Starting phenix.real_space_refine on Thu Jul 25 14:12:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t22_40978/07_2024/8t22_40978.cif" } resolution = 3.83 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= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6357 atoms to isotropic. 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 114 5.16 5 C 15309 2.51 5 N 3980 2.21 5 O 4558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 53": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23961 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5813 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 40, 'TRANS': 707} Chain breaks: 8 Chain: "B" Number of atoms: 5813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5813 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 40, 'TRANS': 707} Chain breaks: 8 Chain: "C" Number of atoms: 7431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7431 Classifications: {'peptide': 954} Link IDs: {'PTRANS': 51, 'TRANS': 902} Chain breaks: 9 Chain: "D" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Time building chain proxies: 14.13, per 1000 atoms: 0.59 Number of scatterers: 23961 At special positions: 0 Unit cell: (135.42, 153.18, 231.99, 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 114 16.00 O 4558 8.00 N 3980 7.00 C 15309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 4.7 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5724 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 30 sheets defined 34.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.715A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.770A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.743A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.560A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.791A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.003A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.634A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.303A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.610A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.697A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.933A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.077A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.980A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 674 through 676 No H-bonds generated for 'chain 'C' and resid 674 through 676' Processing helix chain 'C' and resid 690 through 691 No H-bonds generated for 'chain 'C' and resid 690 through 691' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.284A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.695A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.335A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.238A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.084A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.214A pdb=" N TYR D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.609A pdb=" N GLN D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 109 through 130 removed outlier: 4.975A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 154 removed outlier: 4.254A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 177 removed outlier: 5.549A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.267A pdb=" N GLN D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.648A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 300 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 387 Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.585A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.345A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.552A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 643 through 644 Processing sheet with id=AA3, first strand: chain 'A' and resid 664 through 667 removed outlier: 3.791A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.808A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.507A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.792A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 279 removed outlier: 6.596A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.534A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 664 through 665 removed outlier: 3.815A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'B' and resid 712 through 713 removed outlier: 4.441A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.573A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.619A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.831A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.182A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.623A pdb=" N LEU C 82 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 195 through 197 removed outlier: 4.559A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.637A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 377 through 379 removed outlier: 4.719A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'C' and resid 664 through 667 removed outlier: 4.421A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.745A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.745A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.649A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 348 through 350 885 hydrogen bonds defined for protein. 