Starting phenix.real_space_refine on Tue Mar 19 06:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyk_23593/03_2024/7lyk_23593.pdb" } resolution = 3.65 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= 0.048 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 105 5.16 5 C 14979 2.51 5 N 3866 2.21 5 O 4494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7705 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 7705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7705 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 11.72, per 1000 atoms: 0.50 Number of scatterers: 23444 At special positions: 0 Unit cell: (132.556, 133.625, 194.558, 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 105 16.00 O 4494 8.00 N 3866 7.00 C 14979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.01 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 4.0 seconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5576 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 27.1% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.710A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.131A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.517A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.636A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.521A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 4.262A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.031A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.935A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.838A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A 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 758 through 783 removed outlier: 4.075A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.627A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.836A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.544A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.533A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.561A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.836A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 3.909A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.214A pdb=" N VAL B 991 " --> pdb=" O VAL 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 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.031A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.531A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.537A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.427A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.847A 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 866 through 885 removed outlier: 3.844A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.573A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.846A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.662A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.645A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.582A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.681A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.818A 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: 3.812A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.632A 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 319 removed outlier: 5.302A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.168A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.168A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.869A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.123A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 657 removed outlier: 6.047A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.184A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.196A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.997A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.662A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.507A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.198A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.779A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.921A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.103A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.851A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 720 removed outlier: 3.688A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.806A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.714A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.209A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.198A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.557A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 1002 hydrogen bonds defined for protein. 