Starting phenix.real_space_refine on Sun May 25 11:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.map" model { file = "/net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8khc_37240/05_2025/8khc_37240.cif" } resolution = 3.0 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= -0.004 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17304 2.51 5 N 4458 2.21 5 O 5290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27173 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7729 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 52, 'TRANS': 965} Chain breaks: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 153 Chain: "B" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7738 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 52, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 7642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7642 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 226 Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 917 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 917 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 16.38, per 1000 atoms: 0.60 Number of scatterers: 27173 At special positions: 0 Unit cell: (132.5, 152.64, 222.6, 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 121 16.00 O 5290 8.00 N 4458 7.00 C 17304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 593 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 665 " - pdb=" SG CYS A 674 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 763 " distance=2.03 Simple disulfide: pdb=" SG CYS A 746 " - pdb=" SG CYS A 752 " distance=2.03 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A1046 " distance=2.03 Simple disulfide: pdb=" SG CYS A1085 " - pdb=" SG CYS A1129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 593 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 665 " - pdb=" SG CYS B 674 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 763 " distance=2.02 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B1035 " - pdb=" SG CYS B1046 " distance=2.03 Simple disulfide: pdb=" SG CYS B1085 " - pdb=" SG CYS B1129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 593 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 665 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 763 " distance=2.03 Simple disulfide: pdb=" SG CYS C 746 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C1035 " - pdb=" SG CYS C1046 " distance=2.03 Simple disulfide: pdb=" SG CYS C1085 " - pdb=" SG CYS C1129 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 660 " " NAG A1302 " - " ASN A 334 " " NAG A1303 " - " ASN A 237 " " NAG A1304 " - " ASN A 606 " " NAG A1305 " - " ASN A1077 " " NAG A1306 " - " ASN A1137 " " NAG A1307 " - " ASN A1101 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 619 " " NAG A1310 " - " ASN A 712 " " NAG A1311 " - " ASN A 804 " " NAG A1312 " - " ASN A 285 " " NAG B1301 " - " ASN B1077 " " NAG B1302 " - " ASN B 237 " " NAG B1303 " - " ASN B 285 " " NAG B1304 " - " ASN B1101 " " NAG B1305 " - " ASN B 804 " " NAG B1306 " - " ASN B 712 " " NAG B1307 " - " ASN B 660 " " NAG B1308 " - " ASN B 619 " " NAG B1309 " - " ASN B 606 " " NAG B1310 " - " ASN B 334 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B1137 " " NAG C1301 " - " ASN C 606 " " NAG C1302 " - " ASN C 285 " " NAG C1303 " - " ASN C 660 " " NAG C1304 " - " ASN C 334 " " NAG C1305 " - " ASN C1137 " " NAG C1306 " - " ASN C 237 " " NAG C1307 " - " ASN C 712 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C1101 " " NAG C1310 " - " ASN C 804 " " NAG C1311 " - " ASN C1077 " " NAG C1312 " - " ASN C 619 " " NAG D 1 " - " ASN A 720 " " NAG E 1 " - " ASN B 720 " Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 3.5 seconds 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6560 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 52 sheets defined 21.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.512A pdb=" N GLN A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.519A pdb=" N ASN A 343 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.586A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 740 through 746 Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.627A pdb=" N ASN A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 761 through 786 removed outlier: 3.509A pdb=" N GLN A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 829 Processing helix chain 'A' and resid 869 through 888 Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 915 through 944 removed outlier: 4.282A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 939 " --> pdb=" O GLY A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 968 Processing helix chain 'A' and resid 969 through 971 No H-bonds generated for 'chain 'A' and resid 969 through 971' Processing helix chain 'A' and resid 979 through 986 Processing helix chain 'A' and resid 988 through 1036 removed outlier: 4.561A pdb=" N VAL A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1148 removed outlier: 4.045A pdb=" N GLU A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.960A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.600A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.444A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.558A pdb=" N TYR B 744 " --> pdb=" O ASP B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 786 Processing helix chain 'B' and resid 819 through 829 Processing helix chain 'B' and resid 857 through 859 No H-bonds generated for 'chain 'B' and resid 857 through 859' Processing helix chain 'B' and resid 869 through 888 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 915 through 944 removed outlier: 4.229A pdb=" N LEU B 919 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 925 " --> pdb=" O GLU B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 968 removed outlier: 4.449A pdb=" N VAL B 954 " --> pdb=" O LYS B 950 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 979 through 987 Processing helix chain 'B' and resid 988 through 1036 removed outlier: 4.837A pdb=" N VAL B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 995 " --> pdb=" O GLU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1149 removed outlier: 4.173A pdb=" N GLU B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 340 through 346 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.505A pdb=" N LEU C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 419 through 425 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.618A pdb=" N CYS C 483 " --> pdb=" O ASN C 480 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 484 " --> pdb=" O LYS C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 484' Processing helix chain 'C' and resid 740 through 747 removed outlier: 3.568A pdb=" N TYR C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 747 " --> pdb=" O MET C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.665A pdb=" N LEU C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 757 " --> pdb=" O SER C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 760 No H-bonds generated for 'chain 'C' and resid 758 through 760' Processing helix chain 'C' and resid 761 through 786 removed outlier: 3.987A pdb=" N GLN C 777 " --> pdb=" O ILE C 773 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 778 " --> pdb=" O ALA C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 829 removed outlier: 3.629A pdb=" N VAL C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 887 Processing helix chain 'C' and resid 889 through 893 Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 915 through 921 removed outlier: 4.109A pdb=" N LEU C 919 " --> pdb=" O THR C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 944 Processing helix chain 'C' and resid 948 through 968 removed outlier: 3.628A pdb=" N GLN C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 954 " --> pdb=" O LYS C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 971 No H-bonds generated for 'chain 'C' and resid 969 through 971' Processing helix chain 'C' and resid 979 through 987 Processing helix chain 'C' and resid 988 through 1037 removed outlier: 4.515A pdb=" N VAL C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN C 995 " --> pdb=" O GLU C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.104A pdb=" N ASN A 61 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR A 272 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 63 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 65 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 268 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 267 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 