2550 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: 8.71 Time building geometry restraints manager: 11.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 7777 1.36 - 1.52: 11804 1.52 - 1.69: 4780 1.69 - 1.85: 157 1.85 - 2.02: 3 Bond restraints: 24521 Sorted by residual: bond pdb=" N ASN D 63 " pdb=" CA ASN D 63 " ideal model delta sigma weight residual 1.459 1.679 -0.221 1.16e-02 7.43e+03 3.62e+02 bond pdb=" C MET D 62 " pdb=" N ASN D 63 " ideal model delta sigma weight residual 1.334 1.556 -0.222 1.20e-02 6.94e+03 3.42e+02 bond pdb=" CA GLN D 60 " pdb=" C GLN D 60 " ideal model delta sigma weight residual 1.522 1.744 -0.222 1.40e-02 5.10e+03 2.52e+02 bond pdb=" CA CYS D 542 " pdb=" C CYS D 542 " ideal model delta sigma weight residual 1.521 1.666 -0.146 1.27e-02 6.20e+03 1.32e+02 bond pdb=" CA CYS D 530 " pdb=" C CYS D 530 " ideal model delta sigma weight residual 1.523 1.672 -0.149 1.48e-02 4.57e+03 1.02e+02 ... (remaining 24516 not shown) Histogram of bond angle deviations from ideal: 88.63 - 101.07: 47 101.07 - 113.51: 13668 113.51 - 125.96: 19227 125.96 - 138.40: 413 138.40 - 150.84: 7 Bond angle restraints: 33362 Sorted by residual: angle pdb=" C CYS D 542 " pdb=" N ASP D 543 " pdb=" CA ASP D 543 " ideal model delta sigma weight residual 121.54 150.80 -29.26 1.91e+00 2.74e-01 2.35e+02 angle pdb=" N GLY D 200 " pdb=" CA GLY D 200 " pdb=" C GLY D 200 " ideal model delta sigma weight residual 113.18 148.73 -35.55 2.37e+00 1.78e-01 2.25e+02 angle pdb=" CA PRO C 412 " pdb=" N PRO C 412 " pdb=" CD PRO C 412 " ideal model delta sigma weight residual 112.00 92.45 19.55 1.40e+00 5.10e-01 1.95e+02 angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 93.27 18.73 1.40e+00 5.10e-01 1.79e+02 angle pdb=" CA MET D 62 " pdb=" C MET D 62 " pdb=" O MET D 62 " ideal model delta sigma weight residual 120.42 106.47 13.95 1.06e+00 8.90e-01 1.73e+02 ... (remaining 33357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 12316 18.24 - 36.49: 1808 36.49 - 54.73: 386 54.73 - 72.97: 76 72.97 - 91.22: 39 Dihedral angle restraints: 14625 sinusoidal: 5758 harmonic: 8867 Sorted by residual: dihedral pdb=" CA GLN A 239 " pdb=" C GLN A 239 " pdb=" N THR A 240 " pdb=" CA THR A 240 " ideal model delta harmonic sigma weight residual 180.00 88.78 91.22 0 5.00e+00 4.00e-02 3.33e+02 dihedral pdb=" CA LYS D 61 " pdb=" C LYS D 61 " pdb=" N MET D 62 " pdb=" CA MET D 62 " ideal model delta harmonic sigma weight residual 180.00 95.06 84.94 0 5.00e+00 4.00e-02 2.89e+02 dihedral pdb=" CA ILE D 532 " pdb=" C ILE D 532 " pdb=" N ALA D 533 " pdb=" CA ALA D 533 " ideal model delta harmonic sigma weight residual 180.00 112.92 67.08 0 5.00e+00 4.00e-02 1.80e+02 ... (remaining 14622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3551 0.120 - 0.240: 185 0.240 - 0.360: 22 0.360 - 0.480: 5 0.480 - 0.599: 2 Chirality restraints: 3765 Sorted by residual: chirality pdb=" CA MET D 62 " pdb=" N MET D 62 " pdb=" C MET D 62 " pdb=" CB MET D 62 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA PRO B 80 " pdb=" N PRO B 80 " pdb=" C PRO B 80 " pdb=" CB PRO B 80 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 3762 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 542 " 0.049 2.00e-02 2.50e+03 9.64e-02 9.29e+01 pdb=" C CYS D 542 " -0.167 2.00e-02 2.50e+03 pdb=" O CYS D 542 " 0.060 2.00e-02 2.50e+03 pdb=" N ASP D 543 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 60 " -0.046 2.00e-02 2.50e+03 9.27e-02 8.58e+01 pdb=" C GLN D 60 " 0.160 2.00e-02 2.50e+03 pdb=" O GLN D 60 " -0.059 2.00e-02 2.50e+03 pdb=" N LYS D 61 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 58 " -0.041 2.00e-02 2.50e+03 8.02e-02 6.43e+01 pdb=" C ASN D 58 " 0.139 2.00e-02 2.50e+03 pdb=" O ASN D 58 " -0.050 2.00e-02 2.50e+03 pdb=" N ILE D 59 " -0.048 2.00e-02 2.50e+03 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 131 2.30 - 2.95: 12402 2.95 - 3.60: 37423 3.60 - 4.25: 54344 4.25 - 4.90: 84445 Nonbonded interactions: 188745 Sorted by model distance: nonbonded pdb=" O ILE D 59 " pdb=" O MET D 62 " model vdw 1.654 3.040 nonbonded pdb=" N GLN D 531 " pdb=" N ASP D 543 " model vdw 1.875 3.200 nonbonded pdb=" N GLY A 87 " pdb=" O ARG A 237 " model vdw 1.885 2.520 nonbonded pdb=" O PHE A 84 " pdb=" N PHE A 238 " model vdw 1.913 2.520 nonbonded pdb=" O GLN D 60 " pdb=" N GLY D 66 " model vdw 1.948 2.520 ... (remaining 188740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 68.000 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.261 24521 Z= 0.471 Angle : 1.380 38.142 33362 Z= 0.756 Chirality : 0.064 0.599 3765 Planarity : 0.010 0.172 4320 Dihedral : 17.909 91.219 8814 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 35.98 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.15 % Favored : 86.48 % Rotamer: Outliers : 0.22 % Allowed : 29.71 % Favored : 70.06 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.73 % Twisted General : 1.