2682 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: 9.97 Time building geometry restraints manager: 9.40 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: 6675 1.34 - 1.46: 4078 1.46 - 1.58: 13077 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 23959 Sorted by residual: bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C5 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C5 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.413 1.485 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 23954 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.47: 315 104.47 - 112.16: 10386 112.16 - 119.85: 10242 119.85 - 127.55: 11524 127.55 - 135.24: 144 Bond angle restraints: 32611 Sorted by residual: angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.35 -6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.30e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.37 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA PHE A 342 " pdb=" CB PHE A 342 " pdb=" CG PHE A 342 " ideal model delta sigma weight residual 113.80 119.27 -5.47 1.00e+00 1.00e+00 3.00e+01 angle pdb=" OE1 GLN B1106 " pdb=" CD GLN B1106 " pdb=" NE2 GLN B1106 " ideal model delta sigma weight residual 122.60 117.14 5.46 1.00e+00 1.00e+00 2.98e+01 ... (remaining 32606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13561 17.92 - 35.83: 790 35.83 - 53.75: 133 53.75 - 71.67: 48 71.67 - 89.59: 23 Dihedral angle restraints: 14555 sinusoidal: 5890 harmonic: 8665 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.65 82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.95 76.95 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -151.68 65.68 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 14552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2813 0.104 - 0.208: 910 0.208 - 0.312: 88 0.312 - 0.415: 6 0.415 - 0.519: 2 Chirality restraints: 3819 Sorted by residual: chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CA ASN A 657 " pdb=" N ASN A 657 " pdb=" C ASN A 657 " pdb=" CB ASN A 657 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG B1107 " pdb=" N ARG B1107 " pdb=" C ARG B1107 " pdb=" CB ARG B1107 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 3816 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " 0.336 2.00e-02 2.50e+03 1.93e-01 7.44e+02 pdb=" CG TYR C 453 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " -0.154 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " -0.141 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " -0.108 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " -0.141 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " -0.211 2.00e-02 2.50e+03 1.19e-01 2.83e+02 pdb=" CG TYR B 453 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " 0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.169 2.00e-02 2.50e+03 8.69e-02 1.89e+02 pdb=" CG TRP C 886 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.085 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.121 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.100 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 11096 2.97 - 3.46: 22868 3.46 - 3.94: 38762 3.94 - 4.42: 42467 4.42 - 4.90: 72978 Nonbonded interactions: 188171 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.493 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.497 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.520 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.525 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.532 2.440 ... (remaining 188166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 676 or resid 690 through 744 or (resid 745 and ( \ name N or name CA or name C or name O or name CB )) or resid 746 through 747 or \ (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 749 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 11 \ 47 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (name \ N or name CA or name C or name O or name CB )) or resid 192 through 241 or (resi \ d 242 through 264 and (name N or name CA or name C or name O or name CB )) or re \ sid 265 through 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 676 or resid 690 through 744 or (resid 745 and ( \ name N or name CA or name C or name O or name CB )) or resid 746 through 747 or \ (resid 748 and (name N or name CA or name C or name O or name CB )) or resid 749 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 11 \ 47 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 143 or (re \ sid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 th \ rough 196 or (resid 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 213 or (resid 214 and (name N or name CA or name C or name \ O or name CB )) or resid 215 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 238 or (resid 239 and (nam \ e N or name CA or name C or name O or name CB )) or resid 240 through 308 or (re \ sid 309 and (name N or name CA or name C or name O or name CB )) or resid 310 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 811 or resid 813 through 1141 or (resid 1142 and (name N o \ r name CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid \ 1145 through 1146 and (name N or name CA or name C or name O or name CB )) or r \ esid 1147 or resid 1301 through 1308)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.960 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 61.290 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.013 0.077 23959 Z= 0.849 Angle : 1.734 10.977 32611 Z= 1.167 Chirality : 0.093 0.519 3819 Planarity : 0.014 0.193 4175 Dihedral : 12.835 89.585 8862 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.97 % Favored : 93.72 % Rotamer: Outliers : 0.35 % Allowed : 3.06 % Favored : 96.59 % Cbeta Deviations : 0.14 % 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: -0.98 (0.14), residues: 2931 helix: -0.72 (0.17), residues: 674 sheet: 