Starting phenix.real_space_refine on Tue Mar 19 08:05:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyq_23599/03_2024/7lyq_23599.pdb" } resolution = 3.34 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= 0.064 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 103 5.16 5 C 15097 2.51 5 N 3887 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23641 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7713 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 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: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 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 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" 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 Time building chain proxies: 12.49, per 1000 atoms: 0.53 Number of scatterers: 23641 At special positions: 0 Unit cell: (129.349, 134.694, 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 103 16.00 O 4554 8.00 N 3887 7.00 C 15097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.02 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 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B 801 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " 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 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " Time building additional restraints: 9.12 Conformation dependent library (CDL) restraints added in 4.2 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 46 sheets defined 27.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.749A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.867A 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 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.906A 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: 3.837A 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: 3.929A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.577A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.023A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.679A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.304A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.639A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.474A 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 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.981A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.897A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.613A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) 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: 3.535A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.661A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 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: 3.696A 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: 4.778A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.789A 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 616 through 620 removed outlier: 3.522A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.726A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.632A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.644A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.516A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.670A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.680A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.378A 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: 8.658A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.748A 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: 3.590A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.732A 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: 3.628A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.715A 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: 5.369A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.425A 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 328 removed outlier: 6.053A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.510A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.510A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.826A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.784A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.495A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.197A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.695A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.658A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.794A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.873A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.313A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.886A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.587A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.955A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.546A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LYS