Starting phenix.real_space_refine on Mon Aug 25 07:12:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyh_38773/08_2025/8xyh_38773.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16467 2.51 5 N 4251 2.21 5 O 5046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25878 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8368 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 56, 'TRANS': 1016} Chain breaks: 2 Chain: "B" Number of atoms: 8368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8368 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 56, 'TRANS': 1016} Chain breaks: 2 Chain: "C" Number of atoms: 8368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8368 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 56, 'TRANS': 1016} Chain breaks: 2 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: "F" 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: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 230 Unusual residues: {'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 230 Unusual residues: {'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 230 Unusual residues: {'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 5.35, per 1000 atoms: 0.21 Number of scatterers: 25878 At special positions: 0 Unit cell: (149.73, 156.63, 167.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5046 8.00 N 4251 7.00 C 16467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.04 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.03 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.04 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " 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 F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 30 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 370 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 705 " " NAG A1311 " - " ASN A 713 " " NAG A1312 " - " ASN A 797 " " NAG A1313 " - " ASN A1094 " " NAG A1314 " - " ASN A 17 " " NAG A1316 " - " ASN A 282 " " NAG B1301 " - " ASN B 30 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 149 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 370 " " NAG B1310 " - " ASN B 616 " " NAG B1311 " - " ASN B 705 " " NAG B1312 " - " ASN B 713 " " NAG B1313 " - " ASN B 797 " " NAG B1314 " - " ASN B1094 " " NAG B1315 " - " ASN B 17 " " NAG C1301 " - " ASN C 30 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 705 " " NAG C1310 " - " ASN C 713 " " NAG C1311 " - " ASN C 797 " " NAG C1312 " - " ASN C1094 " " NAG C1313 " - " ASN C 17 " " NAG C1314 " - " ASN C 331 " " NAG C1316 " - " ASN C 149 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN B 122 " " NAG F 1 " - " ASN C 122 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 911.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6006 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 48 sheets defined 25.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.705A pdb=" N THR A 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 74 " --> pdb=" O SER A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.838A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.707A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.537A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.571A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 752 through 779 Processing helix chain 'A' and resid 807 through 811 removed outlier: 3.667A pdb=" N LYS A 810 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG A 811 " --> pdb=" O PRO A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 811' Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.566A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 844 through 851 removed outlier: 3.545A pdb=" N ALA A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 880 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.673A pdb=" N GLY A 885 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.341A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 915 " --> pdb=" O VAL A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 Processing helix chain 'A' and resid 942 through 961 Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1030 removed outlier: 4.741A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.712A pdb=" N THR B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 74' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.541A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.720A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.798A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.637A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.530A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 752 through 779 Processing helix chain 'B' and resid 807 through 811 removed outlier: 3.858A pdb=" N LYS B 810 " --> pdb=" O LYS B 807 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 811 " --> pdb=" O PRO B 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 811' Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.538A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 839 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 862 through 880 Processing helix chain 'B' and resid 882 through 886 removed outlier: 3.807A pdb=" N GLY B 885 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 906 Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.970A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 removed outlier: 3.682A pdb=" N ILE B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.916A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.582A