Starting phenix.real_space_refine on Fri Apr 12 03:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/04_2024/8hri_34974.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15711 2.51 5 N 4086 2.21 5 O 4620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "B" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8191 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 8 Chain: "C" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Time building chain proxies: 12.78, per 1000 atoms: 0.52 Number of scatterers: 24531 At special positions: 0 Unit cell: (139.32, 151.36, 201.24, 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 4620 8.00 N 4086 7.00 C 15711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.67 Conformation dependent library (CDL) restraints added in 4.2 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.891A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.051A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.656A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.538A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.577A pdb=" N ILE A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 806' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.033A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.201A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.066A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.077A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.626A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.871A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.608A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.051A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.557A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.384A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.582A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 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 976 through 984 removed outlier: 3.675A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.226A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.575A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.847A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.540A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.528A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 937 removed outlier: 3.822A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.577A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) 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 984 removed outlier: 3.734A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.900A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.277A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.610A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.577A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.695A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.062A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.643A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.345A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.160A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.805A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 142 removed outlier: 7.615A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.721A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.547A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.471A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.692A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.240A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.601A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.611A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.224A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.639A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1014 hydrogen bonds defined for protein. 2748 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: 11.04 Time building geometry restraints manager: 9.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7684 1.34 - 1.46: 6283 1.46 - 1.59: 10990 1.59 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25098 Sorted by residual: bond pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.27e-02 6.20e+03 8.77e+00 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.53e-02 4.27e+03 8.32e+00 bond pdb=" C PHE A 374 " pdb=" N PHE A 375 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.23e-02 6.61e+03 6.38e+00 bond pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.21e+00 bond pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 5.96e+00 ... (remaining 25093 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.36: 656 106.36 - 113.28: 13378 113.28 - 120.20: 8657 120.20 - 127.11: 11229 127.11 - 134.03: 209 Bond angle restraints: 34129 Sorted by residual: angle pdb=" CA PHE B 375 " pdb=" CB PHE B 375 " pdb=" CG PHE B 375 " ideal model delta sigma weight residual 113.80 120.94 -7.14 1.00e+00 1.00e+00 5.09e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 112.47 99.61 12.86 2.06e+00 2.36e-01 3.90e+01 angle pdb=" CA THR B 376 " pdb=" C THR B 376 " pdb=" O THR B 376 " ideal model delta sigma weight residual 121.88 115.73 6.15 1.13e+00 7.83e-01 2.96e+01 angle pdb=" N PRO B 373 " pdb=" CA PRO B 373 " pdb=" C PRO B 373 " ideal model delta sigma weight residual 112.47 101.82 10.65 2.06e+00 2.36e-01 2.67e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.41 107.87 5.54 1.22e+00 6.72e-01 2.06e+01 ... (remaining 34124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13422 17.62 - 35.24: 1258 35.24 - 52.85: 251 52.85 - 70.47: 45 70.47 - 88.09: 23 Dihedral angle restraints: 14999 sinusoidal: 5882 harmonic: 9117 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.18 80.82 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.03 65.97 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 155.66 -62.66 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 14996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3059 0.052 - 0.104: 652 0.104 - 0.157: 151 0.157 - 0.209: 9 0.209 - 0.261: 2 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" C PRO A 373 " pdb=" CB PRO A 373 " both_signs ideal model delta sigma weight residual False 2.72 2.98 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU A 368 " pdb=" N LEU A 368 " pdb=" C LEU A 368 " pdb=" CB LEU A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU B 368 " pdb=" N LEU B 368 " pdb=" C LEU B 368 " pdb=" CB LEU B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3870 not shown) Planarity restraints: 4411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 498 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 499 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 498 " -0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 499 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " 0.063 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 322 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.051 5.00e-02 4.00e+02 ... (remaining 4408 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1917 2.74 - 3.28: 22777 3.28 - 3.82: 36706 3.82 - 4.36: 41437 4.36 - 4.90: 76836 Nonbonded interactions: 179673 Sorted by model distance: nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.240 2.440 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP A 40 " pdb=" NH1 ARG A 44 " model vdw 2.264 2.520 ... (remaining 179668 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' and (resid 15 through 827 or resid 848 through 1147)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 28.730 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 65.540 Find NCS groups from input model: 1.700 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: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25098 Z= 0.205 Angle : 0.611 12.861 34129 Z= 0.339 Chirality : 0.046 0.261 3873 Planarity : 0.005 0.098 4411 Dihedral : 14.229 88.091 8993 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.76 % Rotamer: Outliers : 0.26 % Allowed : 0.33 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3072 helix: 2.02 (0.21), residues: 679 sheet: 1.05 (0.19), residues: 682 loop : -1.55 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS C1088 PHE 0.020 0.001 PHE A 486 TYR 0.018 0.001 TYR C 351 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.6914 (mtp) cc_final: 0.6618 (mtp) REVERT: A 725 GLU cc_start: 0.8549 (tt0) cc_final: 0.8216 (mt-10) REVERT: A 1107 ARG cc_start: 0.4894 (mpt-90) cc_final: 0.4470 (mtp180) REVERT: B 1019 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.6983 (ttp-110) REVERT: C 676 THR cc_start: 0.3141 (OUTLIER) cc_final: 0.2922 (p) REVERT: C 773 GLU cc_start: 0.7413 (tt0) cc_final: 0.7158 (tt0) outliers start: 7 outliers final: 1 residues processed: 247 average time/residue: 1.2287 time to fit residues: 357.0355 Evaluate side-chains 105 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.2980 chunk 236 optimal weight: 0.0000 chunk 131 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 644 GLN A 914 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1101 HIS B 81 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 564 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 914 ASN C1011 