 TYR cc_start: 0.8198 (p90) cc_final: 0.7974 (p90) REVERT: A 881 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: A 940 CYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6477 (t) REVERT: A 949 ASP cc_start: 0.6525 (m-30) cc_final: 0.6224 (m-30) REVERT: A 1001 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.5086 (mtt) REVERT: A 1059 HIS cc_start: 0.6958 (m170) cc_final: 0.6743 (m170) REVERT: A 1072 MET cc_start: 0.7486 (ppp) cc_final: 0.6931 (ptt) outliers start: 92 outliers final: 68 residues processed: 453 average time/residue: 0.2888 time to fit residues: 183.3482 Evaluate side-chains 468 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 394 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 881 GLN Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 123 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 ASN B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13850 Z= 0.194 Angle : 0.535 10.313 18707 Z= 0.265 Chirality : 0.040 0.294 2134 Planarity : 0.004 0.040 2385 Dihedral : 4.989 61.357 1928 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 6.71 % Allowed : 27.25 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1704 helix: 1.15 (0.21), residues: 609 sheet: -0.01 (0.29), residues: 356 loop : -0.57 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.018 0.001 PHE A1111 TYR 0.014 0.001 TYR A 242 ARG 0.006 0.000 ARG A 896 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 397 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 206 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7768 (mtpp) REVERT: B 408 MET cc_start: 0.7625 (mmm) cc_final: 0.7332 (tpp) REVERT: B 421 CYS cc_start: 0.8252 (m) cc_final: 0.7910 (m) REVERT: B 422 ASP cc_start: 0.8035 (t0) cc_final: 0.7477 (t0) REVERT: B 423 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8033 (mtp) REVERT: B 477 GLU cc_start: 0.7887 (pm20) cc_final: 0.7667 (pm20) REVERT: B 489 SER cc_start: 0.8643 (t) cc_final: 0.8169 (p) REVERT: B 497 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7499 (mtm-85) REVERT: B 782 MET cc_start: 0.8441 (tpt) cc_final: 0.7930 (tpt) REVERT: B 784 LYS cc_start: 0.8117 (pptt) cc_final: 0.7731 (pptt) REVERT: B 811 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7374 (ttp-110) REVERT: B 842 PHE cc_start: 0.7996 (m-10) cc_final: 0.7437 (m-10) REVERT: B 883 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8264 (mm) REVERT: B 924 THR cc_start: 0.4971 (OUTLIER) cc_final: 0.4216 (p) REVERT: B 965 MET cc_start: 0.5320 (tpt) cc_final: 0.4865 (tpt) REVERT: B 973 VAL cc_start: 0.7987 (p) cc_final: 0.7741 (t) REVERT: B 1054 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.5426 (tt0) REVERT: B 1091 LYS cc_start: 0.7182 (tttm) cc_final: 0.6556 (tttt) REVERT: A 99 TYR cc_start: 0.8083 (p90) cc_final: 0.7415 (p90) REVERT: A 286 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8344 (mmtm) REVERT: A 422 ASP cc_start: 0.7877 (t0) cc_final: 0.7465 (t0) REVERT: A 470 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6978 (mt-10) REVERT: A 571 TYR cc_start: 0.8188 (p90) cc_final: 0.7982 (p90) REVERT: A 881 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: A 896 ARG cc_start: 0.7181 (ptt-90) cc_final: 0.6908 (ptt90) REVERT: A 949 ASP cc_start: 0.6539 (m-30) cc_final: 0.6261 (m-30) REVERT: A 1001 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5088 (mtt) REVERT: A 1072 MET cc_start: 0.7454 (ppp) cc_final: 0.7030 (ptt) outliers start: 100 outliers final: 76 residues processed: 447 average time/residue: 0.2875 time to fit residues: 179.6357 Evaluate side-chains 473 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 390 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13850 Z= 0.204 Angle : 0.556 11.900 18707 Z= 0.271 Chirality : 0.041 0.373 2134 Planarity : 0.004 0.040 2385 Dihedral : 4.839 55.686 1925 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.71 % Allowed : 27.65 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1704 helix: 1.17 (0.21), residues: 608 sheet: -0.01 (0.29), residues: 358 loop : -0.58 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.022 0.001 PHE A1111 TYR 0.014 0.001 TYR A 242 ARG 0.007 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 400 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8443 (tt) REVERT: B 206 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7761 (mtpp) REVERT: B 373 ASN cc_start: 0.8045 (t0) cc_final: 0.7760 (t0) REVERT: B 408 MET cc_start: 0.7619 (mmm) cc_final: 0.7330 (tpp) REVERT: B 421 CYS cc_start: 0.8280 (m) cc_final: 0.7960 (m) REVERT: B 422 ASP cc_start: 0.8020 (t0) cc_final: 0.7464 (t0) REVERT: B 423 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: B 489 SER cc_start: 0.8663 (t) cc_final: 0.8198 (p) REVERT: B 497 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7503 (mtm-85) REVERT: B 784 LYS cc_start: 0.8142 (pptt) cc_final: 0.7766 (pptt) REVERT: B 811 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7386 (ttp-110) REVERT: B 842 PHE cc_start: 0.7992 (m-10) cc_final: 0.7471 (m-10) REVERT: B 883 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 924 THR cc_start: 0.4986 (OUTLIER) cc_final: 0.4201 (p) REVERT: B 965 MET cc_start: 0.5334 (tpt) cc_final: 0.4897 (tpt) REVERT: B 973 VAL cc_start: 0.7984 (p) cc_final: 0.7750 (t) REVERT: B 1054 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.5432 (tt0) REVERT: B 1091 LYS cc_start: 0.7185 (tttm) cc_final: 0.6548 (tttt) REVERT: A 99 TYR cc_start: 0.8081 (p90) cc_final: 0.7499 (p90) REVERT: A 229 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6934 (mm-30) REVERT: A 422 ASP cc_start: 0.7892 (t0) cc_final: 0.7476 (t0) REVERT: A 470 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6988 (mm-30) REVERT: A 881 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: A 896 ARG cc_start: 0.7215 (ptt-90) cc_final: 0.6951 (ptt90) REVERT: A 949 ASP cc_start: 0.6545 (m-30) cc_final: 0.6267 (m-30) REVERT: A 1072 MET cc_start: 0.7465 (ppp) cc_final: 0.7148 (ptt) outliers start: 100 outliers final: 78 residues processed: 447 average time/residue: 0.2820 time to fit residues: 176.8044 Evaluate side-chains 481 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 397 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 966 LYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 103 optimal weight: 0.0060 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13850 Z= 0.166 Angle : 0.537 12.394 18707 Z= 0.261 Chirality : 0.040 0.365 2134 Planarity : 0.003 0.038 2385 Dihedral : 4.624 55.851 1925 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.24 % Allowed : 28.05 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1704 helix: 1.28 (0.21), residues: 613 sheet: 0.03 (0.29), residues: 362 loop : -0.55 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.020 0.001 PHE A1111 TYR 0.013 0.001 TYR A 242 ARG 0.007 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 397 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7764 (mtpp) REVERT: B 408 MET cc_start: 0.7632 (mmm) cc_final: 0.7332 (tpp) REVERT: B 421 CYS cc_start: 0.8257 (m) cc_final: 0.7948 (m) REVERT: B 422 ASP cc_start: 0.7983 (t0) cc_final: 0.7419 (t0) REVERT: B 423 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: B 489 SER cc_start: 0.8660 (t) cc_final: 0.8168 (p) REVERT: B 497 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7508 (mtm-85) REVERT: B 518 MET cc_start: 0.7859 (ptp) cc_final: 0.7647 (mtm) REVERT: B 784 LYS cc_start: 0.8092 (pptt) cc_final: 0.7733 (pptt) REVERT: B 883 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8258 (mm) REVERT: B 973 VAL cc_start: 0.7961 (p) cc_final: 0.7709 (t) REVERT: B 1054 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.5284 (tt0) REVERT: B 1082 GLU cc_start: 0.6958 (tp30) cc_final: 0.6534 (tp30) REVERT: B 1091 LYS cc_start: 0.7102 (tttm) cc_final: 0.6486 (tttt) REVERT: B 1116 GLU cc_start: 0.5991 (tm-30) cc_final: 0.5789 (tm-30) REVERT: A 210 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6990 (mtm180) REVERT: A 229 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6371 (mm-30) REVERT: A 301 LEU cc_start: 0.8323 (mt) cc_final: 0.8019 (mt) REVERT: A 422 ASP cc_start: 0.7873 (t0) cc_final: 0.7497 (t0) REVERT: A 435 GLN cc_start: 0.7359 (mp10) cc_final: 0.6923 (mp10) REVERT: A 470 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6954 (mm-30) REVERT: A 573 MET cc_start: 0.7976 (mmp) cc_final: 0.7664 (mmm) REVERT: A 881 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: A 896 ARG cc_start: 0.7144 (ptt-90) cc_final: 0.6934 (ptt90) REVERT: A 949 ASP cc_start: 0.6489 (m-30) cc_final: 0.6212 (m-30) REVERT: A 983 MET cc_start: 0.7559 (tpt) cc_final: 0.7284 (mmm) REVERT: A 1072 MET cc_start: 0.7486 (ppp) cc_final: 0.7206 (ptt) REVERT: A 1091 LYS cc_start: 0.7376 (mttp) cc_final: 0.7165 (mttm) outliers start: 93 outliers final: 66 residues processed: 444 average time/residue: 0.2865 time to fit residues: 178.0101 Evaluate side-chains 463 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 392 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 760 ASN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13850 Z= 0.237 Angle : 0.579 12.573 18707 Z= 0.282 Chirality : 0.042 0.388 2134 Planarity : 0.004 0.040 2385 Dihedral : 4.718 56.461 1925 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.24 % Allowed : 28.52 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1704 helix: 1.17 (0.21), residues: 616 sheet: -0.01 (0.29), residues: 354 loop : -0.54 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS A1059 PHE 0.021 0.001 PHE A1111 TYR 0.022 0.001 TYR A1102 ARG 0.007 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 401 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7776 (mtpp) REVERT: B 373 ASN cc_start: 0.8001 (t0) cc_final: 0.7700 (t0) REVERT: B 408 MET cc_start: 0.7601 (mmm) cc_final: 0.7320 (tpp) REVERT: B 421 CYS cc_start: 0.8280 (m) cc_final: 0.7968 (m) REVERT: B 422 ASP cc_start: 0.8041 (t0) cc_final: 0.7485 (t0) REVERT: B 423 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: B 488 ASP cc_start: 0.7029 (t0) cc_final: 0.6823 (t0) REVERT: B 497 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7531 (mtm-85) REVERT: B 518 MET cc_start: 0.7887 (ptp) cc_final: 0.7673 (mtm) REVERT: B 784 LYS cc_start: 0.8109 (pptt) cc_final: 0.7757 (pptt) REVERT: B 811 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7448 (ttp-110) REVERT: B 824 VAL cc_start: 0.8505 (t) cc_final: 0.8301 (p) REVERT: B 842 PHE cc_start: 0.8014 (m-10) cc_final: 0.7746 (m-10) REVERT: B 883 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8268 (mm) REVERT: B 924 THR cc_start: 0.5040 (OUTLIER) cc_final: 0.4276 (p) REVERT: B 973 VAL cc_start: 0.8003 (p) cc_final: 0.7765 (t) REVERT: B 1054 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.5454 (tt0) REVERT: B 1091 LYS cc_start: 0.7220 (tttm) cc_final: 0.6572 (tttt) REVERT: A 99 TYR cc_start: 0.8093 (p90) cc_final: 0.7553 (p90) REVERT: A 229 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6936 (mm-30) REVERT: A 301 LEU cc_start: 0.8329 (mt) cc_final: 0.7991 (mt) REVERT: A 422 ASP cc_start: 0.7904 (t0) cc_final: 0.7506 (t0) REVERT: A 435 GLN cc_start: 0.7350 (mp10) cc_final: 0.6921 (mp10) REVERT: A 470 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6934 (mm-30) REVERT: A 495 PHE cc_start: 0.8818 (t80) cc_final: 0.8593 (t80) REVERT: A 573 MET cc_start: 0.7929 (mmp) cc_final: 0.7675 (mmm) REVERT: A 881 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: A 896 ARG cc_start: 0.7238 (ptt-90) cc_final: 0.6951 (ptt90) REVERT: A 949 ASP cc_start: 0.6523 (m-30) cc_final: 0.6191 (m-30) REVERT: A 1072 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7286 (ptt) outliers start: 93 outliers final: 78 residues processed: 445 average time/residue: 0.2813 time to fit residues: 174.8364 Evaluate side-chains 482 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 398 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13850 Z= 0.206 Angle : 0.577 12.986 18707 Z= 0.279 Chirality : 0.042 0.386 2134 Planarity : 0.004 0.039 2385 Dihedral : 4.634 55.074 1925 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.84 % Allowed : 28.86 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1704 helix: 1.16 (0.21), residues: 618 sheet: -0.02 (0.30), residues: 345 loop : -0.53 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 521 HIS 0.003 0.001 HIS A1059 PHE 0.015 0.001 PHE A 767 TYR 0.014 0.001 TYR A 242 ARG 0.008 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 390 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7786 (mtpp) REVERT: B 373 ASN cc_start: 0.7989 (t0) cc_final: 0.7663 (t0) REVERT: B 408 MET cc_start: 0.7607 (mmm) cc_final: 0.7315 (tpp) REVERT: B 421 CYS cc_start: 0.8284 (m) cc_final: 0.7952 (m) REVERT: B 422 ASP cc_start: 0.8008 (t0) cc_final: 0.7450 (t0) REVERT: B 423 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8086 (mtp) REVERT: B 497 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7529 (mtm-85) REVERT: B 782 MET cc_start: 0.8440 (tpt) cc_final: 0.7988 (tpt) REVERT: B 784 LYS cc_start: 0.8098 (pptt) cc_final: 0.7738 (pptt) REVERT: B 811 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7575 (ttp-110) REVERT: B 883 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8261 (mm) REVERT: B 920 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6621 (mmm) REVERT: B 924 THR cc_start: 0.5003 (OUTLIER) cc_final: 0.4200 (p) REVERT: B 931 ARG cc_start: 0.7790 (ptt180) cc_final: 0.7097 (mmt180) REVERT: B 1054 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.5424 (tt0) REVERT: B 1091 LYS cc_start: 0.7166 (tttm) cc_final: 0.6528 (tttt) REVERT: A 99 TYR cc_start: 0.8090 (p90) cc_final: 0.7466 (p90) REVERT: A 229 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 301 LEU cc_start: 0.8340 (mt) cc_final: 0.7997 (mt) REVERT: A 422 ASP cc_start: 0.7891 (t0) cc_final: 0.7489 (t0) REVERT: A 435 GLN cc_start: 0.7349 (mp10) cc_final: 0.6943 (mp10) REVERT: A 495 PHE cc_start: 0.8754 (t80) cc_final: 0.8379 (t80) REVERT: A 881 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: A 896 ARG cc_start: 0.7201 (ptt-90) cc_final: 0.6958 (ptt90) REVERT: A 949 ASP cc_start: 0.6528 (m-30) cc_final: 0.6171 (m-30) REVERT: A 1072 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7283 (ptt) REVERT: A 1091 LYS cc_start: 0.7423 (mttp) cc_final: 0.7147 (mttm) outliers start: 87 outliers final: 75 residues processed: 433 average time/residue: 0.2871 time to fit residues: 174.2443 Evaluate side-chains 468 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 386 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1026 PHE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13850 Z= 0.309 Angle : 0.632 13.141 18707 Z= 0.308 Chirality : 0.043 0.405 2134 Planarity : 0.004 0.040 2385 Dihedral : 4.865 54.158 1925 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.11 % Allowed : 28.99 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1704 helix: 0.91 (0.21), residues: 621 sheet: -0.13 (0.29), residues: 356 loop : -0.57 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 521 HIS 0.006 0.001 HIS A1059 PHE 0.021 0.002 PHE A1111 