C 790 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.914A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.914A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.510A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.258A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.608A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.847A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.515A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.899A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.669A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.431A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.431A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.849A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 9.98 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: 6023 1.33 - 1.46: 4721 1.46 - 1.58: 13289 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24160 Sorted by residual: bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG B1314 " pdb=" O5 NAG B1314 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 24155 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.20: 302 104.20 - 111.95: 10004 111.95 - 119.69: 10173 119.69 - 127.44: 12271 127.44 - 135.19: 138 Bond angle restraints: 32888 Sorted by residual: angle pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 angle pdb=" CA PHE C 565 " pdb=" CB PHE C 565 " pdb=" CG PHE C 565 " ideal model delta sigma weight residual 113.80 119.71 -5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N ASN B 137 " pdb=" CA ASN B 137 " pdb=" C ASN B 137 " ideal model delta sigma weight residual 111.36 117.70 -6.34 1.09e+00 8.42e-01 3.39e+01 angle pdb=" CA ASP B 568 " pdb=" CB ASP B 568 " pdb=" CG ASP B 568 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 119.29 -5.49 1.00e+00 1.00e+00 3.01e+01 ... (remaining 32883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13844 17.87 - 35.75: 798 35.75 - 53.62: 124 53.62 - 71.50: 49 71.50 - 89.37: 26 Dihedral angle restraints: 14841 sinusoidal: 6168 harmonic: 8673 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 -171.19 85.19 1 1.00e+01 1.00e-02 8.80e+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 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA PRO A 479 " pdb=" C PRO A 479 " pdb=" N CYS A 480 " pdb=" CA CYS A 480 " ideal model delta harmonic sigma weight residual 180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 3871 0.276 - 0.552: 15 0.552 - 0.828: 0 0.828 - 1.104: 0 1.104 - 1.380: 2 Chirality restraints: 3888 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.75e+01 chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 3885 not shown) Planarity restraints: 4229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.131 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN B 122 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.228 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " 0.130 2.00e-02 2.50e+03 1.43e-01 2.54e+02 pdb=" CG ASN A 122 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " -0.126 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" CG ASN C 709 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " 0.219 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " -0.166 2.00e-02 2.50e+03 ... (remaining 4226 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 11790 3.00 - 3.47: 22714 3.47 - 3.95: 38864 3.95 - 4.42: 42677 4.42 - 4.90: 72907 Nonbonded interactions: 188952 Sorted by model distance: nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.521 2.440 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.526 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.541 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.548 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.550 2.440 ... (remaining 188947 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 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 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 through 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 or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 812 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 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 or resid 1301 through 1311)) 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 130 or (resid 131 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 164 or resid 166 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 190 or (resid 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 192 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 241 or (resid 242 through 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 n \ ame CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 \ and (name N or name CA or name C or name O or name CB )) or resid 569 through 58 \ 2 or (resid 583 and (name N or name CA or name C or name O or name CB )) or resi \ d 584 through 585 or (resid 586 and (name N or name CA or name C or name O or na \ me 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 690 through 744 or (r \ esid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 t \ hrough 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 nam \ e O or name CB )) or resid 812 through 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 or name C \ or name O or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147 or resid \ 1301 through 1311)) 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 130 or (resid 131 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 143 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 195 or (resid 196 through 197 and (name N or name CA or name C or name O \ or name CB )) or resid 198 through 213 or (resid 214 and (name N or name CA or \ name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) o \ r resid 310 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 name O or name CB )) or resid 584 through 585 or (resi \ d 586 and (name N or name CA or name C or name O or name CB )) or resid 587 thro \ ugh 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) o \ r 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 o \ r 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 or name CA or name C or name O or name CB )) or resid \ 1147 or resid 1301 through 1311)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 7.110 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 63.750 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.077 24160 Z= 0.864 Angle : 1.742 12.378 32888 Z= 1.170 Chirality : 0.099 1.380 3888 Planarity : 0.013 0.139 4191 Dihedral : 12.672 89.369 9147 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.21 % Favored : 94.35 % Rotamer: Outliers : 0.43 % Allowed : 1.80 % Favored : 97.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 2937 helix: -0.86 (0.17), residues: 698 sheet: 0.60 (0.22), residues: 495 loop : -0.73 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.156 0.024 TRP A 64 HIS 0.010 0.003 HIS C1058 PHE 0.087 0.011 PHE A 718 TYR 0.168 0.019 TYR B 707 ARG 0.010 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6667 (tttt) cc_final: 0.6122 (tppt) REVERT: A 820 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7629 (t0) REVERT: A 902 MET cc_start: 0.8997 (mmm) cc_final: 0.8749 (mmm) REVERT: B 100 ILE cc_start: 0.8254 (mt) cc_final: 0.7878 (mm) REVERT: B 102 ARG cc_start: 0.6127 (mmp-170) cc_final: 0.5790 (mmp-170) REVERT: B 572 THR cc_start: 0.8026 (m) cc_final: 0.6899 (m) REVERT: B 574 ASP cc_start: 0.8205 (p0) cc_final: 0.7122 (m-30) REVERT: B 587 ILE cc_start: 0.8181 (mt) cc_final: 0.7652 (pt) REVERT: B 816 SER cc_start: 0.9200 (p) cc_final: 0.8779 (t) REVERT: B 820 ASP cc_start: 0.7822 (t70) cc_final: 0.7574 (t0) REVERT: B 988 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 190 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6548 (mmm160) REVERT: C 421 TYR cc_start: 0.7580 (m-80) cc_final: 0.7246 (m-80) REVERT: C 473 TYR cc_start: 0.7448 (t80) cc_final: 0.7202 (t80) REVERT: C 490 PHE cc_start: 0.7671 (t80) cc_final: 0.7003 (t80) REVERT: C 816 SER cc_start: 0.9218 (p) cc_final: 0.8983 (t) outliers start: 11 outliers final: 4 residues processed: 359 average time/residue: 0.3746 time to fit residues: 206.6645 Evaluate side-chains 161 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.5980 chunk 225 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A1048 HIS B 354 ASN B 907 ASN B1119 ASN C 165 ASN C 460 ASN C 506 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24160 Z= 0.193 Angle : 0.615 9.318 32888 Z= 0.330 Chirality : 0.046 0.191 3888 Planarity : 0.004 0.053 4191 Dihedral : 7.018 57.225 3996 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 1.57 % Allowed : 5.53 % Favored : 92.91 % 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: 0.18 (0.15), residues: 2937 helix: 1.25 (0.20), residues: 690 sheet: 0.35 (0.19), residues: 655 loop : -0.45 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.020 0.001 PHE A 497 TYR 0.023 0.002 TYR C 369 ARG 0.007 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 2.645 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8451 (mttt) cc_final: 0.8193 (mmtt) REVERT: A 187 LYS cc_start: 0.6569 (tttt) cc_final: 0.6155 (tppt) REVERT: A 211 ASN cc_start: 0.6519 (m-40) cc_final: 0.6242 (p0) REVERT: A 421 TYR cc_start: 0.7260 (m-80) cc_final: 0.6967 (m-10) REVERT: A 493 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7929 (tm-30) REVERT: B 102 ARG cc_start: 0.6069 (mmp-170) cc_final: 