93 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 230 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 205 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.203A pdb=" N ASP A 290 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.736A pdb=" N ASP A 142 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.731A pdb=" N GLY A 103 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 322 removed outlier: 3.578A pdb=" N THR A 318 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 598 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN A 320 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY A 596 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 652 " --> pdb=" O TYR A 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 546 removed outlier: 3.531A pdb=" N GLY A 551 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 556 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP A 577 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE A 568 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 663 removed outlier: 6.232A pdb=" N GLU A 657 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR A 699 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL A 659 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 731 removed outlier: 6.576A pdb=" N SER A 714 " --> pdb=" O THR A1079 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1079 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 716 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A1077 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU A1075 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A1062 " --> pdb=" O ALA A1059 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR A1070 " --> pdb=" O HIS A1051 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N HIS A1051 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 731 removed outlier: 6.576A pdb=" N SER A 714 " --> pdb=" O THR A1079 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1079 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 716 " --> pdb=" O ASN A1077 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN A1077 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU A1075 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A1081 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A1098 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 736 through 738 removed outlier: 4.645A pdb=" N LYS A 736 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 791 through 793 removed outlier: 5.627A pdb=" N ILE A 791 " --> pdb=" O ASN C 706 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1123 through 1128 removed outlier: 4.700A pdb=" N ALA A1090 " --> pdb=" O SER A1126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.738A pdb=" N ASN B 61 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR B 272 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 63 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 270 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 65 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 268 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 267 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER B 205 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.121A pdb=" N ASP B 290 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.914A pdb=" N GLY B 103 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 322 removed outlier: 5.417A pdb=" N ILE B 315 " --> pdb=" O THR B 602 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B 602 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN B 317 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 600 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 319 " --> pdb=" O VAL B 598 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY B 597 " --> pdb=" O GLN B 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.637A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 465 through 467 removed outlier: 3.684A pdb=" N ARG B 466 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL F 105 " --> pdb=" O ARG B 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 542 through 544 removed outlier: 3.584A pdb=" N GLY B 551 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP B 577 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY B 569 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 657 through 658 removed outlier: 6.137A pdb=" N GLU B 657 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 699 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 673 " --> pdb=" O ILE B 669 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 704 through 707 removed outlier: 6.792A pdb=" N ALA B 704 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LYS C 793 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASN B 706 " --> pdb=" O LYS C 793 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 731 removed outlier: 6.566A pdb=" N SER B 714 " --> pdb=" O THR B1079 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1079 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 716 " --> pdb=" O ASN B1077 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN B1077 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU B1075 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B1062 " --> pdb=" O ALA B1059 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TYR B1070 " --> pdb=" O HIS B1051 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N HIS B1051 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 731 removed outlier: 6.566A pdb=" N SER B 714 " --> pdb=" O THR B1079 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B1079 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA B 716 " --> pdb=" O ASN B1077 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN B1077 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU B1075 " --> pdb=" O PRO B 718 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B1079 " --> pdb=" O SER B1100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 736 through 739 removed outlier: 4.198A pdb=" N LYS B 736 " --> pdb=" O LEU B 864 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1123 through 1128 removed outlier: 4.768A pdb=" N ALA B1090 " --> pdb=" O SER B1126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.965A pdb=" N ASN C 61 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR C 272 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER C 205 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.974A pdb=" N ASP C 290 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.131A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 314 through 322 removed outlier: 5.499A pdb=" N ILE C 315 " --> pdb=" O THR C 602 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR C 602 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN C 317 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C 600 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 319 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY C 597 " --> pdb=" O GLN C 616 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS C 652 " --> pdb=" O TYR C 615 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 328 through 331 removed outlier: 3.634A pdb=" N GLY C 551 " --> pdb=" O PHE C 544 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 556 " --> pdb=" O ASP C 589 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 589 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.267A pdb=" N VAL C 398 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 517 " --> pdb=" O TYR C 399 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 401 " --> pdb=" O VAL C 515 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C 438 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.267A pdb=" N VAL C 398 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 517 " --> pdb=" O TYR C 399 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 401 " --> pdb=" O VAL C 515 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.616A pdb=" N CYS C 364 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 455 through 457 Processing sheet with id=AE4, first strand: chain 'C' and resid 657 through 658 removed outlier: 6.274A pdb=" N GLU C 657 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N THR C 699 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 673 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 714 through 731 removed outlier: 6.721A pdb=" N SER C 714 " --> pdb=" O THR C1079 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C1079 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 716 " --> pdb=" O ASN C1077 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C1077 " --> pdb=" O ALA C 716 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C1075 " --> pdb=" O PRO C 718 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C1070 " --> pdb=" O HIS C1051 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N HIS C1051 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 736 through 739 removed outlier: 4.494A pdb=" N LYS C 736 " --> pdb=" O LEU C 864 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1123 through 1125 Processing sheet with id=AE8, first strand: chain 'C' and resid 1097 through 1099 Processing sheet with id=AE9, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.334A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE F 82 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.676A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.094A pdb=" N GLN G 36 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU G 45 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.883A pdb=" N LEU H 18 " --> pdb=" O MET H 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 82 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 45 through 52 removed outlier: 6.888A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA H 94 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL H 123 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.711A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 18 through 23 1069 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.99 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8632 1.34 - 1.46: 6626 1.46 - 1.58: 12312 1.58 - 1.71: 2 1.71 - 1.83: 154 Bond restraints: 27726 Sorted by residual: bond pdb=" CB PRO C 415 " pdb=" CG PRO C 415 " ideal model delta sigma weight residual 1.492 1.637 -0.145 5.00e-02 4.00e+02 8.42e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" CB PRO B 39 " pdb=" CG PRO B 39 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.83e+00 bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 27721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 37352 2.31 - 4.61: 445 4.61 - 6.92: 35 6.92 - 9.23: 3 9.23 - 11.53: 1 Bond angle restraints: 37836 Sorted by residual: angle pdb=" CA PRO C 415 " pdb=" N PRO C 415 " pdb=" CD PRO C 415 " ideal model delta sigma weight residual 112.00 100.47 11.53 1.40e+00 5.10e-01 6.78e+01 angle pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" CD PRO B 39 " ideal model delta sigma weight residual 112.00 106.29 5.71 1.40e+00 5.10e-01 1.67e+01 angle pdb=" CA LYS B 41 " pdb=" CB LYS B 41 " pdb=" CG LYS B 41 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N GLU B 340 " pdb=" CA GLU B 340 " pdb=" C GLU B 340 " ideal model delta sigma weight residual 111.28 115.00 -3.72 1.09e+00 8.42e-01 1.16e+01 angle pdb=" N PRO C 415 " pdb=" CD PRO C 415 " pdb=" CG PRO C 415 " ideal model delta sigma weight residual 103.20 98.17 5.03 1.50e+00 4.44e-01 1.13e+01 ... (remaining 37831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 15461 17.84 - 35.68: 1120 35.68 - 53.51: 202 53.51 - 71.35: 47 71.35 - 89.19: 20 Dihedral angle restraints: 16850 sinusoidal: 6644 harmonic: 10206 Sorted by residual: dihedral pdb=" CB CYS C 741 " pdb=" SG CYS C 741 " pdb=" SG CYS C 763 " pdb=" CB CYS C 763 " ideal model delta sinusoidal sigma weight residual -86.00 -156.81 70.81 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -152.83 66.83 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CA ASN A 360 " pdb=" C ASN A 360 " pdb=" N CYS A 361 " pdb=" CA CYS A 361 " ideal model delta harmonic sigma weight residual 180.00 142.50 37.50 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 16847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4063 0.085 - 0.170: 409 0.170 - 0.255: 2 0.255 - 0.339: 1 0.339 - 0.424: 2 Chirality restraints: 4477 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 804 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 804 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 606 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4474 not shown) Planarity restraints: 4886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 804 " -0.006 2.00e-02 2.50e+03 5.05e-02 3.18e+01 pdb=" CG ASN A 804 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN A 804 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A 804 " 0.052 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 804 " 0.003 2.00e-02 2.50e+03 3.39e-02 1.43e+01 pdb=" CG ASN B 804 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 804 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN B 804 " 0.039 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 414 " 0.065 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO C 415 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.050 5.00e-02 4.00e+02 ... (remaining 4883 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 563 2.69 - 3.24: 25304 3.24 - 3.79: 40245 3.79 - 4.35: 52822 4.35 - 4.90: 90151 Nonbonded interactions: 209085 Sorted by model distance: nonbonded pdb=" OH TYR B 759 " pdb=" OD1 ASP B 997 " model vdw 2.136 3.040 nonbonded pdb=" O CYS A 379 " pdb=" OH TYR C 492 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR C 759 " pdb=" OD1 ASP C 997 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR A 759 " pdb=" OD1 ASP A 997 " model vdw 2.232 3.040 ... (remaining 209080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 95 or (resid 96 through 98 and (na \ me N or name CA or name C or name O or name CB )) or resid 99 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 123 or (resid 124 and (name N or name CA or name C or name O o \ r name CB )) or resid 125 through 135 or (resid 136 through 138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 139 through 142 or resid 158 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N \ or name CA or name C or name O or name CB )) or resid 207 through 220 or (resid \ 221 and (name N or name CA or name C or name O or name CB )) or resid 222 throu \ gh 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) or \ resid 228 through 247 or (resid 248 through 249 and (name N or name CA or name \ C or name O or name CB )) or resid 250 through 251 or (resid 252 through 253 and \ (name N or name CA or name C or name O or name CB )) or resid 254 through 283 o \ r (resid 284 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 85 through 289 or (resid 290 through 291 and (name N or name CA or name C or nam \ e O or name CB )) or resid 292 through 306 or (resid 307 and (name N or name CA \ or name C or name O or name CB )) or resid 308 through 311 or (resid 312 through \ 313 and (name N or name CA or name C or name O or name CB )) or resid 314 throu \ gh 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or \ resid 325 through 326 or (resid 327 and (name N or name CA or name C or name O \ or name CB )) or resid 328 through 345 or (resid 346 and (name N or name CA or n \ ame C or name O or name CB )) or resid 347 through 355 or (resid 356 and (name N \ or name CA or name C or name O or name CB )) or resid 357 through 368 or (resid \ 369 and (name N or name CA or name C or name O or name CB )) or resid 370 throu \ gh 385 or (resid 386 and (name N or name CA or name C or name O or name CB )) or \ resid 387 or (resid 388 and (name N or name CA or name C or name O or name CB ) \ ) or resid 389 through 405 or (resid 406 and (name N or name CA or name C or nam \ e O or name CB )) or resid 407 through 426 or (resid 427 through 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 438 or (resid \ 439 and (name N or name CA or name C or name O or name CB )) or resid 440 or (r \ esid 441 through 442 and (name N or name CA or name C or name O or name CB )) or \ resid 443 or (resid 444 and (name N or name CA or name C or name O or name CB ) \ ) or resid 445 through 447 or (resid 448 and (name N or name CA or name C or nam \ e O or name CB )) or resid 449 through 461 or (resid 462 and (name N or name CA \ or name C or name O or name CB )) or resid 463 through 473 or (resid 474 through \ 475 and (name N or name CA or name C or name O or name CB )) or resid 476 throu \ gh 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) or \ resid 517 through 522 or (resid 523 and (name N or name CA or name C or name O \ or name CB )) or resid 524 through 531 or resid 533 through 534 or (resid 535 an \ d (name N or name CA or name C or name O or name CB )) or resid 536 through 539 \ or (resid 540 and (name N or name CA or name C or name O or name CB )) or resid \ 541 through 559 or (resid 560 through 561 and (name N or name CA or name C or na \ me O or name CB )) or resid 562 through 571 or (resid 572 through 575 and (name \ N or name CA or name C or name O or name CB )) or resid 576 through 615 or (resi \ d 616 and (name N or name CA or name C or name O or name CB )) or resid 617 thro \ ugh 665 or (resid 666 and (name N or name CA or name C or name O or name CB )) o \ r resid 667 through 704 or (resid 705 and (name N or name CA or name C or name O \ or name CB )) or resid 706 through 739 or (resid 740 and (name N or name CA or \ name C or name O or name CB )) or resid 741 through 742 or (resid 743 and (name \ N or name CA or name C or name O or name CB )) or resid 744 through 747 or (resi \ d 748 and (name N or name CA or name C or name O or name CB )) or resid 749 thro \ ugh 778 or (resid 779 and (name N or name CA or name C or name O or name CB )) o \ r resid 780 through 781 or (resid 782 through 783 and (name N or name CA or name \ C or name O or name CB )) or resid 784 through 797 or (resid 798 and (name N or \ name CA or name C or name O or name CB )) or resid 799 through 810 or (resid 81 \ 1 and (name N or name CA or name C or name 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 re \ sid 815 through 821 or (resid 822 and (name N or name CA or name C or name O or \ name CB )) or resid 823 through 827 or (resid 828 and (name N or name CA or name \ C or name O or name CB )) or resid 829 through 831 or (resid 858 and (name N or \ name CA or name C or name O or name CB )) or resid 859 through 870 or (resid 87 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 872 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 941 or (resid 942 through 947 and (name N or name CA or name C o \ r name O or name CB )) or resid 948 through 949 or (resid 950 and (name N or nam \ e CA or name C or name O or name CB )) or resid 951 through 966 or (resid 967 an \ d (name N or name CA or name C or name O or name CB )) or resid 968 through 997 \ or (resid 998 and (name N or name CA or name C or name O or name CB )) or resid \ 999 through 1016 or (resid 1017 through 1019 and (name N or name CA or name C or \ name O or name CB )) or resid 1020 through 1021 or (resid 1022 through 1023 and \ (name N or name CA or name C or name O or name CB )) or resid 1024 through 1075 \ or (resid 1076 and (name N or name CA or name C or name O or name CB )) or resi \ d 1077 through 1094 or (resid 1095 and (name N or name CA or name C or name O or \ name CB )) or resid 1096 through 1140 or (resid 1141 and (name N or name CA or \ name C or name O or name CB )) or resid 1142 through 1143 or (resid 1144 through \ 1145 and (name N or name CA or name C or name O or name CB )) or resid 1146 thr \ ough 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 51 or (resid 52 throu \ gh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 throu \ gh 68 or resid 81 through 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 95 or (resid 96 through 98 and (name N or \ name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 through 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 133 or (resid 134 and (name N or name CA or name C or name O or n \ ame CB )) or resid 135 or (resid 136 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 142 or resid 158 through 160 or ( \ resid 161 through 164 and (name N or name CA or name C or name O or name CB )) o \ r resid 165 through 205 or (resid 206 and (name N or name CA or name C or name O \ or name CB )) or resid 207 through 209 or (resid 210 and (name N or name CA or \ name C or name O or name CB )) or resid 218 through 247 or (resid 248 through 24 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 250 through \ 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or re \ sid 258 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 289 or (resid 290 through 291 and (name N or nam \ e CA or name C or name O or name CB )) or resid 292 through 311 or (resid 312 th \ rough 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 321 or (resid 322 and (name N or name CA or name C or name O or name CB \ )) or resid 323 through 326 or (resid 327 and (name N or name CA or name C or na \ me O or name CB )) or resid 328 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 355 or (resid 356 and (n \ ame N or name CA or name C or name O or name CB )) or resid 357 through 368 or ( \ resid 369 and (name N or name CA or name C or name O or name CB )) or resid 370 \ through 385 or (resid 386 and (name N or name CA or name C or name O or name CB \ )) or resid 387 or (resid 388 and (name N or name CA or name C or name O or name \ CB )) or resid 389 through 405 or (resid 406 and (name N or name CA or name C o \ r name O or name CB )) or resid 407 through 426 or (resid 427 through 428 and (n \ ame N or name CA or name C or name O or name CB )) or resid 429 through 438 or ( \ resid 439 and (name N or name CA or name C or name O or name CB )) or resid 440 \ or (resid 441 through 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 or (resid 444 and (name N or name CA or name C or name O or name \ CB )) or resid 445 through 447 or (resid 448 and (name N or name CA or name C o \ r name O or name CB )) or resid 449 through 461 or (resid 462 and (name N or nam \ e CA or name C or name O or name CB )) or resid 463 through 473 or (resid 474 th \ rough 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 515 or (resid 516 and (name N or name CA or name C or name O or name CB \ )) or resid 517 through 522 or (resid 523 and (name N or name CA or name C or na \ me O or name CB )) or resid 524 through 534 or (resid 535 and (name N or name CA \ or name C or name O or name CB )) or resid 536 through 539 or (resid 540 and (n \ ame N or name CA or name C or name O or name CB )) or resid 541 through 556 or ( \ resid 557 and (name N or name CA or name C or name O or name CB )) or resid 558 \ or (resid 559 through 561 and (name N or name CA or name C or name O or name CB \ )) or resid 562 through 566 or (resid 567 and (name N or name CA or name C or na \ me O or name CB )) or resid 568 through 573 or (resid 574 through 575 and (name \ N or name CA or name C or name O or name CB )) or resid 576 through 615 or (resi \ d 616 and (name N or name CA or name C or name O or name CB )) or resid 617 thro \ ugh 623 or resid 644 through 679 or resid 694 through 739 or (resid 740 and (nam \ e N or name CA or name C or name O or name CB )) or resid 741 through 747 or (re \ sid 748 and (name N or name CA or name C or name O or name CB )) or resid 749 th \ rough 750 or (resid 751 and (name N or name CA or name C or name O or name CB )) \ or resid 752 through 778 or (resid 779 and (name N or name CA or name C or name \ O or name CB )) or resid 780 through 781 or (resid 782 through 783 and (name N \ or name CA or name C or name O or name CB )) or resid 784 through 813 or (resid \ 814 and (name N or name CA or name C or name O or name CB )) or resid 815 throug \ h 830 or (resid 831 and (name N or name CA or name C or name O or name CB )) or \ (resid 858 and (name N or name CA or name C or name O or name CB )) or resid 859 \ through 870 or (resid 871 and (name N or name CA or name C or name O or name CB \ )) or resid 872 through 941 or (resid 942 through 947 and (name N or name CA or \ name C or name O or name CB )) or resid 948 through 987 or (resid 988 and (name \ N or name CA or name C or name O or name CB )) or resid 989 through 990 or (res \ id 991 through 992 and (name N or name CA or name C or name O or name CB )) or r \ esid 993 through 997 or (resid 998 and (name N or name CA or name C or name O or \ name CB )) or resid 999 through 1016 or (resid 1017 through 1019 and (name N or \ name CA or name C or name O or name CB )) or resid 1020 through 1021 or (resid \ 1022 through 1023 and (name N or name CA or name C or name O or name CB )) or re \ sid 1024 through 1040 or (resid 1041 and (name N or name CA or name C or name O \ or name CB )) or resid 1042 through 1053 or (resid 1054 and (name N or name CA o \ r name C or name O or name CB )) or resid 1055 through 1094 or (resid 1095 and ( \ name N or name CA or name C or name O or name CB )) or resid 1096 through 1113 o \ r (resid 1114 and (name N or name CA or name C or name O or name CB )) or resid \ 1115 through 1146 or (resid 1147 through 1149 and (name N or name CA or name C o \ r name O or name CB )) or resid 1301 through 1312)) selection = (chain 'C' and (resid 27 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 67 or (res \ id 68 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or r \ esid 88 through 107 or (resid 108 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB )) or resid 116 through 120 or (resid 121 through 124 