pdb=" N SER C 256 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.747A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.805A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 748 through 751 removed outlier: 4.069A pdb=" N GLN C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 751' Processing helix chain 'C' and resid 752 through 779 Processing helix chain 'C' and resid 807 through 811 removed outlier: 3.878A pdb=" N LYS C 810 " --> pdb=" O LYS C 807 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ARG C 811 " --> pdb=" O PRO C 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 807 through 811' Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 832 through 839 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 862 through 880 Processing helix chain 'C' and resid 882 through 886 removed outlier: 3.851A pdb=" N GLY C 885 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 906 removed outlier: 3.510A pdb=" N GLY C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 914 removed outlier: 4.041A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 Processing helix chain 'C' and resid 941 through 961 removed outlier: 4.125A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.566A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.824A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.079A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.587A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.697A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.152A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.568A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.721A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.272A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.569A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 598 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.562A pdb=" N GLN A 675 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.527A pdb=" N LYS A1069 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 714 through 724 removed outlier: 3.528A pdb=" N SER A 717 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.703A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 783 through 786 removed outlier: 3.676A pdb=" N ILE A 784 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.208A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.748A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.864A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.714A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.676A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.526A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.515A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 595 through 598 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.142A pdb=" N GLU B 654 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR B 692 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 697 through 699 removed outlier: 3.676A pdb=" N ILE C 784 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.519A pdb=" N ILE B 710 " --> pdb=" O LYS B1069 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B1069 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 724 removed outlier: 3.678A pdb=" N SER B 717 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B1046 " --> pdb=" O VAL B1061 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.582A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1090 through 1093 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.228A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.801A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.025A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.603A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.858A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.594A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.642A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.710A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 595 through 598 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 707 through 711 Processing sheet with id=AE9, first strand: chain 'C' and resid 714 through 724 removed outlier: 3.519A pdb=" N HIS C1060 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C1052 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C1046 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.623A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1077 through 1078 Processing sheet with id=AF3, first strand: chain 'C' and resid 1090 through 1093 997 hydrogen bonds defined for protein. 2742 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: 5.38 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8258 1.34 - 1.47: 6752 1.47 - 1.60: 11315 1.60 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 26469 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.23e-02 6.61e+03 7.70e+00 bond pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.28e+00 ... (remaining 26464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 35802 3.45 - 6.91: 195 6.91 - 10.36: 8 10.36 - 13.82: 3 13.82 - 17.27: 1 Bond angle restraints: 36009 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 114.39 97.12 17.27 1.45e+00 4.76e-01 1.42e+02 angle pdb=" N LEU C 189 " pdb=" CA LEU C 189 " pdb=" C LEU C 189 " ideal model delta sigma weight residual 111.74 123.18 -11.44 1.35e+00 5.49e-01 7.18e+01 angle pdb=" N CYS B 166 " pdb=" CA CYS B 166 " pdb=" C CYS B 166 " ideal model