TYR 0.019 0.002 TYR B1006 ARG 0.008 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 406 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 206 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7783 (mtpp) REVERT: B 373 ASN cc_start: 0.8014 (t0) cc_final: 0.7708 (t0) REVERT: B 408 MET cc_start: 0.7595 (mmm) cc_final: 0.7338 (tpp) REVERT: B 421 CYS cc_start: 0.8238 (m) cc_final: 0.7909 (m) REVERT: B 422 ASP cc_start: 0.8088 (t0) cc_final: 0.7542 (t0) REVERT: B 423 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8130 (mtp) REVERT: B 497 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: B 782 MET cc_start: 0.8477 (tpt) cc_final: 0.8055 (tpt) REVERT: B 784 LYS cc_start: 0.8109 (pptt) cc_final: 0.7755 (pptt) REVERT: B 811 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7609 (ttp-110) REVERT: B 883 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8261 (mm) REVERT: B 920 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6693 (mmm) REVERT: B 924 THR cc_start: 0.4968 (OUTLIER) cc_final: 0.4207 (p) REVERT: B 1054 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.5594 (tt0) REVERT: B 1082 GLU cc_start: 0.7057 (tp30) cc_final: 0.6818 (tp30) REVERT: B 1091 LYS cc_start: 0.7308 (tttm) cc_final: 0.6696 (tttt) REVERT: B 1116 GLU cc_start: 0.5888 (tm-30) cc_final: 0.5649 (tm-30) REVERT: A 99 TYR cc_start: 0.8112 (p90) cc_final: 0.7499 (p90) REVERT: A 229 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 264 TYR cc_start: 0.8028 (m-10) cc_final: 0.7746 (m-10) REVERT: A 301 LEU cc_start: 0.8327 (mt) cc_final: 0.7969 (mt) REVERT: A 422 ASP cc_start: 0.7889 (t0) cc_final: 0.7447 (t0) REVERT: A 435 GLN cc_start: 0.7311 (mp10) cc_final: 0.6892 (mp10) REVERT: A 470 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 495 PHE cc_start: 0.8752 (t80) cc_final: 0.8350 (t80) REVERT: A 576 ILE cc_start: 0.8126 (pt) cc_final: 0.7892 (pt) REVERT: A 881 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 896 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.6996 (ptt90) REVERT: A 949 ASP cc_start: 0.6692 (m-30) cc_final: 0.6336 (m-30) outliers start: 91 outliers final: 75 residues processed: 453 average time/residue: 0.2844 time to fit residues: 181.1396 Evaluate side-chains 484 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 403 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 920 MET Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 968 PHE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1014 GLN Chi-restraints excluded: chain B residue 1053 LEU Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain B residue 1113 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 881 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1018 ASP Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1036 SER Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.6980 chunk 125 optimal weight: 0.0020 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.0070 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136379 restraints weight = 20217.366| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.68 r_work: 0.3607 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13850 Z= 0.171 Angle : 0.587 13.265 18707 Z= 0.281 Chirality : 0.041 0.379 2134 Planarity : 0.004 0.038 2385 Dihedral : 4.547 53.297 1925 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.50 % Allowed : 29.93 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1704 helix: 1.12 (0.21), residues: 620 sheet: -0.09 (0.29), residues: 360 loop : -0.48 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.003 0.001 HIS A 172 PHE 0.021 0.001 PHE A1111 TYR 0.013 0.001 TYR A1102 ARG 0.008 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3968.31 seconds wall clock time: 71 minutes 41.81 seconds (4301.81 seconds total)