an \ d (name N or name CA or name C or name O or name CB )) or resid 125 through 160 \ or (resid 161 through 164 and (name N or name CA or name C or name O or name CB \ )) or resid 165 through 199 or (resid 200 and (name N or name CA or name C or na \ me O or name CB )) or resid 201 through 220 or (resid 221 and (name N or name CA \ or name C or name O or name CB )) or resid 222 through 226 or (resid 227 and (n \ ame N or name CA or name C or name O or name CB )) or resid 228 through 251 or ( \ resid 252 through 253 and (name N or name CA or name C or name O or name CB )) o \ r resid 254 through 256 or (resid 257 and (name N or name CA or name C or name O \ or name CB )) or resid 258 through 323 or (resid 324 and (name N or name CA or \ name C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name \ N or name CA or name C or name O or name CB )) or resid 328 through 334 or resid \ 338 through 531 or resid 533 through 566 or (resid 567 and (name N or name CA o \ r name C or name O or name CB )) or resid 568 through 571 or (resid 572 through \ 575 and (name N or name CA or name C or name O or name CB )) or resid 576 throug \ h 582 or (resid 583 and (name N or name CA or name C or name O or name CB )) or \ resid 584 through 620 or (resid 621 and (name N or name CA or name C or name O o \ r name CB )) or resid 622 through 623 or resid 644 through 679 or resid 694 thro \ ugh 742 or (resid 743 and (name N or name CA or name C or name O or name CB )) o \ r resid 744 through 750 or (resid 751 and (name N or name CA or name C or name O \ or name CB )) or resid 752 through 810 or (resid 811 and (name N or name CA or \ name C or name O or name CB )) or resid 812 through 821 or (resid 822 and (name \ N or name CA or name C or name O or name CB )) or resid 823 through 827 or (resi \ d 828 and (name N or name CA or name C or name O or name CB )) or resid 829 thro \ ugh 831 or resid 858 through 920 or (resid 921 and (name N or name CA or name C \ or name O or name CB )) or resid 922 through 923 or (resid 924 and (name N or na \ me CA or name C or name O or name CB )) or resid 925 through 935 or (resid 936 a \ nd (name N or name CA or name C or name O or name CB )) or resid 937 through 938 \ or (resid 939 and (name N or name CA or name C or name O or name CB )) or resid \ 940 through 943 or (resid 944 through 947 and (name N or name CA or name C or n \ ame O or name CB )) or resid 948 through 949 or (resid 950 and (name N or name C \ A or name C or name O or name CB )) or resid 951 through 966 or (resid 967 and ( \ name N or name CA or name C or name O or name CB )) or resid 968 through 1053 or \ (resid 1054 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 055 through 1109 or (resid 1110 and (name N or name CA or name C or name O or na \ me CB )) or resid 1111 through 1113 or (resid 1114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1115 through 1140 or (resid 1141 and (name \ N or name CA or name C or name O or name CB )) or resid 1142 through 1146 or (re \ sid 1147 through 1149 and (name N or name CA or name C or name O or name CB )) o \ r resid 1301 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 62.290 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 27809 Z= 0.165 Angle : 0.648 13.614 38042 Z= 0.341 Chirality : 0.045 0.424 4477 Planarity : 0.005 0.091 4848 Dihedral : 12.782 89.191 10161 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 0.04 % Allowed : 0.18 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.04 (0.14), residues: 3461 helix: 1.90 (0.21), residues: 649 sheet: 0.92 (0.18), residues: 846 loop : -1.09 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.004 0.001 HIS B1061 PHE 0.019 0.001 PHE A 909 TYR 0.021 0.001 TYR B 91 ARG 0.007 0.000 ARG C 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 38) link_NAG-ASN : angle 3.80469 ( 114) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 1.24572 ( 6) hydrogen bonds : bond 0.21383 ( 1030) hydrogen bonds : angle 8.58974 ( 2919) SS BOND : bond 0.00382 ( 43) SS BOND : angle 1.63347 ( 86) covalent geometry : bond 0.00344 (27726) covalent geometry : angle 0.61060 (37836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1001 THR cc_start: 0.8159 (m) cc_final: 0.7887 (m) REVERT: H 85 MET cc_start: 0.2015 (mpp) cc_final: 0.1145 (tmt) outliers start: 1 outliers final: 2 residues processed: 213 average time/residue: 1.0006 time to fit residues: 262.9812 Evaluate side-chains 150 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain C residue 423 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 178 optimal weight: 0.1980 chunk 141 optimal weight: 0.1980 chunk 273 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 316 optimal weight: 40.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 GLN A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 519 HIS A 616 GLN A 910 ASN B 30 ASN B 317 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 616 GLN C 357 ASN C 706 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.239058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145282 restraints weight = 35174.354| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.61 r_work: 0.3418 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 27809 Z= 0.126 Angle : 0.592 12.549 38042 Z= 0.304 Chirality : 0.046 0.343 4477 Planarity : 0.004 0.055 4848 Dihedral : 5.815 55.846 4598 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 1.32 % Allowed : 5.62 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3461 helix: 2.02 (0.21), residues: 644 sheet: 0.91 (0.17), residues: 891 loop : -1.05 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 439 HIS 0.006 0.001 HIS A 207 PHE 0.024 0.001 PHE A 140 TYR 0.021 0.001 TYR B1070 ARG 0.006 0.000 ARG C 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 38) link_NAG-ASN : angle 3.10944 ( 114) link_BETA1-4 : bond 0.00207 ( 2) link_BETA1-4 : angle 1.13055 ( 6) hydrogen bonds : bond 0.05081 ( 1030) hydrogen bonds : angle 6.20092 ( 2919) SS BOND : bond 0.00384 ( 43) SS BOND : angle 1.49172 ( 86) covalent geometry : bond 0.00291 (27726) covalent geometry : angle 0.56381 (37836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 HIS cc_start: 0.2824 (OUTLIER) cc_final: 0.2554 (p-80) REVERT: A 579 VAL cc_start: 0.8132 (p) cc_final: 0.7916 (m) REVERT: A 953 ASP cc_start: 0.7523 (m-30) cc_final: 0.7245 (m-30) REVERT: B 905 MET cc_start: 0.9195 (mmm) cc_final: 0.8897 (mmt) REVERT: C 287 THR cc_start: 0.7930 (m) cc_final: 0.7633 (p) REVERT: C 468 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6946 (mt-10) REVERT: C 1032 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8074 (tpp) REVERT: H 34 MET cc_start: 0.2664 (OUTLIER) cc_final: 0.2120 (mtp) REVERT: H 85 MET cc_start: -0.0395 (mpp) cc_final: -0.1356 (tpt) outliers start: 37 outliers final: 14 residues processed: 195 average time/residue: 1.0342 time to fit residues: 246.8099 Evaluate side-chains 161 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 1095 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 751 GLU Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 207 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 204 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN B 248 HIS B 317 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN C 463 ASN C 758 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.233585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134053 restraints weight = 34593.078| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.77 r_work: 0.3388 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 27809 Z= 0.196 Angle : 0.657 11.805 38042 Z= 0.335 Chirality : 0.048 0.327 4477 Planarity : 0.005 0.054 4848 Dihedral : 5.814 56.798 4594 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 2.18 % Allowed : 8.12 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3461 helix: 1.80 (0.21), residues: 640 sheet: 0.74 (0.17), residues: 883 loop : -1.18 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 439 HIS 0.038 0.002 HIS A 519 PHE 0.034 0.002 PHE A 909 TYR 0.037 0.002 TYR A 268 ARG 0.005 0.000 ARG C 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 38) link_NAG-ASN : angle 3.23871 ( 114) link_BETA1-4 : bond 0.00510 ( 2) link_BETA1-4 : angle 1.45439 ( 6) hydrogen bonds : bond 0.06494 ( 1030) hydrogen bonds : angle 6.00937 ( 2919) SS BOND : bond 0.00450 ( 43) SS BOND : angle 1.82948 ( 86) covalent geometry : bond 0.00492 (27726) covalent geometry : angle 0.62820 (37836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7892 (m-10) cc_final: 0.7609 (m-10) REVERT: A 43 PHE cc_start: 0.7155 (t80) cc_final: 0.6946 (t80) REVERT: A 519 HIS cc_start: 0.2706 (OUTLIER) cc_final: 0.0903 (t-170) REVERT: B 59 PHE cc_start: 0.7748 (m-80) cc_final: 0.7252 (m-80) REVERT: B 1034 GLU cc_start: 0.8402 (tt0) cc_final: 0.7925 (mt-10) REVERT: C 28 TYR cc_start: 0.7951 (m-10) cc_final: 0.7646 (m-10) REVERT: C 190 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6674 (ptm160) REVERT: C 207 HIS cc_start: 0.7422 (m90) cc_final: 0.7077 (m170) REVERT: C 277 THR cc_start: 0.8690 (m) cc_final: 0.8377 (t) REVERT: C 468 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: C 982 ASP cc_start: 0.7461 (t0) cc_final: 0.6843 (t0) REVERT: C 1020 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: H 34 MET cc_start: 0.2627 (OUTLIER) cc_final: 0.1968 (mtp) REVERT: H 85 MET cc_start: -0.0293 (mpp) cc_final: -0.1628 (ppp) REVERT: H 108 MET cc_start: 0.3991 (ptt) cc_final: 0.3670 (mmm) outliers start: 61 outliers final: 31 residues processed: 201 average time/residue: 1.0537 time to fit residues: 260.2026 Evaluate side-chains 182 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 700 MET Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1095 GLU Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1136 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 60 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 324 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 269 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 616 GLN A 910 ASN B 317 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 81 ASN C 125 ASN C 397 ASN C 807 GLN C 938 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.233414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147123 restraints weight = 34866.513| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 5.21 r_work: 0.3359 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 27809 Z= 0.125 Angle : 0.572 12.204 38042 Z= 0.291 Chirality : 0.045 0.321 4477 Planarity : 0.004 0.061 4848 Dihedral : 5.356 55.983 4594 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.13 % Rotamer: Outliers : 2.18 % Allowed : 9.55 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3461 helix: 2.03 (0.21), residues: 646 sheet: 0.75 (0.18), residues: 840 loop : -1.10 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 439 HIS 0.008 0.001 HIS A 519 PHE 0.023 0.001 PHE B 595 TYR 0.022 0.001 TYR A 268 ARG 0.007 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 38) link_NAG-ASN : angle 3.05327 ( 114) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 1.24277 ( 6) hydrogen bonds : bond 0.05001 ( 1030) hydrogen bonds : angle 5.63517 ( 2919) SS BOND : bond 0.00369 ( 43) SS BOND : angle 1.43580 ( 86) covalent geometry : bond 0.00299 (27726) covalent geometry : angle 0.54434 (37836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 166 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7950 (m-10) cc_final: 0.7704 (m-10) REVERT: B 59 PHE cc_start: 0.7756 (m-80) cc_final: 0.7293 (m-80) REVERT: B 983 ILE cc_start: 0.6664 (mt) cc_final: 0.6126 (mp) REVERT: B 1034 GLU cc_start: 0.8277 (tt0) cc_final: 0.7716 (mt-10) REVERT: C 28 TYR cc_start: 0.7880 (m-10) cc_final: 0.7585 (m-10) REVERT: C 190 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6602 (ptm160) REVERT: C 207 HIS cc_start: 0.7216 (m90) cc_final: 0.6951 (m170) REVERT: C 277 THR cc_start: 0.8541 (m) cc_final: 0.8268 (t) REVERT: C 287 THR cc_start: 0.8242 (m) cc_final: 0.7967 (p) REVERT: C 468 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: C 584 THR cc_start: 0.7192 (p) cc_final: 0.5894 (p) REVERT: C 982 ASP cc_start: 0.7477 (t0) cc_final: 0.6841 (t0) REVERT: C 1005 GLN cc_start: 0.8290 (tp40) cc_final: 0.8006 (tp40) REVERT: C 1020 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: F 85 MET cc_start: -0.3207 (mpt) cc_final: -0.3549 (mpp) REVERT: H 34 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2367 (mtp) REVERT: H 85 MET cc_start: -0.0400 (mpp) cc_final: -0.1577 (ppp) REVERT: H 108 MET cc_start: 0.4121 (ptt) cc_final: 0.3823 (mmm) outliers start: 61 outliers final: 29 residues processed: 206 average time/residue: 1.0008 time to fit residues: 253.2510 Evaluate side-chains 191 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 937 ILE Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain H residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 315 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 209 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 616 GLN A 706 ASN A 758 GLN B 66 HIS B 87 ASN B 125 ASN B 317 GLN B 394 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 938 GLN C 66 HIS C 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.220556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126541 restraints weight = 34230.113| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 4.10 r_work: 0.3173 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.320 27809 Z= 0.469 Angle : 0.973 17.935 38042 Z= 0.499 Chirality : 0.061 0.314 4477 Planarity : 0.007 0.086 4848 Dihedral : 7.355 57.825 4594 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 3.72 % Allowed : 11.16 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.93 (0.14), residues: 3461 helix: 0.88 (0.20), residues: 637 sheet: 0.35 (0.17), residues: 856 loop : -1.66 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 64 HIS 0.010 0.002 HIS C1061 PHE 0.055 0.004 PHE A 201 TYR 0.048 0.003 TYR A 268 ARG 0.009 0.001 ARG C 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00950 ( 38) link_NAG-ASN : angle 4.41313 ( 114) link_BETA1-4 : bond 0.01555 ( 2) link_BETA1-4 : angle 1.84685 ( 6) hydrogen bonds : bond 0.09833 ( 1030) hydrogen bonds : angle 6.61918 ( 2919) SS BOND : bond 0.00880 ( 43) SS BOND : angle 2.94421 ( 86) covalent geometry : bond 0.01187 (27726) covalent geometry : angle 0.93393 (37836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 186 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8464 (m-10) cc_final: 0.8128 (m-80) REVERT: A 219 LEU cc_start: 0.4327 (mt) cc_final: 0.4053 (mm) REVERT: A 272 TYR cc_start: 0.8146 (m-80) cc_final: 0.7871 (m-80) REVERT: A 1005 GLN cc_start: 0.8392 (tt0) cc_final: 0.8047 (tp-100) REVERT: B 201 PHE cc_start: 0.5995 (t80) cc_final: 0.5745 (t80) REVERT: B 312 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7842 (pt0) REVERT: B 361 CYS cc_start: 0.5562 (OUTLIER) cc_final: 0.5109 (t) REVERT: B 538 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7637 (mtmm) REVERT: B 871 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7897 (mp0) REVERT: B 997 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7448 (t0) REVERT: C 84 LEU cc_start: 0.5728 (mt) cc_final: 0.5521 (mt) REVERT: C 426 TYR cc_start: 0.8131 (t80) cc_final: 0.7839 (t80) REVERT: C 468 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: C 568 PHE cc_start: 0.8030 (p90) cc_final: 0.7813 (p90) REVERT: C 982 ASP cc_start: 0.7691 (t0) cc_final: 0.6994 (t0) REVERT: C 1001 THR cc_start: 0.8586 (m) cc_final: 0.8169 (p) REVERT: C 1020 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: F 85 MET cc_start: -0.3413 (mpt) cc_final: -0.3676 (mpp) REVERT: H 34 MET cc_start: 0.2940 (OUTLIER) cc_final: 0.2555 (mtt) REVERT: H 85 MET cc_start: -0.0540 (mpp) cc_final: -0.1678 (ppp) REVERT: H 108 MET cc_start: 0.4271 (ptt) cc_final: 0.3819 (mmm) outliers start: 104 outliers final: 52 residues processed: 269 average time/residue: 0.9558 time to fit residues: 325.6439 Evaluate side-chains 215 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1060 PRO Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 272 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1136 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 811 ASP Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1136 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 178 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 254 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 GLN B 317 GLN B 414 GLN B 487 ASN C 30 ASN C 66 HIS C 81 ASN C 207 HIS ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.228312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132233 restraints weight = 34513.334| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.25 r_work: 0.3289 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 27809 Z= 0.141 Angle : 0.633 14.076 38042 Z= 0.323 Chirality : 0.047 0.303 4477 Planarity : 0.005 0.064 4848 Dihedral : 5.837 59.871 4594 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 2.58 % Allowed : 13.77 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3461 helix: 1.62 (0.21), residues: 639 sheet: 0.56 (0.18), residues: 853 loop : -1.47 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.003 