Starting phenix.real_space_refine on Tue Mar 19 07:14:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwv_23558/03_2024/7lwv_23558.pdb" } resolution = 3.12 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= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 15055 2.51 5 N 3879 2.21 5 O 4526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23561 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7694 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7710 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 46, 'TRANS': 948} Chain breaks: 8 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 51 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': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7681 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 46, 'TRANS': 945} Chain breaks: 8 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 12.34, per 1000 atoms: 0.52 Number of scatterers: 23561 At special positions: 0 Unit cell: (128.28, 135.763, 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 101 16.00 O 4526 8.00 N 3879 7.00 C 15055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 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=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1134 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 234 " Time building additional restraints: 9.06 Conformation dependent library (CDL) restraints added in 4.1 seconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 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: 69 helices and 45 sheets defined 26.8% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.572A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.669A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.878A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.315A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.810A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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: 3.989A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.830A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.684A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.536A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.257A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.237A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.955A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.799A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.861A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.501A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.044A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.548A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.108A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.141A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.406A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.747A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.836A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.851A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.619A 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 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.883A 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 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.843A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.513A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.520A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.538A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.799A 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 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.521A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.817A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.898A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.763A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.772A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.817A 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: 3.864A 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: 5.405A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.414A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.735A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.705A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 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 654 through 655 removed outlier: 6.088A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.739A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 728 removed outlier: 6.127A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.649A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.807A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.862A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.952A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.631A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.424A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.787A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.245A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.827A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.456A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.650A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.511A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.455A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.661A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.19 