0.28 (0.22), residues: 508 loop : -0.88 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.023 TRP C 886 HIS 0.010 0.002 HIS B1083 PHE 0.083 0.012 PHE C 718 TYR 0.336 0.023 TYR C 453 ARG 0.015 0.002 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 230 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6700 (m-80) cc_final: 0.6136 (m-10) REVERT: A 854 LYS cc_start: 0.5422 (tttt) cc_final: 0.4393 (ptmt) REVERT: A 1029 MET cc_start: 0.9144 (tpp) cc_final: 0.8717 (tpp) REVERT: B 117 LEU cc_start: 0.8534 (tp) cc_final: 0.8321 (tp) REVERT: B 168 PHE cc_start: 0.6679 (t80) cc_final: 0.6444 (t80) REVERT: B 265 TYR cc_start: 0.3964 (OUTLIER) cc_final: 0.2885 (p90) REVERT: B 1041 ASP cc_start: 0.7842 (t0) cc_final: 0.7421 (t0) REVERT: C 428 ASP cc_start: 0.8274 (p0) cc_final: 0.7450 (t70) REVERT: C 571 ASP cc_start: 0.6958 (m-30) cc_final: 0.6674 (m-30) REVERT: C 990 GLU cc_start: 0.8415 (tt0) cc_final: 0.8113 (tm-30) outliers start: 9 outliers final: 2 residues processed: 239 average time/residue: 0.3291 time to fit residues: 125.8275 Evaluate side-chains 113 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 586 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 269 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1010 GLN B 913 GLN C 957 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23959 Z= 0.182 Angle : 0.599 8.222 32611 Z= 0.322 Chirality : 0.046 0.185 3819 Planarity : 0.004 0.050 4175 Dihedral : 6.710 57.828 3713 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 1.57 % Allowed : 5.76 % Favored : 92.67 % 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: 0.01 (0.15), residues: 2931 helix: 1.17 (0.20), residues: 653 sheet: 0.12 (0.18), residues: 691 loop : -0.50 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.004 0.001 HIS C 655 PHE 0.033 0.002 PHE A 168 TYR 0.022 0.002 TYR B 265 ARG 0.006 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 2.625 Fit side-chains REVERT: A 133 PHE cc_start: 0.6344 (m-80) cc_final: 0.5955 (m-10) REVERT: A 1031 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: B 975 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8030 (m) REVERT: B 1029 MET cc_start: 0.9084 (tpp) cc_final: 0.8813 (tpp) REVERT: B 1041 ASP cc_start: 0.7919 (t0) cc_final: 0.7600 (t0) REVERT: C 428 ASP cc_start: 0.8440 (p0) cc_final: 0.7937 (m-30) outliers start: 40 outliers final: 17 residues processed: 150 average time/residue: 0.3220 time to fit residues: 80.5663 Evaluate side-chains 97 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 224 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 901 GLN A 913 GLN A 957 GLN B1048 HIS C 519 HIS C 901 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 23959 Z= 0.459 Angle : 0.680 13.888 32611 Z= 0.355 Chirality : 0.048 0.223 3819 Planarity : 0.004 0.051 4175 Dihedral : 6.598 58.747 3709 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.04 % Allowed : 7.56 % Favored : 90.40 % 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: -0.17 (0.15), residues: 2931 helix: 0.95 (0.20), residues: 664 sheet: 0.04 (0.18), residues: 696 loop : -0.60 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 64 HIS 0.008 0.001 HIS A1064 PHE 0.026 0.002 PHE C1089 TYR 0.030 0.002 TYR A 200 ARG 0.005 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 93 time to evaluate : 2.007 Fit side-chains revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6344 (m-80) cc_final: 0.6053 (m-10) REVERT: A 854 LYS cc_start: 0.5908 (tttt) cc_final: 0.4524 (ptmt) REVERT: A 1031 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: B 560 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 1041 ASP cc_start: 0.8028 (t0) cc_final: 0.7805 (t0) REVERT: B 1127 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7123 (p0) outliers start: 52 outliers final: 28 residues processed: 135 average time/residue: 0.2830 time to fit residues: 66.3978 Evaluate side-chains 110 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 79 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 141 optimal weight: 30.0000 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 354 ASN C 955 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23959 Z= 0.179 Angle : 0.519 11.076 32611 Z= 0.274 Chirality : 0.043 0.195 3819 Planarity : 0.003 0.044 4175 Dihedral : 5.916 56.437 3709 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.53 % Allowed : 9.05 % Favored : 89.42 % 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: 0.09 (0.15), residues: 2931 helix: 1.49 (0.21), residues: 661 sheet: 0.06 (0.18), residues: 677 loop : -0.51 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 PHE 0.013 0.001 PHE B 55 TYR 0.021 0.001 TYR B 265 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 98 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6299 (m-80) cc_final: 0.6004 (m-10) REVERT: A 588 THR cc_start: 0.7949 (m) cc_final: 0.7729 (p) REVERT: A 854 LYS cc_start: 0.5876 (tttt) cc_final: 0.4437 (ptmt) REVERT: A 902 MET cc_start: 0.9296 (tpt) cc_final: 0.9031 (tpt) REVERT: A 1031 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: B 1041 ASP cc_start: 0.8024 (t0) cc_final: 0.7770 (t0) REVERT: C 212 LEU cc_start: 0.8044 (tp) cc_final: 0.7819 (tt) REVERT: C 390 LEU cc_start: 0.9414 (mt) cc_final: 0.9156 (mp) REVERT: C 562 PHE cc_start: 0.7262 (p90) cc_final: 0.7057 (p90) outliers start: 39 outliers final: 25 residues processed: 127 average time/residue: 0.2866 time to fit residues: 64.4761 Evaluate side-chains 108 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 20.0000 chunk 162 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 213 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 244 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 804 GLN B 935 GLN B 957 GLN C 388 ASN C 926 GLN C 955 ASN C 965 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23959 Z= 0.246 Angle : 0.532 9.472 32611 Z= 0.277 Chirality : 0.044 0.204 3819 Planarity : 0.003 0.040 4175 Dihedral : 5.754 55.714 3708 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.92 % Allowed : 9.37 % Favored : 88.71 % 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: 0.12 (0.15), residues: 2931 helix: 1.51 (0.21), residues: 662 sheet: 0.10 (0.19), residues: 674 loop : -0.50 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.014 0.001 PHE B1121 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6402 (m-80) cc_final: 0.6119 (m-10) REVERT: A 588 THR cc_start: 0.8212 (m) cc_final: 0.7988 (p) REVERT: A 854 LYS cc_start: 0.5950 (tttt) cc_final: 0.4523 (ptmt) REVERT: A 1029 MET cc_start: 0.8564 (tpp) cc_final: 0.8303 (ttm) REVERT: A 1031 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: B 1041 ASP cc_start: 0.8038 (t0) cc_final: 0.7785 (t0) REVERT: C 118 LEU cc_start: 0.9210 (tp) cc_final: 0.8927 (pp) REVERT: C 140 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6173 (m-80) outliers start: 49 outliers final: 35 residues processed: 130 average time/residue: 0.2740 time to fit residues: 63.4864 Evaluate side-chains 116 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 79 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.6980 chunk 258 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 287 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 133 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23959 Z= 0.182 Angle : 0.496 8.696 32611 Z= 0.258 Chirality : 0.043 0.246 3819 Planarity : 0.003 0.041 4175 Dihedral : 5.571 55.257 3708 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 1.72 % Allowed : 9.80 % Favored : 88.48 % 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: 0.22 (0.15), residues: 2931 helix: 1.66 (0.21), residues: 661 sheet: 0.17 (0.19), residues: 665 loop : -0.47 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.011 0.001 PHE B 92 TYR 0.029 0.001 TYR C 453 ARG 0.004 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6291 (m-80) cc_final: 0.6031 (m-10) REVERT: A 854 LYS cc_start: 0.5941 (tttt) cc_final: 0.4513 (ptmt) REVERT: A 1029 MET cc_start: 0.8564 (tpp) cc_final: 0.8249 (ttm) REVERT: B 226 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7073 (mm) REVERT: B 1041 ASP cc_start: 0.8025 (t0) cc_final: 0.7755 (t0) REVERT: C 118 LEU cc_start: 0.9215 (tp) cc_final: 0.8937 (pp) REVERT: C 140 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6066 (m-80) outliers start: 44 outliers final: 33 residues processed: 124 average time/residue: 0.2846 time to fit residues: 62.0280 Evaluate side-chains 113 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 286 optimal weight: 0.1980 chunk 179 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 784 GLN B 544 ASN B 935 GLN C 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23959 Z= 0.177 Angle : 0.485 7.882 32611 Z= 0.253 Chirality : 0.043 0.229 3819 Planarity : 0.003 0.041 4175 Dihedral : 5.414 55.161 3708 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 10.03 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.30 (0.15), residues: 2931 helix: 1.71 (0.21), residues: 667 sheet: 0.20 (0.19), residues: 662 loop : -0.42 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS C1048 PHE 0.017 0.001 PHE A 168 TYR 0.026 0.001 TYR C 453 ARG 0.003 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 84 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.6967 (p90) cc_final: 0.6759 (p90) REVERT: A 854 LYS cc_start: 0.5941 (tttt) cc_final: 0.4497 (ptmt) REVERT: A 1029 MET cc_start: 0.8541 (tpp) cc_final: 0.8315 (ttm) REVERT: B 1041 ASP cc_start: 0.8052 (t0) cc_final: 0.7794 (t0) REVERT: B 1127 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7395 (p0) REVERT: C 118 LEU cc_start: 0.9205 (tp) cc_final: 0.8944 (pp) REVERT: C 140 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5920 (m-80) REVERT: C 858 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7244 (pp) outliers start: 47 outliers final: 39 residues processed: 125 average time/residue: 0.2725 time to fit residues: 60.4190 Evaluate side-chains 121 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 170 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23959 Z= 0.187 Angle : 0.486 7.550 32611 Z= 0.253 Chirality : 0.043 0.221 3819 Planarity : 0.003 0.042 4175 Dihedral : 5.366 55.109 3708 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.88 % Allowed : 10.07 % Favored : 88.05 % 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: 0.32 (0.15), residues: 2931 helix: 1.72 (0.21), residues: 667 sheet: 0.25 (0.19), residues: 665 loop : -0.41 