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2988 helix: -0.61 (0.18), residues: 914 sheet: -1.17 (0.29), residues: 298 loop : -3.05 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP D 594 HIS 0.016 0.002 HIS B 207 PHE 0.041 0.002 PHE D 464 TYR 0.040 0.002 TYR A 91 ARG 0.024 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 317 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7798 (tp) cc_final: 0.7494 (tt) REVERT: A 765 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8223 (tmm-80) REVERT: B 104 TRP cc_start: 0.4374 (m-90) cc_final: 0.3999 (m100) REVERT: B 918 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 994 ASP cc_start: 0.8309 (p0) cc_final: 0.7572 (p0) REVERT: B 1005 GLN cc_start: 0.7213 (tp-100) cc_final: 0.6715 (mm110) REVERT: C 28 TYR cc_start: 0.6366 (m-80) cc_final: 0.5417 (m-80) REVERT: C 303 LEU cc_start: 0.9154 (mp) cc_final: 0.8925 (tp) REVERT: C 387 LEU cc_start: 0.6903 (tt) cc_final: 0.6588 (pp) REVERT: C 505 TYR cc_start: 0.7667 (m-80) cc_final: 0.7118 (m-80) REVERT: C 725 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 43 ASN cc_start: 0.5030 (t0) cc_final: 0.4528 (t0) REVERT: D 62 MET cc_start: 0.1419 (tmm) cc_final: 0.1031 (tpt) REVERT: D 74 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6676 (pt0) REVERT: D 100 LEU cc_start: 0.5281 (tp) cc_final: 0.4918 (tp) REVERT: D 152 MET cc_start: 0.2460 (tpt) cc_final: 0.1862 (ttp) REVERT: D 237 TYR cc_start: 0.2793 (t80) cc_final: 0.2232 (m-10) REVERT: D 249 MET cc_start: 0.1207 (mmm) cc_final: 0.0755 (mtm) REVERT: D 270 MET cc_start: 0.1442 (mpp) cc_final: 0.1139 (ttp) REVERT: D 361 CYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4679 (m) REVERT: D 408 MET cc_start: 0.6278 (mpp) cc_final: 0.5803 (tpp) REVERT: D 453 THR cc_start: 0.1521 (m) cc_final: 0.1230 (m) REVERT: D 455 MET cc_start: 0.2736 (ppp) cc_final: 0.2163 (tpp) REVERT: D 523 PHE cc_start: 0.3627 (t80) cc_final: 0.3299 (t80) outliers start: 6 outliers final: 2 residues processed: 319 average time/residue: 0.3659 time to fit residues: 180.6087 Evaluate side-chains 193 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain B residue 1000 ARG Chi-restraints excluded: chain D residue 361 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 154 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 777 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN D 437 ASN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.198 24521 Z= 0.329 Angle : 1.068 21.161 33362 Z= 0.571 Chirality : 0.056 0.430 3765 Planarity : 0.007 0.095 4320 Dihedral : 8.559 81.196 3250 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.88 % Favored : 86.81 % Rotamer: Outliers : 5.13 % Allowed : 26.11 % Favored : 68.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2988 helix: -0.18 (0.18), residues: 905 sheet: -0.99 (0.31), residues: 286 loop : -2.95 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 594 HIS 0.009 0.001 HIS D 493 PHE 0.036 0.002 PHE C 559 TYR 0.035 0.002 TYR D 158 ARG 0.006 0.001 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 213 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7881 (tp) cc_final: 0.7657 (pt) REVERT: A 202 LYS cc_start: 0.7301 (tppt) cc_final: 0.6598 (ttpp) REVERT: A 765 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8286 (tmm-80) REVERT: B 187 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.4503 (tttt) REVERT: B 918 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 970 PHE cc_start: 0.5987 (m-80) cc_final: 0.5738 (m-80) REVERT: B 978 ASN cc_start: 0.7939 (t0) cc_final: 0.7028 (p0) REVERT: B 982 SER cc_start: 0.7604 (OUTLIER) cc_final: 0.7400 (m) REVERT: B 994 ASP cc_start: 0.8172 (p0) cc_final: 0.7949 (p0) REVERT: B 1005 GLN cc_start: 0.7316 (tp-100) cc_final: 0.6755 (mm-40) REVERT: B 1009 THR cc_start: 0.7561 (p) cc_final: 0.6642 (p) REVERT: C 28 TYR cc_start: 0.6348 (m-80) cc_final: 0.5294 (m-80) REVERT: C 91 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6483 (t80) REVERT: C 241 LEU cc_start: 0.4324 (OUTLIER) cc_final: 0.4118 (pp) REVERT: C 286 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9084 (p) REVERT: C 303 LEU cc_start: 0.9166 (mp) cc_final: 0.8920 (tp) REVERT: C 505 TYR cc_start: 0.7656 (m-80) cc_final: 0.7172 (m-80) REVERT: C 515 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.4680 (p90) REVERT: C 725 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8341 (mm-30) REVERT: C 753 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8458 (tt) REVERT: D 74 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6768 (pt0) REVERT: D 220 ASN cc_start: 0.4176 (OUTLIER) cc_final: 0.3774 (t0) REVERT: D 249 MET cc_start: 0.0871 (mmm) cc_final: 0.0296 (mtm) REVERT: D 424 LEU cc_start: 0.1526 (OUTLIER) cc_final: 0.0477 (tp) REVERT: D 455 MET cc_start: 0.3457 (ppp) cc_final: 0.2928 (tpp) REVERT: D 480 MET cc_start: 0.0289 (tmm) cc_final: -0.0678 (tpp) REVERT: D 481 LYS cc_start: 0.3444 (OUTLIER) cc_final: 0.2959 (tptp) REVERT: D 523 PHE cc_start: 0.3978 (t80) cc_final: 0.3706 (t80) REVERT: D 542 CYS cc_start: 0.0088 (OUTLIER) cc_final: -0.0498 (m) outliers start: 137 outliers final: 58 residues processed: 336 average time/residue: 0.3261 time to fit residues: 177.0704 Evaluate side-chains 252 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 183 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 296 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 613 GLN A 777 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 165 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 345 HIS ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN ** D 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 24521 Z= 0.409 Angle : 1.064 17.485 33362 Z= 0.572 Chirality : 0.056 0.381 3765 Planarity : 0.008 0.091 4320 Dihedral : 8.503 83.478 3245 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 31.