0.5510 (mmt180) REVERT: B 816 SER cc_start: 0.9004 (p) cc_final: 0.8754 (t) REVERT: B 820 ASP cc_start: 0.7589 (t70) cc_final: 0.7215 (t0) REVERT: C 403 ARG cc_start: 0.6977 (ptm160) cc_final: 0.6698 (ptm160) REVERT: C 421 TYR cc_start: 0.7482 (m-80) cc_final: 0.7244 (m-80) REVERT: C 816 SER cc_start: 0.9112 (p) cc_final: 0.8842 (p) REVERT: C 1029 MET cc_start: 0.8814 (mmt) cc_final: 0.8289 (tpt) outliers start: 40 outliers final: 27 residues processed: 222 average time/residue: 0.3344 time to fit residues: 119.8047 Evaluate side-chains 168 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN A 856 ASN B1002 GLN B1048 HIS B1135 ASN C 613 GLN C 901 GLN C 935 GLN C1005 GLN C1048 HIS C1083 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24160 Z= 0.301 Angle : 0.589 9.104 32888 Z= 0.309 Chirality : 0.046 0.226 3888 Planarity : 0.004 0.053 4191 Dihedral : 6.536 57.479 3990 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.84 % Allowed : 7.21 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2937 helix: 1.62 (0.21), residues: 672 sheet: 0.23 (0.19), residues: 663 loop : -0.49 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS B1058 PHE 0.016 0.002 PHE A 559 TYR 0.033 0.002 TYR A 369 ARG 0.006 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.7994 (tptt) cc_final: 0.7763 (tptm) REVERT: A 421 TYR cc_start: 0.7274 (m-80) cc_final: 0.6981 (m-10) REVERT: A 465 GLU cc_start: 0.7621 (tt0) cc_final: 0.7192 (tt0) REVERT: A 820 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7863 (t0) REVERT: B 102 ARG cc_start: 0.6099 (mmp-170) cc_final: 0.5629 (mmt180) REVERT: B 816 SER cc_start: 0.9056 (p) cc_final: 0.8850 (t) REVERT: B 820 ASP cc_start: 0.7674 (t70) cc_final: 0.7437 (t0) REVERT: B 1051 SER cc_start: 0.8947 (p) cc_final: 0.8651 (m) REVERT: C 34 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7920 (mmp80) REVERT: C 403 ARG cc_start: 0.7054 (ptm160) cc_final: 0.6723 (ptm160) REVERT: C 421 TYR cc_start: 0.7559 (m-80) cc_final: 0.7315 (m-80) REVERT: C 436 TRP cc_start: 0.7676 (p90) cc_final: 0.7307 (p90) REVERT: C 569 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8349 (mt) outliers start: 47 outliers final: 38 residues processed: 205 average time/residue: 0.3336 time to fit residues: 110.6517 Evaluate side-chains 188 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 207 HIS B 675 GLN B1119 ASN C 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24160 Z= 0.260 Angle : 0.547 13.457 32888 Z= 0.285 Chirality : 0.044 0.232 3888 Planarity : 0.004 0.048 4191 Dihedral : 6.263 56.586 3990 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.20 % Favored : 96.77 % Rotamer: Outliers : 2.23 % Allowed : 8.27 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2937 helix: 1.75 (0.21), residues: 675 sheet: 0.25 (0.19), residues: 680 loop : -0.48 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.021 0.001 PHE B 329 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8014 (tptt) cc_final: 0.7806 (tptm) REVERT: A 403 ARG cc_start: 0.6483 (ptm160) cc_final: 0.6043 (ptp-110) REVERT: A 421 TYR cc_start: 0.7251 (m-80) cc_final: 0.6950 (m-10) REVERT: A 492 LEU cc_start: 0.8558 (mp) cc_final: 0.8356 (tt) REVERT: B 102 ARG cc_start: 0.6054 (mmp-170) cc_final: 0.5176 (mmt180) REVERT: B 816 SER cc_start: 0.9048 (p) cc_final: 0.8842 (p) REVERT: B 820 ASP cc_start: 0.7640 (t70) cc_final: 0.7200 (t0) REVERT: C 34 ARG cc_start: 0.8189 (mmp-170) cc_final: 0.7841 (mmm160) REVERT: C 403 ARG cc_start: 0.7199 (ptm160) cc_final: 0.6931 (ptm160) REVERT: C 421 TYR cc_start: 0.7524 (m-80) cc_final: 0.7130 (m-80) REVERT: C 436 TRP cc_start: 0.7619 (p90) cc_final: 0.7279 (p90) outliers start: 57 outliers final: 44 residues processed: 214 average time/residue: 0.3065 time to fit residues: 107.5309 Evaluate side-chains 200 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 0.0670 chunk 118 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 207 HIS C 30 ASN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24160 Z= 0.224 Angle : 0.525 12.062 32888 Z= 0.272 Chirality : 0.044 0.235 3888 Planarity : 0.003 0.045 4191 Dihedral : 5.982 55.903 3988 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 9.29 % Favored : 88.56 % 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: 0.36 (0.15), residues: 2937 helix: 1.86 (0.21), residues: 672 sheet: 0.31 (0.19), residues: 687 loop : -0.48 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.028 0.001 PHE B 329 TYR 0.026 0.001 TYR A 369 ARG 0.003 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8023 (tptt) cc_final: 0.7814 (tptm) REVERT: A 383 SER cc_start: 0.8549 (t) cc_final: 0.8158 (p) REVERT: A 403 ARG cc_start: 0.6378 (ptm160) cc_final: 0.5995 (ptp-110) REVERT: A 492 LEU cc_start: 0.8587 (mp) cc_final: 0.8353 (tt) REVERT: B 95 THR cc_start: 0.7624 (p) cc_final: 0.7311 (t) REVERT: B 102 ARG cc_start: 0.6090 (mmp-170) cc_final: 0.5451 (mmt180) REVERT: B 572 THR cc_start: 0.8581 (m) cc_final: 0.8306 (p) REVERT: B 1051 SER cc_start: 0.8952 (p) cc_final: 0.8535 (m) REVERT: C 351 TYR cc_start: 0.8624 (p90) cc_final: 0.8183 (p90) REVERT: C 403 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6965 (ptm160) REVERT: C 421 TYR cc_start: 0.7569 (m-80) cc_final: 0.7267 (m-80) REVERT: C 436 TRP cc_start: 0.7647 (p90) cc_final: 0.7305 (p90) REVERT: C 985 ASP cc_start: 0.7582 (t0) cc_final: 0.6987 (t70) outliers start: 55 outliers final: 45 residues processed: 210 average time/residue: 0.3280 time to fit residues: 113.3051 Evaluate side-chains 193 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 148 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24160 Z= 0.235 Angle : 0.518 11.930 32888 Z= 0.269 Chirality : 0.044 0.239 3888 Planarity : 0.003 0.044 4191 Dihedral : 5.872 56.051 3988 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 2.55 % Allowed : 9.33 % Favored : 88.13 % 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: 2937 helix: 1.88 (0.21), residues: 672 sheet: 0.29 (0.19), residues: 680 loop : -0.50 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.023 0.001 PHE B 329 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 157 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8021 (tptt) cc_final: 0.7809 (tptm) REVERT: A 383 SER cc_start: 0.8493 (t) cc_final: 0.8161 (p) REVERT: A 403 ARG cc_start: 0.6342 (ptm160) cc_final: 0.6073 (ttm-80) REVERT: A 492 LEU cc_start: 0.8598 (mp) cc_final: 0.8307 (tt) REVERT: B 95 THR cc_start: 0.7567 (p) cc_final: 0.7243 (t) REVERT: B 102 ARG cc_start: 0.6217 (mmp-170) cc_final: 0.5601 (mmt180) REVERT: B 572 THR cc_start: 0.8612 (m) cc_final: 0.7413 (p) REVERT: B 574 ASP cc_start: 0.8336 (p0) cc_final: 0.7834 (m-30) REVERT: C 351 TYR cc_start: 0.8521 (p90) cc_final: 0.8070 (p90) REVERT: C 403 ARG cc_start: 0.7232 (ptm160) cc_final: 0.6972 (ptm160) REVERT: C 436 TRP cc_start: 0.7743 (p90) cc_final: 0.7535 (p90) outliers start: 65 outliers final: 52 residues processed: 206 average time/residue: 0.3098 time to fit residues: 104.9990 Evaluate side-chains 197 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 145 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1128 VAL 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: 0.8980 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 0.0030 chunk 160 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 907 ASN C 49 HIS C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 24160 Z= 0.143 Angle : 0.480 11.680 32888 Z= 0.250 Chirality : 0.043 0.226 3888 Planarity : 0.003 0.041 4191 Dihedral : 5.611 55.741 3988 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.00 % Allowed : 9.91 % Favored : 88.09 % 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: 0.49 (0.15), residues: 2937 helix: 2.12 (0.21), residues: 665 sheet: 0.30 (0.19), residues: 683 loop : -0.41 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.000 HIS C 207 PHE 0.021 0.001 PHE B 329 TYR 0.020 0.001 TYR A 369 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 165 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8027 (tptt) cc_final: 0.7819 (tptm) REVERT: A 383 SER cc_start: 0.8479 (t) cc_final: 0.8151 (p) REVERT: A 403 ARG cc_start: 0.6339 (ptm160) cc_final: 0.5841 (ptp-110) REVERT: A 492 LEU cc_start: 0.8580 (mp) cc_final: 0.8282 (tt) REVERT: B 95 THR cc_start: 0.7497 (p) cc_final: 0.7179 (t) REVERT: B 102 ARG cc_start: 0.6133 (mmp-170) cc_final: 0.5503 (mmt180) REVERT: B 572 THR cc_start: 0.8670 (m) cc_final: 0.7558 (p) REVERT: B 574 ASP cc_start: 0.8288 (p0) cc_final: 0.7965 (m-30) REVERT: C 351 TYR cc_start: 0.8504 (p90) cc_final: 0.8123 (p90) REVERT: C 979 ASP cc_start: 0.7252 (t0) cc_final: 0.6929 (t0) REVERT: C 985 ASP cc_start: 0.7510 (t0) cc_final: 0.6978 (t70) outliers start: 51 outliers final: 42 residues processed: 204 average time/residue: 0.3364 time to fit residues: 113.5119 Evaluate side-chains 192 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN B 207 HIS B 907 ASN B1002 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24160 Z= 0.229 Angle : 0.509 11.458 32888 Z= 0.263 Chirality : 0.043 0.239 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.643 56.153 3988 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 2.23 % Allowed : 10.15 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.15), residues: 2937 helix: 2.07 (0.21), residues: 660 sheet: 0.28 (0.19), residues: 682 loop : -0.42 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.004 0.001 HIS C 207 PHE 0.021 0.001 PHE B 329 TYR 0.025 0.001 TYR C 421 ARG 0.004 