delta sigma weight residual 111.28 120.38 -9.10 1.35e+00 5.49e-01 4.54e+01 angle pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 109.24 119.65 -10.41 1.63e+00 3.76e-01 4.08e+01 angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" C ASN B 616 " ideal model delta sigma weight residual 110.80 97.96 12.84 2.13e+00 2.20e-01 3.63e+01 ... (remaining 36004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 15129 18.00 - 35.99: 1069 35.99 - 53.99: 183 53.99 - 71.99: 55 71.99 - 89.99: 19 Dihedral angle restraints: 16455 sinusoidal: 7098 harmonic: 9357 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.52 -63.52 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" C ASN B 616 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta harmonic sigma weight residual -122.60 -106.13 -16.47 0 2.50e+00 1.60e-01 4.34e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 144.98 -51.98 1 1.00e+01 1.00e-02 3.69e+01 ... (remaining 16452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.301: 4186 0.301 - 0.602: 11 0.602 - 0.904: 2 0.904 - 1.205: 1 1.205 - 1.506: 3 Chirality restraints: 4203 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 705 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.67e+01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 705 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.06 -1.34 2.00e-01 2.50e+01 4.49e+01 ... (remaining 4200 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " 0.330 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B1306 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " -0.510 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1314 " 0.274 2.00e-02 2.50e+03 2.36e-01 6.97e+02 pdb=" C7 NAG A1314 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A1314 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A1314 " -0.415 2.00e-02 2.50e+03 pdb=" O7 NAG A1314 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1315 " 0.193 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" C7 NAG B1315 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG B1315 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG B1315 " -0.277 2.00e-02 2.50e+03 pdb=" O7 NAG B1315 " 0.147 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 808 2.71 - 3.26: 24002 3.26 - 3.80: 37726 3.80 - 4.35: 48389 4.35 - 4.90: 84241 Nonbonded interactions: 195166 Sorted by model distance: nonbonded pdb=" OD1 ASN B 122 " pdb=" N ALA B 123 " model vdw 2.159 3.120 nonbonded pdb=" O GLN A 800 " pdb=" OG SER A 812 " model vdw 2.219 3.040 nonbonded pdb=" OG SER C 640 " pdb=" OD1 ASN C 641 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.231 3.040 nonbonded pdb=" O SER A 704 " pdb=" NE2 GLN B 891 " model vdw 2.236 3.120 ... (remaining 195161 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 1314) selection = (chain 'B' and resid 16 through 1314) selection = (chain 'C' and resid 16 through 1314) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.300 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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 : 0.005 0.077 26559 Z= 0.227 Angle : 0.831 22.755 36240 Z= 0.426 Chirality : 0.070 1.506 4203 Planarity : 0.010 0.285 4614 Dihedral : 12.947 89.986 10332 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.62 % Favored : 93.22 % Rotamer: Outliers : 0.14 % Allowed : 0.39 % Favored : 99.46 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3201 helix: 1.25 (0.20), residues: 690 sheet: 0.15 (0.20), residues: 687 loop : -1.89 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.024 0.002 TYR B 505 PHE 0.028 0.002 PHE B 902 TRP 0.013 0.002 TRP C 64 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00462 (26469) covalent geometry : angle 0.73787 (36009) SS BOND : bond 0.00525 ( 39) SS BOND : angle 2.69400 ( 78) hydrogen bonds : bond 0.21318 ( 988) hydrogen bonds : angle 7.26504 ( 2742) link_BETA1-4 : bond 0.03208 ( 3) link_BETA1-4 : angle 6.64574 ( 9) link_NAG-ASN : bond 0.01186 ( 48) link_NAG-ASN : angle 5.56403 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 284 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 TRP cc_start: 0.7857 (p-90) cc_final: 0.7525 (p-90) REVERT: B 865 MET cc_start: 0.9080 (mtt) cc_final: 0.8855 (mtt) REVERT: B 1101 THR cc_start: 0.8409 (t) cc_final: 0.8157 (t) REVERT: C 776 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7754 (mt-10) REVERT: C 1100 VAL cc_start: 0.6279 (p) cc_final: 0.5526 (t) REVERT: C 1103 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7395 (mmt-90) outliers start: 4 outliers final: 4 residues processed: 288 average time/residue: 0.6243 time to fit residues: 206.6623 Evaluate side-chains 123 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 839 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 897 GLN A1006 GLN B 115 GLN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN C 493 GLN C 780 GLN C 921 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.077840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059670 restraints weight = 75835.614| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.25 r_work: 0.2992 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26559 Z= 0.195 Angle : 0.716 20.002 36240 Z= 0.365 Chirality : 0.050 0.672 4203 Planarity : 0.005 0.057 4614 Dihedral : 7.392 115.816 4583 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 1.25 % Allowed : 7.07 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3201 helix: 1.55 (0.20), residues: 687 sheet: 0.24 (0.20), residues: 738 