GLN C1083 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4530 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25098 Z= 0.197 Angle : 0.593 10.354 34129 Z= 0.312 Chirality : 0.045 0.186 3873 Planarity : 0.005 0.073 4411 Dihedral : 4.413 55.925 3352 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.32 % Allowed : 9.28 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3072 helix: 1.90 (0.21), residues: 703 sheet: 0.80 (0.19), residues: 677 loop : -1.55 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.002 PHE B 275 TYR 0.020 0.001 TYR C 453 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 2.471 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: -0.0816 (mmm) cc_final: -0.1533 (ttm) REVERT: A 697 MET cc_start: 0.7350 (mtp) cc_final: 0.7096 (mtp) REVERT: A 916 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6994 (tt) REVERT: A 935 GLN cc_start: 0.7444 (tt0) cc_final: 0.7158 (tm-30) REVERT: B 44 ARG cc_start: 0.4950 (OUTLIER) cc_final: 0.4106 (ptp-170) REVERT: B 1019 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7455 (ttp-110) outliers start: 36 outliers final: 15 residues processed: 165 average time/residue: 1.2585 time to fit residues: 245.0367 Evaluate side-chains 112 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.1980 chunk 192 optimal weight: 0.9980 chunk 78 optimal weight: 0.0170 chunk 283 optimal weight: 0.5980 chunk 306 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 0.0870 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 644 GLN A1002 GLN A1135 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 165 ASN C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4870 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25098 Z= 0.174 Angle : 0.547 11.264 34129 Z= 0.286 Chirality : 0.044 0.189 3873 Planarity : 0.005 0.088 4411 Dihedral : 4.071 52.363 3351 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 1.50 % Allowed : 12.31 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3072 helix: 2.24 (0.21), residues: 683 sheet: 0.92 (0.19), residues: 670 loop : -1.47 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS A1101 PHE 0.021 0.001 PHE C 201 TYR 0.016 0.001 TYR C1067 ARG 0.037 0.001 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.6282 (tpp80) cc_final: 0.5501 (mmp-170) REVERT: A 697 MET cc_start: 0.7644 (mtp) cc_final: 0.7433 (mtp) REVERT: A 869 MET cc_start: 0.6690 (mtt) cc_final: 0.6007 (mtt) REVERT: B 44 ARG cc_start: 0.5214 (ptp-170) cc_final: 0.4303 (ptp-170) REVERT: B 153 MET cc_start: 0.0389 (tpp) cc_final: -0.0856 (tmm) REVERT: B 646 ARG cc_start: 0.6721 (mmp80) cc_final: 0.5890 (mpp80) REVERT: B 921 LYS cc_start: 0.5624 (mtpp) cc_final: 0.5368 (pttm) REVERT: B 955 ASN cc_start: 0.6470 (t0) cc_final: 0.6201 (m-40) outliers start: 41 outliers final: 16 residues processed: 166 average time/residue: 1.1853 time to fit residues: 233.6821 Evaluate side-chains 120 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 804 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 901 GLN C 52 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25098 Z= 0.369 Angle : 0.797 14.102 34129 Z= 0.429 Chirality : 0.052 0.471 3873 Planarity : 0.007 0.103 4411 Dihedral : 5.079 24.233 3349 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.63 % Allowed : 15.16 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3072 helix: 0.82 (0.19), residues: 706 sheet: 0.62 (0.20), residues: 617 loop : -1.76 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 886 HIS 0.006 0.002 HIS B 505 PHE 0.032 0.003 PHE C 55 TYR 0.036 0.003 TYR C 37 ARG 0.032 0.001 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 162 time to evaluate : 2.911 Fit side-chains revert: symmetry clash REVERT: A 644 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6642 (tp40) REVERT: A 914 ASN cc_start: 0.7175 (t0) cc_final: 0.6892 (t0) REVERT: A 957 GLN cc_start: 0.7857 (tp40) cc_final: 0.7506 (tt0) REVERT: A 1031 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: A 1113 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: A 1138 TYR cc_start: 0.6691 (t80) cc_final: 0.6364 (m-80) REVERT: B 1005 GLN cc_start: 0.7035 (mm110) cc_final: 0.6785 (mt0) REVERT: C 310 LYS cc_start: 0.7299 (ttpt) cc_final: 0.6263 (tptt) REVERT: C 814 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6426 (tttp) REVERT: C 1010 GLN cc_start: 0.7808 (mm110) cc_final: 0.7288 (mt0) REVERT: C 1123 SER cc_start: 0.9278 (t) cc_final: 0.8997 (m) outliers start: 72 outliers final: 27 residues processed: 218 average time/residue: 1.1318 time to fit residues: 