0.001 HIS A1067 PHE 0.028 0.001 PHE B 86 TYR 0.018 0.001 TYR B1070 ARG 0.006 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 38) link_NAG-ASN : angle 3.41590 ( 114) link_BETA1-4 : bond 0.00423 ( 2) link_BETA1-4 : angle 1.49132 ( 6) hydrogen bonds : bond 0.05536 ( 1030) hydrogen bonds : angle 5.81560 ( 2919) SS BOND : bond 0.00408 ( 43) SS BOND : angle 1.83047 ( 86) covalent geometry : bond 0.00336 (27726) covalent geometry : angle 0.59976 (37836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8493 (m-10) cc_final: 0.8279 (m-80) REVERT: A 129 LYS cc_start: 0.8237 (ptmm) cc_final: 0.8017 (ptpp) REVERT: A 329 ILE cc_start: 0.5658 (pt) cc_final: 0.5086 (tt) REVERT: A 618 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8432 (m) REVERT: A 997 ASP cc_start: 0.8144 (t70) cc_final: 0.7867 (t0) REVERT: B 274 GLN cc_start: 0.7198 (mt0) cc_final: 0.6947 (mt0) REVERT: B 312 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8072 (pt0) REVERT: B 361 CYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4591 (t) REVERT: B 414 GLN cc_start: 0.2173 (OUTLIER) cc_final: 0.1941 (tt0) REVERT: B 567 GLN cc_start: 0.6684 (mt0) cc_final: 0.5849 (mp10) REVERT: B 997 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7157 (t0) REVERT: B 1034 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: C 101 ILE cc_start: 0.8277 (mm) cc_final: 0.7933 (mm) REVERT: C 190 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7476 (ptm160) REVERT: C 207 HIS cc_start: 0.7430 (m90) cc_final: 0.7105 (m90) REVERT: C 277 THR cc_start: 0.8718 (m) cc_final: 0.8465 (t) REVERT: C 287 THR cc_start: 0.8315 (m) cc_final: 0.8096 (p) REVERT: C 360 ARG cc_start: 0.7800 (ptm160) cc_final: 0.7522 (ptm160) REVERT: C 406 ARG cc_start: 0.3331 (OUTLIER) cc_final: 0.3047 (mmp80) REVERT: C 468 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: C 568 PHE cc_start: 0.7773 (p90) cc_final: 0.7572 (p90) REVERT: C 580 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8177 (ptp-110) REVERT: C 982 ASP cc_start: 0.7586 (t0) cc_final: 0.7005 (t0) REVERT: C 1001 THR cc_start: 0.8619 (m) cc_final: 0.8318 (p) REVERT: C 1005 GLN cc_start: 0.8505 (tp40) cc_final: 0.8288 (tp40) REVERT: C 1020 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: F 85 MET cc_start: -0.3420 (mpt) cc_final: -0.3717 (mpp) REVERT: H 34 MET cc_start: 0.3082 (OUTLIER) cc_final: 0.2561 (mtt) REVERT: H 85 MET cc_start: -0.0427 (mpp) cc_final: -0.1534 (ppp) REVERT: H 108 MET cc_start: 0.4167 (ptt) cc_final: 0.3752 (mmm) outliers start: 72 outliers final: 36 residues processed: 223 average time/residue: 0.9571 time to fit residues: 265.9125 Evaluate side-chains 208 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1034 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 354 TYR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 1020 GLU Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 180 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 127 optimal weight: 0.0040 chunk 106 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 169 optimal weight: 0.0870 chunk 272 optimal weight: 0.0470 chunk 307 optimal weight: 20.0000 overall best weight: 0.2668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 519 HIS B 317 GLN B 938 GLN C 66 HIS C 81 ASN C1008 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.232061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.140824 restraints weight = 34738.736| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.75 r_work: 0.3384 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.146 27809 Z= 0.109 Angle : 0.568 12.965 38042 Z= 0.289 Chirality : 0.045 0.312 4477 Planarity : 0.004 0.059 4848 Dihedral : 5.109 55.002 4594 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 2.18 % Allowed : 14.52 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.21 (0.14), residues: 3461 helix: 1.96 (0.21), residues: 645 sheet: 0.68 (0.18), residues: 868 loop : -1.33 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 439 HIS 0.004 0.000 HIS A 207 PHE 0.020 0.001 PHE B 32 TYR 0.019 0.001 TYR B1070 ARG 0.007 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 38) link_NAG-ASN : angle 2.96517 ( 114) link_BETA1-4 : bond 0.00401 ( 2) link_BETA1-4 : angle 1.29682 ( 6) hydrogen bonds : bond 0.04309 ( 1030) hydrogen bonds : angle 5.37912 ( 2919) SS BOND : bond 0.00379 ( 43) SS BOND : angle 1.38903 ( 86) covalent geometry : bond 0.00247 (27726) covalent geometry : angle 0.54173 (37836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8430 (m-10) cc_final: 0.8010 (m-80) REVERT: A 61 ASN cc_start: 0.7717 (p0) cc_final: 0.7484 (p0) REVERT: A 129 LYS cc_start: 0.7906 (ptmm) cc_final: 0.7697 (ptpp) REVERT: B 274 GLN cc_start: 0.6859 (mt0) cc_final: 0.6579 (mt0) REVERT: B 361 CYS cc_start: 0.5077 (OUTLIER) cc_final: 0.4061 (t) REVERT: B 567 GLN cc_start: 0.6641 (mt0) cc_final: 0.5859 (mp10) REVERT: B 997 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6242 (m-30) REVERT: B 1034 GLU cc_start: 0.8667 (tt0) cc_final: 0.7588 (mt-10) REVERT: C 101 ILE cc_start: 0.8236 (mm) cc_final: 0.7900 (mm) REVERT: C 190 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7256 (ptm160) REVERT: C 207 HIS cc_start: 0.7193 (m90) cc_final: 0.6898 (m90) REVERT: C 401 ASP cc_start: 0.7640 (t0) cc_final: 0.7401 (t0) REVERT: C 468 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: C 580 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8050 (ptp-110) REVERT: C 982 ASP cc_start: 0.7628 (t0) cc_final: 0.7102 (t0) REVERT: C 984 PHE cc_start: 0.6103 (m-10) cc_final: 0.5832 (m-10) REVERT: C 1005 GLN cc_start: 0.8343 (tp40) cc_final: 0.8129 (tp40) REVERT: F 85 MET cc_start: -0.3415 (mpt) cc_final: -0.3654 (mpp) REVERT: H 34 MET cc_start: 0.2960 (OUTLIER) cc_final: 0.2494 (mtt) REVERT: H 85 MET cc_start: -0.0524 (mpp) cc_final: -0.1762 (ppp) REVERT: H 108 MET cc_start: 0.4437 (ptt) cc_final: 0.3993 (mmm) outliers start: 61 outliers final: 30 residues processed: 215 average time/residue: 0.9531 time to fit residues: 255.7037 Evaluate side-chains 192 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 328 optimal weight: 0.0470 chunk 185 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 246 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 333 optimal weight: 30.0000 chunk 77 optimal weight: 0.4980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 616 GLN A 758 GLN B 317 GLN C 66 HIS C 81 ASN C1008 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.232223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140084 restraints weight = 34721.256| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.61 r_work: 0.3378 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.130 27809 Z= 0.107 Angle : 0.556 12.884 38042 Z= 0.281 Chirality : 0.045 0.312 4477 Planarity : 0.004 0.059 4848 Dihedral : 4.837 54.619 4594 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 2.04 % Allowed : 15.34 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3461 helix: 2.06 (0.21), residues: 649 sheet: 0.67 (0.17), residues: 879 loop : -1.27 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 439 HIS 0.002 0.000 HIS A 207 PHE 0.024 0.001 PHE B 595 TYR 0.018 0.001 TYR B1070 ARG 0.005 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 38) link_NAG-ASN : angle 2.92025 ( 114) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 1.15666 ( 6) hydrogen bonds : bond 0.04243 ( 1030) hydrogen bonds : angle 5.22652 ( 2919) SS BOND : bond 0.00332 ( 43) SS BOND : angle 1.30549 ( 86) covalent geometry : bond 0.00246 (27726) covalent geometry : angle 0.52966 (37836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8438 (m-10) cc_final: 0.8000 (m-80) REVERT: A 320 ASN cc_start: 0.5636 (m110) cc_final: 0.5320 (m110) REVERT: B 201 PHE cc_start: 0.5126 (m-80) cc_final: 0.4753 (m-80) REVERT: B 274 GLN cc_start: 0.6982 (mt0) cc_final: 0.6759 (mt0) REVERT: B 567 GLN cc_start: 0.6696 (mt0) cc_final: 0.5922 (mp10) REVERT: B 740 ASP cc_start: 0.6638 (t0) cc_final: 0.6419 (t0) REVERT: B 997 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6145 (m-30) REVERT: B 1034 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: C 101 ILE cc_start: 0.8289 (mm) cc_final: 0.7921 (mm) REVERT: C 190 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7217 (ptm160) REVERT: C 207 HIS cc_start: 0.7165 (m90) cc_final: 0.6892 (m90) REVERT: C 401 ASP cc_start: 0.7596 (t0) cc_final: 0.7380 (t0) REVERT: C 468 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: C 580 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (ptp-110) REVERT: C 982 ASP cc_start: 0.7575 (t0) cc_final: 0.6998 (t0) REVERT: C 984 PHE cc_start: 0.6203 (m-10) cc_final: 