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.005 0.001 HIS C1048 PHE 0.026 0.001 PHE A 133 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 82 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6871 (m-10) cc_final: 0.6388 (m-10) REVERT: A 854 LYS cc_start: 0.6008 (tttt) cc_final: 0.4526 (ptmt) REVERT: A 1029 MET cc_start: 0.8563 (tpp) cc_final: 0.8292 (ttm) REVERT: B 697 MET cc_start: 0.7879 (ttm) cc_final: 0.7622 (ttt) REVERT: B 1041 ASP cc_start: 0.8056 (t0) cc_final: 0.7797 (t0) REVERT: B 1127 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7330 (p0) REVERT: C 118 LEU cc_start: 0.9201 (tp) cc_final: 0.8952 (pp) REVERT: C 140 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: C 858 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7287 (pp) outliers start: 48 outliers final: 39 residues processed: 124 average time/residue: 0.2875 time to fit residues: 62.9768 Evaluate side-chains 121 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 3.9990 chunk 274 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 209 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 0.0070 chunk 265 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23959 Z= 0.136 Angle : 0.468 7.444 32611 Z= 0.243 Chirality : 0.042 0.208 3819 Planarity : 0.003 0.041 4175 Dihedral : 5.210 54.825 3708 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.57 % Allowed : 10.46 % Favored : 87.97 % 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: 0.45 (0.15), residues: 2931 helix: 1.85 (0.21), residues: 667 sheet: 0.28 (0.19), residues: 664 loop : -0.33 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS C1048 PHE 0.018 0.001 PHE A 168 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 87 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6664 (m-10) cc_final: 0.6067 (m-10) REVERT: A 854 LYS cc_start: 0.5999 (tttt) cc_final: 0.4538 (ptmt) REVERT: A 1029 MET cc_start: 0.8494 (tpp) cc_final: 0.8262 (ttm) REVERT: B 697 MET cc_start: 0.7786 (ttm) cc_final: 0.7535 (ttt) REVERT: B 1041 ASP cc_start: 0.8036 (t0) cc_final: 0.7789 (t0) REVERT: C 118 LEU cc_start: 0.9199 (tp) cc_final: 0.8965 (pp) REVERT: C 140 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: C 858 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7245 (pp) REVERT: C 1029 MET cc_start: 0.8893 (tpp) cc_final: 0.8356 (ttm) outliers start: 40 outliers final: 34 residues processed: 122 average time/residue: 0.2867 time to fit residues: 62.2287 Evaluate side-chains 115 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 79 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23959 Z= 0.221 Angle : 0.493 6.965 32611 Z= 0.255 Chirality : 0.043 0.214 3819 Planarity : 0.003 0.041 4175 Dihedral : 5.269 55.167 3708 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.45 % Allowed : 10.62 % Favored : 87.93 % 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: 0.42 (0.15), residues: 2931 helix: 1.77 (0.21), residues: 673 sheet: 0.31 (0.19), residues: 668 loop : -0.34 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.006 0.001 HIS C1048 PHE 0.016 0.001 PHE A 133 TYR 0.021 0.001 TYR C 904 ARG 0.002 0.000 ARG A 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 83 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6736 (m-10) cc_final: 0.6137 (m-10) REVERT: A 854 LYS cc_start: 0.6032 (tttt) cc_final: 0.4548 (ptmt) REVERT: A 1029 MET cc_start: 0.8586 (tpp) cc_final: 0.8276 (ttm) REVERT: B 697 MET cc_start: 0.7879 (ttm) cc_final: 0.7630 (ttt) REVERT: B 1041 ASP cc_start: 0.8065 (t0) cc_final: 0.7812 (t0) REVERT: C 118 LEU cc_start: 0.9195 (tp) cc_final: 0.8973 (pp) REVERT: C 140 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: C 858 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7260 (pp) REVERT: C 900 MET cc_start: 0.8305 (mtm) cc_final: 0.7874 (mtm) REVERT: C 1029 MET cc_start: 0.8871 (tpp) cc_final: 0.8386 (ttm) outliers start: 37 outliers final: 33 residues processed: 115 average time/residue: 0.2735 time to fit residues: 55.8748 Evaluate side-chains 114 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 79 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 chunk 34 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN C 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.133260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085557 restraints weight = 54963.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087850 restraints weight = 29844.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089634 restraints weight = 20581.374| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23959 Z= 0.264 Angle : 0.515 7.453 32611 Z= 0.265 Chirality : 0.043 0.226 3819 Planarity : 0.003 0.040 4175 Dihedral : 5.379 55.370 3708 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.49 % Allowed : 10.66 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.35 (0.15), residues: 2931 helix: 1.65 (0.21), residues: 679 sheet: 0.30 (0.19), residues: 674 loop : -0.38 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.008 0.001 HIS C1048 PHE 0.018 0.001 PHE B 392 TYR 0.021 0.001 TYR C 501 ARG 0.002 0.000 ARG A 995 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3390.63 seconds wall clock time: 63 minutes 16.84 seconds (3796.84 seconds total)