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.36 % Favored : 85.41 % Rotamer: Outliers : 7.61 % Allowed : 24.58 % Favored : 67.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.73 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.14), residues: 2988 helix: -0.43 (0.17), residues: 909 sheet: -1.14 (0.30), residues: 281 loop : -3.07 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 594 HIS 0.011 0.002 HIS D 374 PHE 0.025 0.002 PHE C 559 TYR 0.030 0.003 TYR A 38 ARG 0.009 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 183 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8043 (tp) cc_final: 0.7833 (pt) REVERT: A 765 ARG cc_start: 0.8878 (ttp-170) cc_final: 0.8576 (tmm-80) REVERT: A 869 MET cc_start: 0.8784 (pmm) cc_final: 0.8513 (pmm) REVERT: A 1144 GLU cc_start: 0.8758 (mp0) cc_final: 0.8419 (pm20) REVERT: B 187 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.4445 (tttt) REVERT: B 266 TYR cc_start: 0.5529 (m-80) cc_final: 0.5187 (m-80) REVERT: B 869 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: B 918 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 994 ASP cc_start: 0.8177 (p0) cc_final: 0.7975 (p0) REVERT: C 28 TYR cc_start: 0.6780 (m-80) cc_final: 0.5671 (m-80) REVERT: C 275 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.6335 (t80) REVERT: C 387 LEU cc_start: 0.8659 (pp) cc_final: 0.8241 (mp) REVERT: C 393 THR cc_start: 0.2505 (OUTLIER) cc_final: 0.2142 (p) REVERT: C 505 TYR cc_start: 0.7630 (m-80) cc_final: 0.7245 (m-80) REVERT: C 515 PHE cc_start: 0.5191 (OUTLIER) cc_final: 0.4837 (p90) REVERT: C 753 LEU cc_start: 0.8895 (tt) cc_final: 0.8667 (tt) REVERT: C 1029 MET cc_start: 0.8441 (tmm) cc_final: 0.8119 (tmm) REVERT: D 74 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6689 (pt0) REVERT: D 123 MET cc_start: 0.2614 (OUTLIER) cc_final: 0.2294 (ttt) REVERT: D 190 MET cc_start: 0.4844 (ptt) cc_final: 0.4597 (ptm) REVERT: D 220 ASN cc_start: 0.3908 (OUTLIER) cc_final: 0.3399 (t0) REVERT: D 249 MET cc_start: 0.0826 (mmm) cc_final: 0.0294 (mtm) REVERT: D 345 HIS cc_start: 0.1395 (t70) cc_final: 0.1152 (m170) REVERT: D 424 LEU cc_start: 0.1318 (OUTLIER) cc_final: 0.0654 (tp) REVERT: D 455 MET cc_start: 0.3734 (ppp) cc_final: 0.3245 (tpp) REVERT: D 480 MET cc_start: 0.0655 (tmm) cc_final: -0.0445 (tpp) REVERT: D 481 LYS cc_start: 0.3682 (OUTLIER) cc_final: 0.3310 (tmtt) REVERT: D 512 PHE cc_start: 0.2100 (OUTLIER) cc_final: 0.1803 (m-80) REVERT: D 516 TYR cc_start: 0.5471 (m-10) cc_final: 0.5050 (m-10) REVERT: D 582 ARG cc_start: 0.0479 (OUTLIER) cc_final: 0.0196 (ttp-110) outliers start: 203 outliers final: 100 residues processed: 356 average time/residue: 0.3296 time to fit residues: 187.4056 Evaluate side-chains 279 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 168 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 582 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 144 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 644 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 24521 Z= 0.351 Angle : 0.992 17.929 33362 Z= 0.531 Chirality : 0.054 0.355 3765 Planarity : 0.007 0.086 4320 Dihedral : 8.330 84.439 3245 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.49 % Favored : 86.24 % Rotamer: Outliers : 7.04 % Allowed : 25.63 % Favored : 67.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.73 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 2988 helix: -0.33 (0.17), residues: 917 sheet: -1.29 (0.29), residues: 305 loop : -3.10 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 594 HIS 0.010 0.002 HIS D 374 PHE 0.025 0.002 PHE C 559 TYR 0.035 0.002 TYR A 38 ARG 0.014 0.001 ARG D 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 174 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8083 (tp) cc_final: 0.7641 (tt) REVERT: A 201 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 740 MET cc_start: 0.8082 (ppp) cc_final: 0.7849 (tmm) REVERT: A 765 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8472 (tmm-80) REVERT: A 1106 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: A 1144 GLU cc_start: 0.8746 (mp0) cc_final: 0.8518 (mp0) REVERT: B 187 LYS cc_start: 0.5636 (OUTLIER) cc_final: 0.4441 (tttt) REVERT: B 266 TYR cc_start: 0.5506 (m-80) cc_final: 0.5127 (m-80) REVERT: B 869 MET cc_start: 0.8560 (pmm) cc_final: 0.8285 (pmm) REVERT: B 918 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 1000 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7420 (tpp-160) REVERT: B 1005 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: C 28 TYR cc_start: 0.6523 (m-80) cc_final: 0.5538 (m-80) REVERT: C 270 LEU cc_start: 0.8192 (tp) cc_final: 0.7985 (tp) REVERT: C 275 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6332 (t80) REVERT: C 505 TYR cc_start: 0.7576 (m-80) cc_final: 0.7205 (m-80) REVERT: C 515 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4813 (p90) REVERT: C 1029 MET cc_start: 0.8513 (tmm) cc_final: 0.8122 (tmm) REVERT: D 74 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6931 (pt0) REVERT: D 123 MET cc_start: 0.2517 (OUTLIER) cc_final: 