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 150 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8024 (tptt) cc_final: 0.7817 (tptm) REVERT: A 383 SER cc_start: 0.8503 (t) cc_final: 0.8157 (p) REVERT: A 403 ARG cc_start: 0.6293 (ptm160) cc_final: 0.5861 (ptp-110) REVERT: B 95 THR cc_start: 0.7454 (p) cc_final: 0.7100 (t) REVERT: B 102 ARG cc_start: 0.6170 (mmp-170) cc_final: 0.5603 (mmt180) REVERT: B 572 THR cc_start: 0.8661 (m) cc_final: 0.7538 (p) REVERT: B 574 ASP cc_start: 0.8332 (p0) cc_final: 0.8095 (m-30) REVERT: C 351 TYR cc_start: 0.8501 (p90) cc_final: 0.8074 (p90) REVERT: C 985 ASP cc_start: 0.7471 (t0) cc_final: 0.6867 (t70) outliers start: 57 outliers final: 52 residues processed: 192 average time/residue: 0.3232 time to fit residues: 102.4531 Evaluate side-chains 199 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 252 optimal weight: 0.0470 chunk 265 optimal weight: 0.8980 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN B 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24160 Z= 0.188 Angle : 0.494 11.297 32888 Z= 0.256 Chirality : 0.043 0.233 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.561 55.805 3988 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.27 % Allowed : 10.27 % Favored : 87.46 % 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: 0.48 (0.15), residues: 2937 helix: 2.17 (0.21), residues: 655 sheet: 0.28 (0.19), residues: 681 loop : -0.42 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS C 207 PHE 0.020 0.001 PHE B 329 TYR 0.022 0.001 TYR C 421 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8027 (tptt) cc_final: 0.7823 (tptm) REVERT: A 383 SER cc_start: 0.8493 (t) cc_final: 0.8153 (p) REVERT: A 403 ARG cc_start: 0.6265 (ptm160) cc_final: 0.5891 (ptp-110) REVERT: B 95 THR cc_start: 0.7335 (p) cc_final: 0.6946 (t) REVERT: B 102 ARG cc_start: 0.6185 (mmp-170) cc_final: 0.5403 (mmt180) REVERT: B 572 THR cc_start: 0.8678 (m) cc_final: 0.7571 (p) REVERT: C 351 TYR cc_start: 0.8495 (p90) cc_final: 0.8028 (p90) REVERT: C 490 PHE cc_start: 0.8161 (t80) cc_final: 0.7773 (t80) outliers start: 58 outliers final: 56 residues processed: 196 average time/residue: 0.3229 time to fit residues: 103.4886 Evaluate side-chains 198 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.2980 chunk 282 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 196 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 235 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24160 Z= 0.130 Angle : 0.477 11.190 32888 Z= 0.247 Chirality : 0.042 0.222 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.385 55.660 3988 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.80 % Allowed : 10.74 % Favored : 87.46 % 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: 0.60 (0.16), residues: 2937 helix: 2.30 (0.21), residues: 657 sheet: 0.33 (0.19), residues: 669 loop : -0.35 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.000 HIS C 207 PHE 0.020 0.001 PHE B 329 TYR 0.022 0.001 TYR C 421 ARG 0.005 0.000 ARG A 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8044 (tptt) cc_final: 0.7844 (tptm) REVERT: A 383 SER cc_start: 0.8491 (t) cc_final: 0.8139 (p) REVERT: A 403 ARG cc_start: 0.6215 (ptm160) cc_final: 0.5840 (ptp-110) REVERT: A 465 GLU cc_start: 0.7134 (tt0) cc_final: 0.6815 (tt0) REVERT: A 529 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8097 (ptmm) REVERT: B 95 THR cc_start: 0.7417 (p) cc_final: 0.7026 (t) REVERT: B 102 ARG cc_start: 0.6189 (mmp-170) cc_final: 0.5623 (mmt180) REVERT: C 351 TYR cc_start: 0.8394 (p90) cc_final: 0.7888 (p90) REVERT: C 490 PHE cc_start: 0.8149 (t80) cc_final: 0.7761 (t80) REVERT: C 979 ASP cc_start: 0.7293 (t0) cc_final: 0.7024 (t0) outliers start: 46 outliers final: 43 residues processed: 191 average time/residue: 0.3484 time to fit residues: 110.1987 Evaluate side-chains 191 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 235 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113527 restraints weight = 37973.540| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.80 r_work: 0.3177 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24160 Z= 0.218 Angle : 0.498 11.158 32888 Z= 0.257 Chirality : 0.043 0.233 3888 Planarity : 0.003 0.040 4191 Dihedral : 5.458 55.927 3988 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 10.93 % Favored : 87.03 % 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: 2937 helix: 2.18 (0.21), residues: 656 sheet: 0.30 (0.19), residues: 673 loop : -0.39 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.003 0.001 HIS C 207 PHE 0.020 0.001 PHE B 329 TYR 0.024 0.001 TYR A 369 ARG 0.004 0.000 ARG A 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.31 seconds wall clock time: 84 minutes 11.99 seconds (5051.99 seconds total)