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6227 1.33 - 1.46: 4529 1.46 - 1.58: 13194 1.58 - 1.70: 0 1.70 - 1.83: 125 Bond restraints: 24075 Sorted by residual: bond pdb=" C5 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 24070 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.73: 352 104.73 - 112.40: 10648 112.40 - 120.06: 11397 120.06 - 127.73: 10250 127.73 - 135.39: 116 Bond angle restraints: 32763 Sorted by residual: angle pdb=" CA ASP C 570 " pdb=" CB ASP C 570 " pdb=" CG ASP C 570 " ideal model delta sigma weight residual 112.60 121.02 -8.42 1.00e+00 1.00e+00 7.10e+01 angle pdb=" OE1 GLN A1106 " pdb=" CD GLN A1106 " pdb=" NE2 GLN A1106 " ideal model delta sigma weight residual 122.60 116.17 6.43 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 119.03 -6.43 1.00e+00 1.00e+00 4.14e+01 angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 133.17 -11.63 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 32758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 13763 17.68 - 35.37: 762 35.37 - 53.05: 139 53.05 - 70.73: 44 70.73 - 88.42: 25 Dihedral angle restraints: 14733 sinusoidal: 6073 harmonic: 8660 Sorted by residual: 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 -168.55 82.55 1 1.00e+01 1.00e-02 8.36e+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 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+01 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 -161.02 75.02 1 1.00e+01 1.00e-02 7.12e+01 ... (remaining 14730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.274: 3835 0.274 - 0.549: 25 0.549 - 0.823: 0 0.823 - 1.098: 0 1.098 - 1.372: 3 Chirality restraints: 3863 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.71e+01 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.58e+01 ... (remaining 3860 not shown) Planarity restraints: 4211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " 0.228 2.00e-02 2.50e+03 1.20e-01 3.58e+02 pdb=" CG TRP C 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.096 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.163 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.149 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " -0.133 2.00e-02 2.50e+03 1.43e-01 2.54e+02 pdb=" CG ASN C 282 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.094 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" CG ASN A 234 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.158 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.123 2.00e-02 2.50e+03 ... (remaining 4208 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11052 2.99 - 3.47: 21962 3.47 - 3.94: 38354 3.94 - 4.42: 42515 4.42 - 4.90: 73386 Nonbonded interactions: 187269 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.513 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.525 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.530 2.440 nonbonded pdb=" OG SER A 975 " pdb=" OD2 ASP C 571 " model vdw 2.531 2.440 ... (remaining 187264 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 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name 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 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 through 166 and (name N or name CA or name C or name \ O or name CB )) or resid 167 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 171 or (resid 172 and (nam \ e N or name CA or name C or name O or name CB )) or resid 186 through 190 or (re \ sid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 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 through 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O o \ r name CB )) or resid 529 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 o \ r (resid 867 through 868 and (name N or name CA or name C or name O or name CB ) \ ) or resid 869 through 1141 or (resid 1142 and (name N or name CA or name C or n \ ame 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 resid 1147 or resid 1301 \ through 1310)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N o \ r name CA or name C or name O or name CB )) or resid 139 through 164 or (resid 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 195 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 241 or (resid 242 t \ hrough 264 and (name N or name CA or name C or name O or name CB )) or resid 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 479 or (resid 480 and (name N or name CA or name C or n \ ame O or name CB )) or resid 481 through 483 or resid 485 through 487 or (resid \ 488 and (name N or name CA or name C or name O or name CB )) or resid 489 throug \ h 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) or \ resid 569 through 582 or (resid 583 and (name N or name CA or name C or name O o \ r name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or na \ me C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 676 or resid 6 \ 90 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 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 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 1091 or (resid 1092 and (name N or name CA o \ r name C or name O or name CB )) or resid 1093 through 1143 or (resid 1144 throu \ gh 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147 o \ r resid 1301 through 1310)) 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 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 134 or (resid 