294.8518 Evaluate side-chains 139 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0270 chunk 171 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 755 GLN A 901 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 675 GLN B 901 GLN B1101 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1058 HIS C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25098 Z= 0.184 Angle : 0.575 8.426 34129 Z= 0.307 Chirality : 0.044 0.177 3873 Planarity : 0.005 0.066 4411 Dihedral : 4.344 24.628 3349 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.83 % Allowed : 17.25 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3072 helix: 1.71 (0.21), residues: 686 sheet: 0.55 (0.19), residues: 667 loop : -1.68 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.002 0.001 HIS B 505 PHE 0.018 0.001 PHE C 201 TYR 0.017 0.001 TYR C 265 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 117 time to evaluate : 2.760 Fit side-chains REVERT: A 654 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: A 851 CYS cc_start: 0.7206 (m) cc_final: 0.6970 (m) REVERT: A 957 GLN cc_start: 0.7736 (tp40) cc_final: 0.7408 (tt0) REVERT: A 1029 MET cc_start: 0.7878 (tpp) cc_final: 0.7642 (tpp) REVERT: A 1113 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: A 1114 ILE cc_start: 0.8260 (mm) cc_final: 0.8058 (tp) REVERT: A 1117 THR cc_start: 0.8041 (m) cc_final: 0.7707 (p) REVERT: A 1138 TYR cc_start: 0.6789 (t80) cc_final: 0.6495 (m-80) REVERT: B 755 GLN cc_start: 0.8047 (mt0) cc_final: 0.7790 (mt0) REVERT: C 310 LYS cc_start: 0.7380 (ttpt) cc_final: 0.6170 (tptt) REVERT: C 740 MET cc_start: 0.8189 (mmm) cc_final: 0.7948 (ttt) REVERT: C 814 LYS cc_start: 0.7335 (mmpt) cc_final: 0.6407 (tttp) REVERT: C 1123 SER cc_start: 0.9254 (t) cc_final: 0.8986 (m) outliers start: 50 outliers final: 18 residues processed: 159 average time/residue: 1.0997 time to fit residues: 212.8210 Evaluate side-chains 121 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 0.0010 chunk 301 optimal weight: 0.5980 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 158 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 914 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 978 ASN C1058 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25098 Z= 0.174 Angle : 0.544 6.558 34129 Z= 0.290 Chirality : 0.044 0.173 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.147 24.271 3349 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 1.86 % Allowed : 17.94 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3072 helix: 1.96 (0.21), residues: 679 sheet: 0.64 (0.20), residues: 645 loop : -1.65 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.003 0.001 HIS A1088 PHE 0.015 0.001 PHE C 201 TYR 0.017 0.001 TYR A 796 ARG 0.004 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 108 time to evaluate : 3.591 Fit side-chains REVERT: A 333 THR cc_start: 0.3220 (OUTLIER) cc_final: 0.3016 (t) REVERT: A 654 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7166 (pt0) REVERT: A 851 CYS cc_start: 0.7327 (m) cc_final: 0.7076 (m) REVERT: A 957 GLN cc_start: 0.7759 (tp40) cc_final: 0.7447 (tt0) REVERT: A 1113 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: A 1117 THR cc_start: 0.8260 (m) cc_final: 0.8007 (p) REVERT: A 1138 TYR cc_start: 0.6853 (t80) cc_final: 0.6537 (m-80) REVERT: B 723 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7473 (p) REVERT: B 755 GLN cc_start: 0.8014 (mt0) cc_final: 0.7774 (mt0) REVERT: B 957 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: C 644 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.5662 (tt0) REVERT: C 664 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 795 LYS cc_start: 0.7145 (mptm) cc_final: 0.6565 (mtpp) REVERT: C 814 LYS cc_start: 0.7384 (mmpt) cc_final: 0.6394 (tttp) REVERT: C 1010 GLN cc_start: 0.7742 (mm110) cc_final: 0.7207 (mt0) REVERT: C 1123 SER cc_start: 0.9290 (t) cc_final: 0.9021 (m) outliers start: 51 outliers final: 20 residues processed: 149 average time/residue: 1.1249 time to fit residues: 201.5681 Evaluate side-chains 119 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 49 HIS B 613 GLN B 675 GLN B 901 GLN C 49 HIS ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN C 965 GLN C1058 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 25098 Z= 0.276 Angle : 0.668 8.307 34129 Z= 0.362 Chirality : 0.047 0.235 3873 Planarity : 0.006 0.067 4411 Dihedral : 4.689 26.020 3349 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.59 % Allowed : 18.30 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3072 helix: 1.51 (0.20), residues: 678 sheet: 0.42 (0.19), residues: 683 loop : -1.80 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 353 HIS 0.005 0.001 HIS A1083 PHE 0.031 0.002 PHE B 377 TYR 0.023 0.002 TYR C1067 ARG 0.010 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 112 time to evaluate : 2.762 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8082 (mtt) cc_final: 0.7880 (mtt) REVERT: A 957 GLN cc_start: 0.7783 (tp40) cc_final: 0.7485 (tt0) REVERT: A 1010 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: A 1031 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: A 1113 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 1117 THR cc_start: 0.8571 (m) cc_final: 0.8340 (p) REVERT: A 1138 TYR cc_start: 0.6918 (t80) cc_final: 0.6619 (m-80) REVERT: B 655 TYR cc_start: 0.6461 (t80) cc_final: 0.6250 (t80) REVERT: B 723 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7529 (p) REVERT: B 755 GLN cc_start: 0.8164 (mt0) cc_final: 0.7894 (mt0) REVERT: B 964 LYS cc_start: 0.7457 (ttmm) cc_final: 0.7158 (tttm) REVERT: B 969 LYS cc_start: 0.7028 (tppp) cc_final: 0.6811 (tppt) REVERT: B 1005 GLN cc_start: 0.7113 (mm110) cc_final: 0.6822 (mt0) REVERT: C 664 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7941 (mt) REVERT: C 748 GLU cc_start: 0.5964 (mp0) cc_final: 0.5670 (mp0) REVERT: C 795 LYS cc_start: 0.7230 (mptm) cc_final: 0.6547 (mtpp) REVERT: C 814 LYS cc_start: 0.7489 (mmpt) cc_final: 0.6408 (tttp) REVERT: C 1010 GLN cc_start: 0.7791 (mm110) cc_final: 0.7270 (mt0) REVERT: C 1123 SER cc_start: 0.9295 (t) cc_final: 0.8874 (m) outliers start: 71 outliers final: 38 residues processed: 168 average time/residue: 1.1523 time to fit residues: 234.1181 Evaluate side-chains 139 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 0.0270 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 914 ASN B 613 GLN B 675 GLN B 914 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C1058 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25098 Z= 0.202 Angle : 0.576 8.158 34129 Z= 0.309 Chirality : 0.045 0.172 3873 Planarity : 0.005 0.064 4411 Dihedral : 4.400 23.900 3349 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 1.94 % Allowed : 19.44 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3072 helix: 1.79 (0.21), residues: 687 sheet: 0.33 (0.20), residues: 630 loop : -1.78 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.053 0.001 PHE B 541 TYR 0.017 0.001 TYR C 265 ARG 0.010 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 105 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.1532 (OUTLIER) cc_final: 0.0456 (t) REVERT: A 957 GLN cc_start: 0.7771 (tp40) cc_final: 0.7498 (tt0) REVERT: A 1010 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: A 1113 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: A 1117 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 1138 TYR cc_start: 0.6946 (t80) cc_final: 0.6631 (m-80) REVERT: B 664 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7767 (mt) REVERT: B 723 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7541 (p) REVERT: B 755 GLN cc_start: 0.8177 (mt0) cc_final: 0.7908 (mt0) REVERT: B 964 LYS cc_start: 0.7231 (ttmm) cc_final: 0.6970 (tttp) REVERT: B 969 LYS cc_start: 0.7090 (tppp) cc_final: 0.6873 (tppt) REVERT: B 1005 GLN cc_start: 0.7119 (mm110) cc_final: 0.6889 (mt0) REVERT: C 226 LEU cc_start: 0.0400 (OUTLIER) cc_final: -0.0232 (pp) REVERT: C 664 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7970 (mt) REVERT: C 748 GLU cc_start: 0.5892 (mp0) cc_final: 0.5602 (mp0) REVERT: C 795 LYS cc_start: 0.7201 (mptm) cc_final: 0.6516 (mtpp) REVERT: C 814 LYS cc_start: 0.7535 (mmpt) cc_final: 0.6462 (tttp) REVERT: C 1010 GLN cc_start: 0.7796 (mm110) cc_final: 0.7272 (mt0) REVERT: C 1123 SER cc_start: 0.9286 (t) cc_final: 0.8941 (m) outliers start: 53 outliers final: 29 residues processed: 145 average time/residue: 1.2529 time to fit residues: 214.4878 Evaluate side-chains 135 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 0.4980 chunk 262 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 220 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 914 ASN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.8332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25098 Z= 0.265 Angle : 0.651 8.384 34129 Z= 0.351 Chirality : 0.047 0.241 3873 Planarity : 0.006 0.063 4411 Dihedral : 4.662 23.871 3349 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 1.90 % Allowed : 20.06 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3072 helix: 1.46 (0.20), residues: 700 sheet: 0.49 (0.20), residues: 631 loop : -1.96 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.028 0.002 PHE B 377 TYR 0.028 0.002 TYR C 917 ARG 0.017 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 2.698 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.1538 (OUTLIER) cc_final: 0.0470 (t) REVERT: A 957 GLN cc_start: 0.7785 (tp40) cc_final: 0.7504 (tt0) REVERT: A 1010 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: A 1113 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: A 1117 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 1138 TYR cc_start: 0.6977 (t80) cc_final: 0.6665 (m-80) REVERT: B 664 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7766 (mt) REVERT: B 723 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7652 (p) REVERT: B 755 GLN cc_start: 0.8319 (mt0) cc_final: 0.8073 (mt0) REVERT: B 964 LYS cc_start: 0.7628 (ttmm) cc_final: 0.7327 (tttm) REVERT: B 979 ASP cc_start: 0.6083 (t0) cc_final: 0.5797 (m-30) REVERT: B 1005 GLN cc_start: 0.7311 (mm110) cc_final: 0.7001 (mt0) REVERT: C 748 GLU cc_start: 0.6106 (mp0) cc_final: 0.5899 (mp0) REVERT: C 795 LYS cc_start: 0.7200 (mptm) cc_final: 0.6487 (mtpp) REVERT: C 814 LYS cc_start: 0.7510 (mmpt) cc_final: 0.6311 (ttpp) REVERT: C 1010 GLN cc_start: 0.7772 (mm110) cc_final: 0.7275 (mt0) REVERT: C 1123 SER cc_start: 0.9250 (t) cc_final: 0.8893 (m) outliers start: 52 outliers final: 28 residues processed: 157 average time/residue: 1.2324 time to fit residues: 231.3996 Evaluate side-chains 134 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.0000 chunk 296 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 310 optimal weight: 0.3980 chunk 286 optimal weight: 0.4980 chunk 247 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 914 ASN C1058 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25098 Z= 0.177 Angle : 0.560 8.906 34129 Z= 0.299 Chirality : 0.044 0.159 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.313 23.315 3349 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 1.57 % Allowed : 20.64 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3072 helix: 1.81 (0.21), residues: 694 sheet: 0.39 (0.21), residues: 595 loop : -1.86 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.006 0.001 HIS A1083 PHE 0.016 0.001 PHE C 562 TYR 0.015 0.001 TYR C1067 ARG 0.011 0.000 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 111 time to evaluate : 2.782 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.1604 (OUTLIER) cc_final: 0.0541 (t) REVERT: A 957 GLN cc_start: 0.7756 (tp40) cc_final: 0.7491 (tt0) REVERT: A 1010 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: A 1113 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: A 1117 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (p) REVERT: A 1138 TYR cc_start: 0.6992 (t80) cc_final: 0.6638 (m-80) REVERT: B 664 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 723 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (p) REVERT: B 755 GLN cc_start: 0.8283 (mt0) cc_final: 0.8023 (mt0) REVERT: B 964 LYS cc_start: 0.7274 (ttmm) cc_final: 0.7037 (tttp) REVERT: B 1005 GLN cc_start: 0.7193 (mm110) cc_final: 0.6930 (mt0) REVERT: C 795 LYS cc_start: 0.7173 (mptm) cc_final: 0.6480 (mtpp) REVERT: C 814 LYS cc_start: 0.7526 (mmpt) cc_final: 0.6476 (tmtp) REVERT: C 1010 GLN cc_start: 0.7766 (mm110) cc_final: 0.7243 (mt0) REVERT: C 1123 SER cc_start: 0.9247 (t) cc_final: 0.8877 (m) outliers start: 43 outliers final: 26 residues processed: 146 average time/residue: 1.1375 time to fit residues: 199.2088 Evaluate side-chains 133 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 228 optimal weight: 0.0060 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1058 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.273052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.212858 restraints weight = 31313.634| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.50 r_work: 0.3820 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25098 Z= 0.195 Angle : 0.575 8.986 34129 Z= 0.307 Chirality : 0.044 0.177 3873 Planarity : 0.005 0.068 4411 Dihedral : 4.304 22.606 3349 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 1.42 % Allowed : 20.83 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3072 helix: 1.89 (0.21), residues: 686 sheet: 0.45 (0.21), residues: 588 loop : -1.88 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.017 0.001 PHE C 562 TYR 0.018 0.001 TYR C 279 ARG 0.018 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7127.20 seconds wall clock time: 129 minutes 51.40 seconds (7791.40 seconds total)