0.5848 (m-10) REVERT: C 1005 GLN cc_start: 0.8322 (tp40) cc_final: 0.8085 (tp40) REVERT: F 85 MET cc_start: -0.3410 (mpt) cc_final: -0.3656 (mpp) REVERT: H 34 MET cc_start: 0.2997 (OUTLIER) cc_final: 0.2533 (mtt) REVERT: H 85 MET cc_start: -0.0252 (mpp) cc_final: -0.1478 (ppp) REVERT: H 108 MET cc_start: 0.4832 (ptt) cc_final: 0.4293 (mmm) REVERT: H 122 MET cc_start: 0.6656 (tpt) cc_final: 0.5699 (mmm) outliers start: 57 outliers final: 35 residues processed: 204 average time/residue: 0.9804 time to fit residues: 250.3016 Evaluate side-chains 196 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1034 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 212 optimal weight: 20.0000 chunk 69 optimal weight: 0.0970 chunk 231 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 616 GLN A 758 GLN B 317 GLN C 66 HIS C1008 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.227790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135005 restraints weight = 34399.249| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.57 r_work: 0.3309 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 27809 Z= 0.168 Angle : 0.618 14.541 38042 Z= 0.314 Chirality : 0.047 0.305 4477 Planarity : 0.004 0.063 4848 Dihedral : 5.073 56.547 4594 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 2.15 % Allowed : 15.24 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.27 (0.14), residues: 3461 helix: 1.89 (0.21), residues: 647 sheet: 0.65 (0.18), residues: 868 loop : -1.36 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 439 HIS 0.004 0.001 HIS C1051 PHE 0.021 0.002 PHE B 86 TYR 0.024 0.001 TYR A 268 ARG 0.004 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 38) link_NAG-ASN : angle 3.10679 ( 114) link_BETA1-4 : bond 0.00501 ( 2) link_BETA1-4 : angle 1.29770 ( 6) hydrogen bonds : bond 0.05833 ( 1030) hydrogen bonds : angle 5.47831 ( 2919) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.70042 ( 86) covalent geometry : bond 0.00415 (27726) covalent geometry : angle 0.58992 (37836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8463 (m-10) cc_final: 0.8051 (m-80) REVERT: A 320 ASN cc_start: 0.5949 (m110) cc_final: 0.5685 (m110) REVERT: B 274 GLN cc_start: 0.7228 (mt0) cc_final: 0.6964 (mt0) REVERT: B 312 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7881 (pt0) REVERT: B 567 GLN cc_start: 0.6754 (mt0) cc_final: 0.5968 (mp10) REVERT: B 740 ASP cc_start: 0.6997 (t0) cc_final: 0.6758 (t0) REVERT: B 905 MET cc_start: 0.9100 (mmm) cc_final: 0.8894 (mmt) REVERT: B 1034 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: C 101 ILE cc_start: 0.8281 (mm) cc_final: 0.7912 (mm) REVERT: C 190 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: C 207 HIS cc_start: 0.7128 (m90) cc_final: 0.6853 (m90) REVERT: C 401 ASP cc_start: 0.7914 (t0) cc_final: 0.7432 (m-30) REVERT: C 468 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: C 580 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8187 (ptp-110) REVERT: C 982 ASP cc_start: 0.7633 (t0) cc_final: 0.7060 (t0) REVERT: C 984 PHE cc_start: 0.6326 (m-10) cc_final: 0.6004 (m-10) REVERT: C 1005 GLN cc_start: 0.8367 (tp40) cc_final: 0.8108 (tp40) REVERT: F 85 MET cc_start: -0.3397 (mpt) cc_final: -0.3643 (mpp) REVERT: H 34 MET cc_start: 0.2950 (OUTLIER) cc_final: 0.2500 (mtt) REVERT: H 85 MET cc_start: -0.0200 (mpp) cc_final: -0.1258 (ppp) REVERT: H 108 MET cc_start: 0.4572 (ptt) cc_final: 0.4201 (mmm) outliers start: 60 outliers final: 44 residues processed: 204 average time/residue: 0.9840 time to fit residues: 248.3485 Evaluate side-chains 202 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1034 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 85 optimal weight: 0.7980 chunk 139 optimal weight: 40.0000 chunk 223 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 340 optimal weight: 30.0000 chunk 344 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 GLN C 66 HIS C1008 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.228871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135282 restraints weight = 34425.499| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.21 r_work: 0.3323 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 27809 Z= 0.144 Angle : 0.602 14.556 38042 Z= 0.304 Chirality : 0.046 0.306 4477 Planarity : 0.004 0.061 4848 Dihedral : 5.008 56.205 4594 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 1.86 % Allowed : 15.84 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3461 helix: 1.86 (0.21), residues: 652 sheet: 0.67 (0.18), residues: 862 loop : -1.32 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 439 HIS 0.004 0.001 HIS C1051 PHE 0.039 0.001 PHE C 568 TYR 0.019 0.001 TYR B1070 ARG 0.005 0.000 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 38) link_NAG-ASN : angle 3.03265 ( 114) link_BETA1-4 : bond 0.00275 ( 2) link_BETA1-4 : angle 1.29814 ( 6) hydrogen bonds : bond 0.05300 ( 1030) hydrogen bonds : angle 5.41610 ( 2919) SS BOND : bond 0.00358 ( 43) SS BOND : angle 1.57113 ( 86) covalent geometry : bond 0.00352 (27726) covalent geometry : angle 0.57502 (37836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6922 Ramachandran restraints generated. 3461 Oldfield, 0 Emsley, 3461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8428 (m-10) cc_final: 0.7997 (m-80) REVERT: A 320 ASN cc_start: 0.5980 (m110) cc_final: 0.5690 (m110) REVERT: B 32 PHE cc_start: 0.6439 (m-10) cc_final: 0.6141 (m-10) REVERT: B 274 GLN cc_start: 0.7197 (mt0) cc_final: 0.6892 (mt0) REVERT: B 312 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7872 (pt0) REVERT: B 567 GLN cc_start: 0.6765 (mt0) cc_final: 0.5993 (mp10) REVERT: B 740 ASP cc_start: 0.7142 (t0) cc_final: 0.6882 (t0) REVERT: B 1034 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: C 190 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: C 207 HIS cc_start: 0.7118 (m90) cc_final: 0.6852 (m90) REVERT: C 401 ASP cc_start: 0.7778 (t0) cc_final: 0.7436 (t0) REVERT: C 468 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 580 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8194 (ptp-110) REVERT: C 982 ASP cc_start: 0.7662 (t0) cc_final: 0.7084 (t0) REVERT: C 984 PHE cc_start: 0.6317 (m-10) cc_final: 0.5962 (m-10) REVERT: C 1005 GLN cc_start: 0.8333 (tp40) cc_final: 0.8088 (tp40) REVERT: F 85 MET cc_start: -0.3428 (mpt) cc_final: -0.3668 (mpp) REVERT: H 34 MET cc_start: 0.2917 (OUTLIER) cc_final: 0.2476 (mtt) REVERT: H 85 MET cc_start: -0.0188 (mpp) cc_final: -0.1257 (ppp) REVERT: H 108 MET cc_start: 0.4581 (ptt) cc_final: 0.4191 (mmm) outliers start: 52 outliers final: 41 residues processed: 191 average time/residue: 0.9955 time to fit residues: 237.8104 Evaluate side-chains 194 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1139 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 593 CYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 1034 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 406 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 611 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 905 MET Chi-restraints excluded: chain C residue 1079 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 161 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 245 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN A 790 GLN B 317 GLN B 938 GLN C 66 HIS C1008 GLN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.225925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133735 restraints weight = 34391.815| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.87 r_work: 0.3258 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 27809 Z= 0.202 Angle : 0.665 15.612 38042 Z= 0.338 Chirality : 0.048 0.302 4477 Planarity : 0.005 0.064 4848 Dihedral : 5.361 57.940 4594 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.18 % Allowed : 15.67 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.40 (0.14), residues: 3461 helix: 1.70 (0.21), residues: 643 sheet: 0.62 (0.17), residues: 870 loop : -1.44 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.006 0.001 HIS C1051 PHE 0.071 0.002 PHE B 92 TYR 0.027 0.002 TYR A 268 ARG 0.008 0.001 ARG C 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 38) link_NAG-ASN : angle 3.25827 ( 114) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 1.46138 ( 6) hydrogen bonds : bond 0.06514 ( 1030) hydrogen bonds : angle 5.68034 ( 2919) SS BOND : bond 0.00423 ( 43) SS BOND : angle 1.91561 ( 86) covalent geometry : bond 0.00507 (27726) covalent geometry : angle 0.63604 (37836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19616.24 seconds wall clock time: 338 minutes 57.48 seconds (20337.48 seconds total)