0.2055 (ttt) REVERT: D 220 ASN cc_start: 0.3588 (OUTLIER) cc_final: 0.3157 (t0) REVERT: D 249 MET cc_start: 0.0771 (mmm) cc_final: 0.0255 (mtt) REVERT: D 424 LEU cc_start: 0.1372 (OUTLIER) cc_final: 0.0300 (tp) REVERT: D 455 MET cc_start: 0.4104 (ppp) cc_final: 0.3712 (tpp) REVERT: D 480 MET cc_start: 0.0591 (tmm) cc_final: -0.0349 (tpp) REVERT: D 481 LYS cc_start: 0.3341 (OUTLIER) cc_final: 0.2892 (tmtt) REVERT: D 512 PHE cc_start: 0.2228 (OUTLIER) cc_final: 0.1919 (m-80) REVERT: D 516 TYR cc_start: 0.5569 (m-10) cc_final: 0.5171 (m-10) outliers start: 188 outliers final: 112 residues processed: 338 average time/residue: 0.3210 time to fit residues: 175.7043 Evaluate side-chains 283 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 160 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 217 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 201 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 710 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 24521 Z= 0.293 Angle : 0.949 16.005 33362 Z= 0.502 Chirality : 0.052 0.446 3765 Planarity : 0.007 0.174 4320 Dihedral : 8.036 83.992 3245 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.39 % Favored : 86.41 % Rotamer: Outliers : 6.93 % Allowed : 25.70 % Favored : 67.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 2988 helix: -0.04 (0.18), residues: 905 sheet: -1.19 (0.29), residues: 302 loop : -3.03 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 478 HIS 0.009 0.001 HIS D 374 PHE 0.030 0.002 PHE A 65 TYR 0.025 0.002 TYR B 38 ARG 0.005 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 180 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8187 (tp) cc_final: 0.7831 (pt) REVERT: A 201 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: A 740 MET cc_start: 0.8209 (ppp) cc_final: 0.7913 (tmm) REVERT: A 765 ARG cc_start: 0.8792 (ttp-170) cc_final: 0.8465 (tmm-80) REVERT: A 1106 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: A 1144 GLU cc_start: 0.8653 (mp0) cc_final: 0.8365 (mp0) REVERT: B 120 VAL cc_start: 0.6625 (OUTLIER) cc_final: 0.6408 (m) REVERT: B 125 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7634 (t0) REVERT: B 187 LYS cc_start: 0.4344 (OUTLIER) cc_final: 0.3360 (tttt) REVERT: B 266 TYR cc_start: 0.5493 (m-80) cc_final: 0.5030 (m-80) REVERT: B 869 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8297 (pmm) REVERT: B 918 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 938 LEU cc_start: 0.8245 (mt) cc_final: 0.8002 (mm) REVERT: B 1000 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7635 (tpp-160) REVERT: B 1005 GLN cc_start: 0.7360 (tp-100) cc_final: 0.6992 (mm-40) REVERT: C 28 TYR cc_start: 0.6331 (m-80) cc_final: 0.5314 (m-80) REVERT: C 275 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.6359 (t80) REVERT: C 505 TYR cc_start: 0.7649 (m-80) cc_final: 0.7130 (m-80) REVERT: C 515 PHE cc_start: 0.5289 (OUTLIER) cc_final: 0.4940 (p90) REVERT: C 725 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8446 (mm-30) REVERT: C 1029 MET cc_start: 0.8447 (tmm) cc_final: 0.8044 (tmm) REVERT: D 74 GLU cc_start: 0.7228 (mm-30) cc_final: 0.7009 (pt0) REVERT: D 123 MET cc_start: 0.2225 (ttt) cc_final: 0.1992 (ttt) REVERT: D 220 ASN cc_start: 0.4060 (OUTLIER) cc_final: 0.3533 (t0) REVERT: D 249 MET cc_start: 0.0561 (mmm) cc_final: 0.0106 (mtt) REVERT: D 364 VAL cc_start: 0.4848 (OUTLIER) cc_final: 0.4569 (p) REVERT: D 424 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0061 (tp) REVERT: D 455 MET cc_start: 0.4282 (OUTLIER) cc_final: 0.3882 (tpp) REVERT: D 480 MET cc_start: 0.0744 (tmm) cc_final: -0.0115 (tpp) REVERT: D 481 LYS cc_start: 0.3320 (OUTLIER) cc_final: 0.2881 (tmtt) REVERT: D 512 PHE cc_start: 0.2410 (OUTLIER) cc_final: 0.2128 (m-80) REVERT: D 516 TYR cc_start: 0.5480 (m-10) cc_final: 0.4955 (m-10) REVERT: D 562 ARG cc_start: 0.3755 (OUTLIER) cc_final: 0.3418 (mtt180) REVERT: D 594 TRP cc_start: 0.6613 (t60) cc_final: 0.5653 (m-10) outliers start: 185 outliers final: 116 residues processed: 341 average time/residue: 0.3281 time to fit residues: 180.7251 Evaluate side-chains 292 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 161 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 180 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 562 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 57 optimal weight: 0.0870 chunk 171 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 292 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 644 GLN A 658 ASN A 690 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN D 388 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24521 Z= 0.269 Angle : 0.918 16.083 33362 Z= 0.484 Chirality : 0.051 0.392 3765 Planarity : 0.006 0.089 4320 Dihedral : 7.725 84.886 3245 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.45 % Favored : 87.38 % Rotamer: Outliers : 6.78 % Allowed : 26.04 % Favored : 67.18 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2988 helix: -0.01 (0.18), residues: 914 sheet: -1.15 (0.29), residues: 312 loop : -2.92 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 478 HIS 0.009 0.001 HIS D 374 PHE 0.027 0.001 PHE A 238 TYR 0.035 0.001 TYR D 183 ARG 0.005 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 175 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8101 (tp) cc_final: 0.7775 (pt) REVERT: A 135 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6643 (p90) REVERT: A 201 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: A 740 MET cc_start: 0.8420 (ppp) cc_final: 0.8026 (tmm) REVERT: A 765 ARG cc_start: 0.8779 (ttp-170) cc_final: 0.8431 (tmm-80) REVERT: A 1106 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (pt0) REVERT: A 1144 GLU cc_start: 0.8663 (mp0) cc_final: 0.8361 (mp0) REVERT: B 40 ASP cc_start: 0.7240 (p0) cc_final: 0.6712 (t0) REVERT: B 120 VAL cc_start: 0.6640 (OUTLIER) cc_final: 0.6431 (m) REVERT: B 125 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7663 (t0) REVERT: B 187 LYS cc_start: 0.4786 (OUTLIER) cc_final: 0.3942 (tttt) REVERT: B 198 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7419 (p0) REVERT: B 266 TYR cc_start: 0.5206 (m-80) cc_final: 0.5000 (m-80) REVERT: B 869 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8268 (pmm) REVERT: B 918 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 1005 GLN cc_start: 0.7214 (tp-100) cc_final: 0.6872 (mm-40) REVERT: B 1009 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7134 (p) REVERT: C 28 TYR cc_start: 0.6222 (m-80) cc_final: 0.5245 (m-80) REVERT: C 64 TRP cc_start: 0.7972 (t60) cc_final: 0.7622 (t60) REVERT: C 266 TYR cc_start: 0.7597 (m-10) cc_final: 0.7286 (m-10) REVERT: C 275 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.6292 (t80) REVERT: C 276 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7432 (tp) REVERT: C 505 TYR cc_start: 0.7540 (m-80) cc_final: 0.6988 (m-80) REVERT: C 515 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.5175 (p90) REVERT: C 725 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8493 (mm-30) REVERT: C 1029 MET cc_start: 0.8384 (tmm) cc_final: 0.8024 (tmm) REVERT: C 1031 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 74 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6803 (tt0) REVERT: D 106 SER cc_start: 0.3158 (OUTLIER) cc_final: 0.2782 (t) REVERT: D 123 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2013 (ttt) REVERT: D 152 MET cc_start: 0.1974 (tpp) cc_final: 0.1205 (ttp) REVERT: D 249 MET cc_start: 0.1144 (mmm) cc_final: 0.0759 (mtt) REVERT: D 455 MET cc_start: 0.4230 (OUTLIER) cc_final: 0.3851 (tpp) REVERT: D 480 MET cc_start: 0.0579 (tmm) cc_final: -0.0366 (tpp) REVERT: D 512 PHE cc_start: 0.1997 (OUTLIER) cc_final: 0.1758 (m-80) REVERT: D 516 TYR cc_start: 0.5390 (m-10) cc_final: 0.4926 (m-10) REVERT: D 562 ARG cc_start: 0.3754 (OUTLIER) cc_final: 0.3443 (mtt180) REVERT: D 594 TRP cc_start: 0.6639 (t60) cc_final: 0.5755 (m-10) outliers start: 181 outliers final: 125 residues processed: 330 average time/residue: 0.3208 time to fit residues: 171.9871 Evaluate side-chains 301 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 159 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 509 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 562 ARG Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 644 GLN A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24521 Z= 0.333 Angle : 0.947 14.490 33362 Z= 0.498 Chirality : 0.052 0.411 3765 Planarity : 0.007 0.088 4320 Dihedral : 7.757 84.263 3243 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.19 % Favored : 85.68 % Rotamer: Outliers : 7.53 % Allowed : 26.08 % Favored : 66.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.11 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 2988 helix: -0.14 (0.17), residues: 930 sheet: -1.33 (0.28), residues: 318 loop : -2.99 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 436 HIS 0.008 0.001 HIS D 374 PHE 0.037 0.002 PHE D 32 TYR 0.024 0.002 TYR B 38 ARG 0.011 0.001 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 158 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8116 (tp) cc_final: 0.7647 (tt) REVERT: A 135 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6562 (p90) REVERT: A 201 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: A 765 ARG cc_start: 0.8866 (ttp-170) cc_final: 0.8565 (tmm-80) REVERT: A 1106 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: B 125 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7752 (t0) REVERT: B 187 LYS cc_start: 0.4920 (OUTLIER) cc_final: 0.4002 (tttt) REVERT: B 198 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (p0) REVERT: B 266 TYR cc_start: 0.4834 (m-80) cc_final: 0.4514 (m-80) REVERT: B 869 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (pmm) REVERT: B 918 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 28 TYR cc_start: 0.6332 (m-80) cc_final: 0.5322 (m-80) REVERT: C 275 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.6459 (t80) REVERT: C 276 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7527 (tp) REVERT: C 505 TYR cc_start: 0.7558 (m-80) cc_final: 0.6958 (m-80) REVERT: C 515 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.5070 (p90) REVERT: C 1029 MET cc_start: 0.8501 (tmm) cc_final: 0.8236 (tmm) REVERT: D 74 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6839 (tt0) REVERT: D 220 ASN cc_start: 0.4104 (OUTLIER) cc_final: 0.3604 (t0) REVERT: D 249 MET cc_start: 0.0883 (mmm) cc_final: 0.0533 (mtt) REVERT: D 455 MET cc_start: 0.4230 (OUTLIER) cc_final: 0.3817 (tpp) REVERT: D 516 TYR cc_start: 0.5428 (m-10) cc_final: 