135 through 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 143 or (resid 165 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 through 195 or ( \ resid 196 through 197 and (name N or name CA or name C or name O or name CB )) o \ r resid 198 through 213 or (resid 214 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 217 or (resid 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 through 238 or (resid 23 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 483 or resid 485 through 487 or (resid 488 and ( \ name N or name CA or name C or name O or name CB )) or resid 489 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 \ through 567 or (resid 568 and (name N or name CA or name C or name O or name CB \ )) or resid 569 through 582 or (resid 583 and (name N or name CA or name C or n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1141 or (resid 1142 and (name N or name CA or name C \ or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N o \ r name CA or name C or name O or name CB )) or resid 1147 or resid 1301 through \ 1310)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.900 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 64.050 Find NCS groups from input model: 1.870 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 0.076 24075 Z= 0.865 Angle : 1.782 11.629 32763 Z= 1.200 Chirality : 0.101 1.372 3863 Planarity : 0.013 0.133 4177 Dihedral : 12.527 88.418 9046 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.82 % Favored : 94.87 % Rotamer: Outliers : 0.63 % Allowed : 2.20 % Favored : 97.17 % 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: -0.77 (0.14), residues: 2924 helix: -0.94 (0.17), residues: 674 sheet: 0.68 (0.21), residues: 544 loop : -0.69 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.228 0.026 TRP C 886 HIS 0.014 0.003 HIS A1048 PHE 0.067 0.012 PHE B 718 TYR 0.128 0.019 TYR B 279 ARG 0.009 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 350 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8581 (m) cc_final: 0.8277 (p) REVERT: A 427 ASP cc_start: 0.6931 (m-30) cc_final: 0.6701 (m-30) REVERT: A 776 LYS cc_start: 0.8567 (tttt) cc_final: 0.8361 (tttm) REVERT: A 1125 ASN cc_start: 0.7250 (p0) cc_final: 0.7011 (p0) REVERT: B 100 ILE cc_start: 0.8876 (mt) cc_final: 0.8618 (mt) REVERT: B 740 MET cc_start: 0.8195 (tpt) cc_final: 0.7249 (tpt) REVERT: B 1050 MET cc_start: 0.8811 (ptp) cc_final: 0.8414 (ptp) REVERT: C 28 TYR cc_start: 0.7994 (m-80) cc_final: 0.7781 (m-80) REVERT: C 1144 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7580 (mt-10) outliers start: 16 outliers final: 7 residues processed: 365 average time/residue: 0.3655 time to fit residues: 203.6395 Evaluate side-chains 201 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 343 ASN A 370 ASN A 394 ASN A 675 GLN A 856 ASN A1010 GLN B 370 ASN B 764 ASN C 188 ASN C 239 GLN C 360 ASN C 394 ASN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24075 Z= 0.192 Angle : 0.600 10.502 32763 Z= 0.322 Chirality : 0.046 0.425 3863 Planarity : 0.004 0.052 4177 Dihedral : 7.183 58.400 3900 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Rotamer: Outliers : 0.98 % Allowed : 5.98 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2924 helix: 1.58 (0.20), residues: 657 sheet: 0.69 (0.19), residues: 698 loop : -0.52 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.026 0.001 PHE C 168 TYR 0.019 0.002 TYR C 380 ARG 0.005 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7287 (OUTLIER) cc_final: 0.6792 (m-70) REVERT: A 269 TYR cc_start: 0.8486 (m-80) cc_final: 0.8260 (m-10) REVERT: A 307 THR cc_start: 0.8623 (m) cc_final: 0.8367 (p) REVERT: A 427 ASP cc_start: 0.7227 (m-30) cc_final: 0.6935 (m-30) REVERT: A 859 THR cc_start: 0.8612 (p) cc_final: 0.8307 (m) REVERT: B 697 MET cc_start: 0.8606 (ptp) cc_final: 0.8182 (ptm) REVERT: B 1050 MET cc_start: 0.8631 (ptp) cc_final: 0.8253 (ptp) REVERT: C 105 ILE cc_start: 0.8206 (mt) cc_final: 0.8002 (mt) REVERT: C 118 LEU cc_start: 0.7503 (tp) cc_final: 0.7058 (mt) REVERT: C 886 TRP cc_start: 0.7339 (p90) cc_final: 0.7097 (p90) outliers start: 25 outliers final: 10 residues processed: 238 average time/residue: 0.3136 time to fit residues: 120.5530 Evaluate side-chains 171 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 291 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 914 ASN A 969 ASN A1010 GLN A1088 HIS A1106 GLN A1119 ASN A1125 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1119 ASN C 87 ASN C 188 ASN C 207 HIS C 394 ASN C1048 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24075 Z= 0.275 Angle : 0.576 9.671 32763 Z= 0.304 Chirality : 0.047 0.401 3863 Planarity : 0.004 0.044 4177 Dihedral : 6.690 58.468 3895 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.61 % Allowed : 7.79 % Favored : 90.60 % 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: 0.39 (0.15), residues: 2924 helix: 1.76 (0.21), residues: 661 sheet: 0.62 (0.18), residues: 698 loop : -0.55 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 886 HIS 0.008 0.001 HIS A1048 PHE 0.023 0.002 PHE C 565 TYR 0.020 0.002 TYR A1067 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8488 (m-80) cc_final: 0.8241 (m-10) REVERT: A 427 ASP cc_start: 0.7236 (m-30) cc_final: 0.6971 (m-30) REVERT: B 745 ASP cc_start: 0.6467 (t0) cc_final: 0.6197 (t0) REVERT: B 1050 MET cc_start: 0.8628 (ptp) cc_final: 0.8269 (ptp) REVERT: C 105 ILE cc_start: 0.8198 (mt) cc_final: 0.7985 (mt) REVERT: C 239 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: C 369 TYR cc_start: 0.7488 (t80) cc_final: 0.7248 (t80) outliers start: 41 outliers final: 25 residues processed: 214 average time/residue: 0.3121 time to fit residues: 109.6930 Evaluate side-chains 187 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 chunk 128 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 287 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 762 GLN A 856 ASN A1010 GLN A1125 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 188 ASN C 218 GLN C 239 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24075 Z= 0.177 Angle : 0.510 8.334 32763 Z= 0.268 Chirality : 0.044 0.387 3863 Planarity : 0.003 0.038 4177 Dihedral : 6.375 55.173 3895 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 1.45 % Allowed : 8.89 % Favored : 89.66 % 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: 0.51 (0.15), residues: 2924 helix: 1.99 (0.21), residues: 671 sheet: 0.54 (0.18), residues: 721 loop : -0.49 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.005 0.001 HIS A1048 PHE 0.026 0.001 PHE C 565 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 2.671 Fit side-chains revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8461 (m-80) cc_final: 0.8156 (m-10) REVERT: A 427 ASP cc_start: 0.7199 (m-30) cc_final: 0.6931 (m-30) REVERT: A 1010 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7114 (mp-120) REVERT: B 29 THR cc_start: 0.8124 (m) cc_final: 0.7872 (m) REVERT: B 745 ASP cc_start: 0.6488 (t0) cc_final: 0.6288 (t0) REVERT: B 1050 MET cc_start: 0.8598 (ptp) cc_final: 0.8261 (ptp) REVERT: C 105 ILE cc_start: 0.8254 (mt) cc_final: 0.7972 (mt) REVERT: C 118 LEU cc_start: 0.7685 (tp) cc_final: 0.7259 (mp) REVERT: C 886 TRP cc_start: 0.7534 (p90) cc_final: 0.7003 (p90) outliers start: 37 outliers final: 22 residues processed: 202 average time/residue: 0.3321 time to fit residues: 111.1485 Evaluate side-chains 183 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A1010 GLN A1048 HIS A1119 ASN A1125 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 188 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 24075 Z= 0.524 Angle : 0.656 10.062 32763 Z= 0.342 Chirality : 0.050 0.361 3863 Planarity : 0.004 0.046 4177 Dihedral : 6.824 59.759 3895 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 9.67 % Favored : 88.12 % 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: 2924 helix: 1.42 (0.21), residues: 666 sheet: 0.37 (0.18), residues: 732 loop : -0.81 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 886 HIS 0.013 0.002 HIS A1048 PHE 0.028 0.002 PHE C 565 TYR 0.021 0.002 TYR A1067 ARG 0.004 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8538 (m-80) cc_final: 0.8236 (m-10) REVERT: A 501 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: A 747 THR cc_start: 0.8763 (m) cc_final: 0.8562 (p) REVERT: B 233 ILE cc_start: 0.7662 (tt) cc_final: 0.7202 (pt) REVERT: C 99 ASN cc_start: 0.7422 (t0) cc_final: 0.7047 (t0) outliers start: 56 outliers final: 40 residues processed: 222 average time/residue: 0.3202 time to fit residues: 117.4490 Evaluate side-chains 204 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 1098 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 238 optimal weight: 7.9990 chunk 133 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1010 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 239 GLN C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24075 Z= 0.173 Angle : 0.504 10.043 32763 Z= 0.263 Chirality : 0.044 0.365 3863 Planarity : 0.003 0.041 4177 Dihedral : 6.326 56.411 3895 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.57 % Allowed : 10.38 % 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: 0.43 (0.15), residues: 2924 helix: 1.99 (0.21), residues: 666 sheet: 0.52 (0.18), residues: 733 loop : -0.60 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS A1118 PHE 0.027 0.001 PHE C 565 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 2.802 Fit side-chains REVERT: A 207 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6885 (m-70) REVERT: A 269 TYR cc_start: 0.8475 (m-80) cc_final: 0.8161 (m-10) REVERT: A 501 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: A 855 PHE cc_start: 0.6018 (m-80) cc_final: 0.5784 (m-80) REVERT: A 856 ASN cc_start: 0.7469 (p0) cc_final: 0.7232 (p0) REVERT: B 29 THR cc_start: 0.8131 (m) cc_final: 0.7909 (m) REVERT: B 190 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7293 (mtt90) REVERT: C 886 TRP cc_start: 0.7573 (p90) cc_final: 0.7007 (p90) outliers start: 40 outliers final: 27 residues processed: 211 average time/residue: 0.3130 time to fit residues: 109.0795 Evaluate side-chains 193 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 162 optimal weight: 0.3980 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1119 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24075 Z= 0.191 Angle : 0.505 9.651 32763 Z= 0.262 Chirality : 0.044 0.360 3863 Planarity : 0.003 0.037 4177 Dihedral : 6.152 56.161 3894 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.65 % Allowed : 10.74 % Favored : 87.61 % 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: 0.51 (0.15), residues: 2924 helix: 2.11 (0.21), residues: 666 sheet: 0.55 (0.18), residues: 735 loop : -0.56 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B 66 PHE 0.022 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6864 (m-70) REVERT: A 269 TYR cc_start: 0.8455 (m-80) cc_final: 0.8118 (m-10) REVERT: A 501 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: B 190 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7278 (mtt90) REVERT: C 394 ASN cc_start: 0.6999 (m-40) cc_final: 0.6770 (m-40) REVERT: C 886 TRP cc_start: 0.7643 (p90) cc_final: 0.7161 (p90) outliers start: 42 outliers final: 34 residues processed: 208 average time/residue: 0.3230 time to fit residues: 110.4505 Evaluate side-chains 206 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 170 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 0.4980 chunk 195 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1119 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24075 Z= 0.138 Angle : 0.481 8.807 32763 Z= 0.249 Chirality : 0.043 0.358 3863 Planarity : 0.003 0.036 4177 Dihedral : 5.937 56.803 3894 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 1.38 % Allowed : 11.01 % Favored : 87.61 % 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: 0.63 (0.15), residues: 2924 helix: 2.26 (0.21), residues: 669 sheet: 0.55 (0.18), residues: 741 loop : -0.47 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.000 HIS B 66 PHE 0.027 0.001 PHE C 168 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6838 (m-70) REVERT: A 269 TYR cc_start: 0.8465 (m-80) cc_final: 0.8105 (m-10) REVERT: A 904 TYR cc_start: 0.7255 (m-10) cc_final: 0.7012 (m-10) REVERT: B 190 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7341 (mtt90) REVERT: C 886 TRP cc_start: 0.7563 (p90) cc_final: 0.7205 (p90) outliers start: 35 outliers final: 30 residues processed: 207 average time/residue: 0.3351 time to fit residues: 113.1884 Evaluate side-chains 198 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 856 ASN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 24075 Z= 0.350 Angle : 0.563 9.030 32763 Z= 0.291 Chirality : 0.047 0.341 3863 Planarity : 0.004 0.038 4177 Dihedral : 6.236 57.566 3894 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 1.85 % Allowed : 10.85 % Favored : 87.30 % 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: 0.34 (0.15), residues: 2924 helix: 1.88 (0.21), residues: 678 sheet: 0.46 (0.18), residues: 737 loop : -0.65 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.006 0.001 HIS A1048 PHE 0.023 0.002 PHE C 168 TYR 0.020 0.002 TYR A1067 ARG 0.004 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6824 (mtt180) cc_final: 0.6545 (mtt90) REVERT: A 207 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6850 (m-70) REVERT: A 269 TYR cc_start: 0.8524 (m-80) cc_final: 0.8128 (m-10) REVERT: B 190 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7247 (mtm-85) REVERT: C 886 TRP cc_start: 0.7741 (p90) cc_final: 0.7263 (p90) outliers start: 47 outliers final: 38 residues processed: 211 average time/residue: 0.3239 time to fit residues: 113.1691 Evaluate side-chains 208 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9990 chunk 282 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 181 optimal weight: 0.0770 chunk 144 optimal weight: 4.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 24075 Z= 0.156 Angle : 0.495 10.305 32763 Z= 0.256 Chirality : 0.044 0.350 3863 Planarity : 0.003 0.036 4177 Dihedral : 5.996 56.010 3894 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.26 % Allowed : 11.48 % Favored : 87.26 % 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: 0.53 (0.15), residues: 2924 helix: 2.15 (0.21), residues: 675 sheet: 0.49 (0.18), residues: 745 loop : -0.55 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 PHE 0.027 0.001 PHE C 168 TYR 0.031 0.001 TYR A 904 ARG 0.008 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6817 (m-70) REVERT: A 856 ASN cc_start: 0.7369 (p0) cc_final: 0.7119 (p0) REVERT: A 904 TYR cc_start: 0.7065 (m-10) cc_final: 0.6844 (m-10) REVERT: B 190 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7383 (mtm-85) REVERT: C 886 TRP cc_start: 0.7581 (p90) cc_final: 0.7203 (p90) outliers start: 32 outliers final: 29 residues processed: 199 average time/residue: 0.3186 time to fit residues: 104.7122 Evaluate side-chains 199 residues out of total 2604 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS 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: 7.9990 chunk 72 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 235 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.170359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140414 restraints weight = 28197.046| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.39 r_work: 0.3288 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24075 Z= 0.256 Angle : 0.523 9.891 32763 Z= 0.269 Chirality : 0.045 0.341 3863 Planarity : 0.004 0.037 4177 Dihedral : 6.061 56.409 3894 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.53 % Allowed : 11.44 % Favored : 87.02 % 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: 2924 helix: 2.01 (0.21), residues: 681 sheet: 0.45 (0.18), residues: 740 loop : -0.60 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.025 0.001 PHE C 168 TYR 0.029 0.001 TYR A 904 ARG 0.003 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4466.96 seconds wall clock time: 81 minutes 48.34 seconds (4908.34 seconds total)