0.5015 (m-10) REVERT: D 530 CYS cc_start: 0.5354 (OUTLIER) cc_final: 0.5020 (m) REVERT: D 594 TRP cc_start: 0.6511 (t60) cc_final: 0.5651 (m-10) outliers start: 201 outliers final: 150 residues processed: 332 average time/residue: 0.3309 time to fit residues: 182.2318 Evaluate side-chains 311 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 148 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 chunk 173 optimal weight: 0.0270 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 24521 Z= 0.256 Angle : 0.924 14.627 33362 Z= 0.480 Chirality : 0.050 0.386 3765 Planarity : 0.006 0.088 4320 Dihedral : 7.553 84.790 3243 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.15 % Favored : 87.68 % Rotamer: Outliers : 4.87 % Allowed : 28.25 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.48 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 2988 helix: 0.11 (0.18), residues: 920 sheet: -1.02 (0.29), residues: 306 loop : -2.89 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 478 HIS 0.008 0.001 HIS D 374 PHE 0.035 0.001 PHE D 32 TYR 0.033 0.001 TYR D 183 ARG 0.010 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 173 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8020 (tp) cc_final: 0.7545 (tt) REVERT: A 135 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6687 (p90) REVERT: A 201 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: A 765 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8419 (tmm-80) REVERT: B 40 ASP cc_start: 0.7458 (p0) cc_final: 0.6716 (t0) REVERT: B 125 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 187 LYS cc_start: 0.3738 (OUTLIER) cc_final: 0.2968 (tttt) REVERT: B 198 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7597 (p0) REVERT: B 266 TYR cc_start: 0.4859 (m-80) cc_final: 0.4631 (m-80) REVERT: B 869 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8283 (pmm) REVERT: B 918 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 28 TYR cc_start: 0.6095 (m-80) cc_final: 0.5175 (m-80) REVERT: C 64 TRP cc_start: 0.7879 (t60) cc_final: 0.7614 (t60) REVERT: C 266 TYR cc_start: 0.7480 (m-10) cc_final: 0.7248 (m-10) REVERT: C 275 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.6304 (t80) REVERT: C 276 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7457 (tp) REVERT: C 336 CYS cc_start: 0.4103 (OUTLIER) cc_final: 0.3484 (m) REVERT: C 505 TYR cc_start: 0.7707 (m-80) cc_final: 0.7041 (m-80) REVERT: C 725 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8507 (mm-30) REVERT: C 1005 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8228 (mm-40) REVERT: C 1029 MET cc_start: 0.8360 (tmm) cc_final: 0.7982 (tmm) REVERT: D 74 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6792 (tt0) REVERT: D 152 MET cc_start: 0.2490 (tpp) cc_final: 0.1643 (ttp) REVERT: D 220 ASN cc_start: 0.4088 (OUTLIER) cc_final: 0.3602 (t0) REVERT: D 249 MET cc_start: 0.0960 (mmm) cc_final: 0.0715 (mtt) REVERT: D 455 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3961 (tpp) REVERT: D 594 TRP cc_start: 0.6658 (t60) cc_final: 0.5815 (m-10) outliers start: 130 outliers final: 96 residues processed: 285 average time/residue: 0.3066 time to fit residues: 143.7666 Evaluate side-chains 260 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 153 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 254 optimal weight: 0.0980 chunk 271 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 212 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 270 optimal weight: 0.0370 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 644 GLN A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 24521 Z= 0.263 Angle : 0.914 18.198 33362 Z= 0.475 Chirality : 0.050 0.391 3765 Planarity : 0.006 0.089 4320 Dihedral : 7.425 83.272 3243 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.82 % Favored : 87.05 % Rotamer: Outliers : 4.53 % Allowed : 28.66 % Favored : 66.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2988 helix: 0.16 (0.18), residues: 910 sheet: -0.90 (0.29), residues: 306 loop : -2.84 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 459 HIS 0.007 0.001 HIS D 374 PHE 0.040 0.001 PHE D 32 TYR 0.022 0.001 TYR D 183 ARG 0.006 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 164 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8107 (tp) cc_final: 0.7603 (tt) REVERT: A 129 LYS cc_start: 0.7536 (tmtt) cc_final: 0.6962 (tptp) REVERT: A 135 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6724 (p90) REVERT: A 166 CYS cc_start: 0.4323 (OUTLIER) cc_final: 0.4043 (m) REVERT: A 201 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6278 (m-80) REVERT: A 765 ARG cc_start: 0.8792 (ttp-170) cc_final: 0.8459 (tmm-80) REVERT: B 40 ASP cc_start: 0.7425 (p0) cc_final: 0.6718 (t0) REVERT: B 125 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7596 (t0) REVERT: B 187 LYS cc_start: 0.4100 (OUTLIER) cc_final: 0.3262 (tttt) REVERT: B 198 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7588 (p0) REVERT: B 869 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (pmm) REVERT: B 994 ASP cc_start: 0.8999 (t0) cc_final: 0.8245 (p0) REVERT: C 28 TYR cc_start: 0.6146 (m-80) cc_final: 0.5228 (m-80) REVERT: C 64 TRP cc_start: 0.7925 (t60) cc_final: 0.7720 (t60) REVERT: C 275 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6284 (t80) REVERT: C 276 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7481 (tp) REVERT: C 336 CYS cc_start: 0.4075 (OUTLIER) cc_final: 0.3541 (m) REVERT: C 505 TYR cc_start: 0.7729 (m-80) cc_final: 0.7076 (m-80) REVERT: C 515 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.5118 (p90) REVERT: C 725 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 1005 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8276 (mm-40) REVERT: C 1029 MET cc_start: 0.8376 (tmm) cc_final: 0.7996 (tmm) REVERT: D 74 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6805 (tp30) REVERT: D 106 SER cc_start: 0.2431 (OUTLIER) cc_final: 0.1892 (t) REVERT: D 152 MET cc_start: 0.2324 (tpp) cc_final: 0.1467 (ttp) REVERT: D 220 ASN cc_start: 0.4019 (OUTLIER) cc_final: 0.3555 (t0) REVERT: D 455 MET cc_start: 0.4304 (OUTLIER) cc_final: 0.3906 (tpp) REVERT: D 594 TRP cc_start: 0.6575 (t60) cc_final: 0.5729 (m-10) outliers start: 121 outliers final: 98 residues processed: 266 average time/residue: 0.3126 time to fit residues: 136.3988 Evaluate side-chains 260 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 148 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 175 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 644 GLN A 658 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24521 Z= 0.316 Angle : 0.948 19.055 33362 Z= 0.495 Chirality : 0.051 0.359 3765 Planarity : 0.007 0.087 4320 Dihedral : 7.520 81.635 3243 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.69 % Favored : 86.08 % Rotamer: Outliers : 4.76 % Allowed : 28.55 % Favored : 66.69 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.15), residues: 2988 helix: 0.08 (0.17), residues: 912 sheet: -1.12 (0.28), residues: 333 loop : -2.86 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 302 HIS 0.007 0.001 HIS D 374 PHE 0.024 0.002 PHE A 32 TYR 0.045 0.002 TYR D 183 ARG 0.009 0.001 ARG D 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 150 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8123 (tp) cc_final: 0.7561 (tt) REVERT: A 129 LYS cc_start: 0.7593 (tmtt) cc_final: 0.6998 (tptp) REVERT: A 135 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6836 (p90) REVERT: A 166 CYS cc_start: 0.4299 (OUTLIER) cc_final: 0.4044 (m) REVERT: A 201 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6172 (m-80) REVERT: B 40 ASP cc_start: 0.7523 (p0) cc_final: 0.6795 (t0) REVERT: B 125 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7743 (t0) REVERT: B 187 LYS cc_start: 0.4548 (OUTLIER) cc_final: 0.3831 (tttt) REVERT: B 198 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 869 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: C 28 TYR cc_start: 0.6234 (m-80) cc_final: 0.5298 (m-80) REVERT: C 64 TRP cc_start: 0.7909 (t60) cc_final: 0.7640 (t60) REVERT: C 275 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6448 (t80) REVERT: C 276 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7774 (tp) REVERT: C 505 TYR cc_start: 0.7719 (m-80) cc_final: 0.7111 (m-80) REVERT: C 515 PHE cc_start: 0.5179 (OUTLIER) cc_final: 0.4914 (p90) REVERT: C 1005 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8307 (mm-40) REVERT: C 1029 MET cc_start: 0.8504 (tmm) cc_final: 0.8228 (tmm) REVERT: D 74 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6734 (tp30) REVERT: D 106 SER cc_start: 0.2475 (OUTLIER) cc_final: 0.1977 (p) REVERT: D 152 MET cc_start: 0.2558 (tpp) cc_final: 0.1659 (ttp) REVERT: D 220 ASN cc_start: 0.4069 (OUTLIER) cc_final: 0.3597 (t0) REVERT: D 302 TRP cc_start: 0.2463 (m-90) cc_final: 0.2037 (m-10) REVERT: D 455 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.4314 (tpp) REVERT: D 594 TRP cc_start: 0.6553 (t60) cc_final: 0.5740 (m-10) outliers start: 127 outliers final: 106 residues processed: 259 average time/residue: 0.3384 time to fit residues: 145.7365 Evaluate side-chains 262 residues out of total 2669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 143 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 158 TYR Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 613 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 0.1980 chunk 255 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.118260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.090153 restraints weight = 115046.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.091332 restraints weight = 70460.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.091754 restraints weight = 44348.920| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24521 Z= 0.253 Angle : 0.917 17.507 33362 Z= 0.475 Chirality : 0.050 0.361 3765 Planarity : 0.006 0.088 4320 Dihedral : 7.349 82.893 3243 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.45 % Favored : 87.45 % Rotamer: Outliers : 4.50 % Allowed : 28.66 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.86 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2988 helix: 0.19 (0.18), residues: 917 sheet: -0.96 (0.29), residues: 309 loop : -2.80 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 478 HIS 0.008 0.001 HIS D 374 PHE 0.026 0.001 PHE D 314 TYR 0.052 0.001 TYR D 183 ARG 0.006 0.000 ARG D 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4880.45 seconds wall clock time: 88 minutes 34.45 seconds (5314.45 seconds total)