loop : -1.90 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.018 0.001 TYR B 145 PHE 0.025 0.002 PHE B 884 TRP 0.013 0.002 TRP C 436 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00452 (26469) covalent geometry : angle 0.66057 (36009) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.71341 ( 78) hydrogen bonds : bond 0.07078 ( 988) hydrogen bonds : angle 5.62760 ( 2742) link_BETA1-4 : bond 0.00439 ( 3) link_BETA1-4 : angle 3.94478 ( 9) link_NAG-ASN : bond 0.00789 ( 48) link_NAG-ASN : angle 4.15930 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.6394 (p90) REVERT: A 571 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8601 (t0) REVERT: A 891 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: B 69 HIS cc_start: 0.5837 (m90) cc_final: 0.5632 (m90) REVERT: B 258 TRP cc_start: 0.7948 (p-90) cc_final: 0.7408 (p-90) REVERT: B 865 MET cc_start: 0.9115 (mtt) cc_final: 0.8897 (mtt) REVERT: B 883 THR cc_start: 0.8797 (p) cc_final: 0.8540 (t) REVERT: B 1101 THR cc_start: 0.8271 (t) cc_final: 0.8068 (m) REVERT: C 984 GLU cc_start: 0.8539 (tp30) cc_final: 0.8313 (tp30) REVERT: C 1103 ARG cc_start: 0.7795 (mtt90) cc_final: 0.7464 (mmt-90) REVERT: C 1107 GLU cc_start: 0.7587 (mp0) cc_final: 0.7331 (mp0) outliers start: 35 outliers final: 13 residues processed: 146 average time/residue: 0.5557 time to fit residues: 94.7948 Evaluate side-chains 117 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 97 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 292 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS C 493 GLN C1109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.077944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059707 restraints weight = 76072.282| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.29 r_work: 0.2994 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26559 Z= 0.151 Angle : 0.640 19.757 36240 Z= 0.325 Chirality : 0.047 0.587 4203 Planarity : 0.004 0.045 4614 Dihedral : 6.568 58.762 4577 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 1.50 % Allowed : 8.57 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.14), residues: 3201 helix: 1.72 (0.20), residues: 684 sheet: 0.41 (0.20), residues: 741 loop : -1.86 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.016 0.001 TYR C 248 PHE 0.018 0.001 PHE B 884 TRP 0.013 0.001 TRP A 882 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00347 (26469) covalent geometry : angle 0.58895 (36009) SS BOND : bond 0.00293 ( 39) SS BOND : angle 1.68653 ( 78) hydrogen bonds : bond 0.06185 ( 988) hydrogen bonds : angle 5.24052 ( 2742) link_BETA1-4 : bond 0.00751 ( 3) link_BETA1-4 : angle 3.37793 ( 9) link_NAG-ASN : bond 0.00674 ( 48) link_NAG-ASN : angle 3.77266 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8287 (mtp) cc_final: 0.7817 (mtt) REVERT: A 565 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.6553 (p90) REVERT: A 571 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8610 (t0) REVERT: B 169 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: B 258 TRP cc_start: 0.7977 (p-90) cc_final: 0.7401 (p-90) REVERT: B 865 MET cc_start: 0.9088 (mtt) cc_final: 0.8872 (mtt) REVERT: B 883 THR cc_start: 0.8747 (p) cc_final: 0.8468 (t) REVERT: B 984 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8344 (mt-10) REVERT: B 1101 THR cc_start: 0.8267 (t) cc_final: 0.8057 (m) REVERT: C 153 MET cc_start: 0.8351 (ptp) cc_final: 0.8133 (ptt) REVERT: C 565 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7548 (p90) REVERT: C 984 GLU cc_start: 0.8622 (tp30) cc_final: 0.8313 (tp30) REVERT: C 1034 LYS cc_start: 0.8804 (mppt) cc_final: 0.8380 (mmtm) REVERT: C 1103 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7525 (mmt-90) REVERT: C 1107 GLU cc_start: 0.7607 (mp0) cc_final: 0.7374 (mp0) outliers start: 42 outliers final: 15 residues processed: 142 average time/residue: 0.6033 time to fit residues: 101.4513 Evaluate side-chains 115 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 125 optimal weight: 0.2980 chunk 247 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 245 HIS B 481 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN B1084 HIS C 493 GLN C1109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060204 restraints weight = 75319.726| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.28 r_work: 0.3007 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26559 Z= 0.131 Angle : 0.605 19.487 36240 Z= 0.306 Chirality : 0.046 0.549 4203 Planarity : 0.004 0.043 4614 Dihedral : 6.157 59.934 4577 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 1.43 % Allowed : 9.81 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3201 helix: 1.88 (0.21), residues: 681 sheet: 0.56 (0.20), residues: 729 loop : -1.85 (0.12), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.019 0.001 TYR B1063 PHE 0.015 0.001 PHE B1071 TRP 0.014 0.001 TRP B 882 HIS 0.003 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00295 (26469) covalent geometry : angle 0.56002 (36009) SS BOND : bond 0.00240 ( 39) SS BOND : angle 1.36361 ( 78) hydrogen bonds : bond 0.05537 ( 988) hydrogen bonds : angle 4.96893 ( 2742) link_BETA1-4 : bond 0.00596 ( 3) link_BETA1-4 : angle 2.94923 ( 9) link_NAG-ASN : bond 0.00622 ( 48) link_NAG-ASN : angle 3.49166 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.6678 (p90) REVERT: A 571 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8608 (t0) REVERT: A 865 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8938 (mtp) REVERT: A 984 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8300 (mp0) REVERT: B 52 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8138 (tp40) REVERT: B 169 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: B 258 TRP cc_start: 0.7912 (p-90) cc_final: 0.7112 (p-90) REVERT: B 865 MET cc_start: 0.9071 (mtt) cc_final: 0.8870 (mtt) REVERT: B 883 THR cc_start: 0.8719 (p) cc_final: 0.8428 (t) REVERT: B 984 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 1101 THR cc_start: 0.8200 (t) cc_final: 0.7984 (m) REVERT: C 153 MET cc_start: 0.8257 (ptp) cc_final: 0.8020 (ptt) REVERT: C 565 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7532 (p90) REVERT: C 984 GLU cc_start: 0.8651 (tp30) cc_final: 0.8352 (tp30) REVERT: C 1034 LYS cc_start: 0.8788 (mppt) cc_final: 0.8358 (mmtm) REVERT: C 1103 ARG cc_start: 0.7670 (mtt90) cc_final: 0.7283 (mmt-90) REVERT: C 1107 GLU cc_start: 0.7572 (mp0) cc_final: 0.7309 (mp0) outliers start: 40 outliers final: 17 residues processed: 137 average time/residue: 0.5470 time to fit residues: 89.8104 Evaluate side-chains 119 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 261 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C1109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.077582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059441 restraints weight = 75603.575| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.25 r_work: 0.2989 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26559 Z= 0.146 Angle : 0.608 19.352 36240 Z= 0.309 Chirality : 0.046 0.542 4203 Planarity : 0.004 0.043 4614 Dihedral : 6.037 59.853 4577 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 2.00 % Allowed : 10.10 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.14), residues: 3201 helix: 1.86 (0.21), residues: 684 sheet: 0.82 (0.20), residues: 690 loop : -1.85 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.013 0.001 TYR B 265 PHE 0.024 0.001 PHE B 923 TRP 0.017 0.002 TRP A 882 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00339 (26469) covalent geometry : angle 0.56409 (36009) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.38924 ( 78) hydrogen bonds : bond 0.05709 ( 988) hydrogen bonds : angle 4.91580 ( 2742) link_BETA1-4 : bond 0.00505 ( 3) link_BETA1-4 : angle 2.77987 ( 9) link_NAG-ASN : bond 0.00585 ( 48) link_NAG-ASN : angle 3.43780 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.6772 (p90) REVERT: A 571 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8621 (t0) REVERT: A 896 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7028 (mtp) REVERT: B 52 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: B 169 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8584 (mm-30) REVERT: B 258 TRP cc_start: 0.7962 (p-90) cc_final: 0.7002 (p-90) REVERT: B 883 THR cc_start: 0.8718 (p) cc_final: 0.8448 (t) REVERT: B 984 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8340 (mt-10) REVERT: B 1101 THR cc_start: 0.8147 (t) cc_final: 0.7916 (m) REVERT: C 153 MET cc_start: 0.8202 (ptp) cc_final: 0.7939 (ptt) REVERT: C 565 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7591 (p90) REVERT: C 892 ILE cc_start: 0.7801 (mm) cc_final: 0.7268 (tp) REVERT: C 984 GLU cc_start: 0.8653 (tp30) cc_final: 0.8361 (tp30) REVERT: C 1034 LYS cc_start: 0.8816 (mppt) cc_final: 0.8334 (mmtm) REVERT: C 1103 ARG cc_start: 0.7594 (mtt90) cc_final: 0.7214 (tpp80) outliers start: 56 outliers final: 24 residues processed: 143 average time/residue: 0.4880 time to fit residues: 84.4950 Evaluate side-chains 123 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 236 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 613 GLN C1109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059219 restraints weight = 76072.789| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.27 r_work: 0.2983 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26559 Z= 0.147 Angle : 0.614 19.281 36240 Z= 0.310 Chirality : 0.046 0.539 4203 Planarity : 0.004 0.044 4614 Dihedral : 6.010 59.883 4577 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 1.82 % Allowed : 10.39 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.14), residues: 3201 helix: 1.85 (0.21), residues: 684 sheet: 0.86 (0.20), residues: 681 loop : -1.83 (0.12), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 567 TYR 0.019 0.001 TYR B1063 PHE 0.019 0.001 PHE B 923 TRP 0.018 0.002 TRP A 882 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00345 (26469) covalent geometry : angle 0.57089 (36009) SS BOND : bond 0.00266 ( 39) SS BOND : angle 1.67677 ( 78) hydrogen bonds : bond 0.05700 ( 988) hydrogen bonds : angle 4.86825 ( 2742) link_BETA1-4 : bond 0.00488 ( 3) link_BETA1-4 : angle 2.70368 ( 9) link_NAG-ASN : bond 0.00565 ( 48) link_NAG-ASN : angle 3.38823 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7643 (ptp) REVERT: A 565 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.6856 (p90) REVERT: A 571 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8637 (t0) REVERT: A 896 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7048 (mtp) REVERT: B 52 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8105 (tp40) REVERT: B 169 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: B 258 TRP cc_start: 0.7944 (p-90) cc_final: 0.7040 (p-90) REVERT: B 883 THR cc_start: 0.8732 (p) cc_final: 0.8450 (t) REVERT: B 984 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 1101 THR cc_start: 0.8141 (t) cc_final: 0.7894 (m) REVERT: C 153 MET cc_start: 0.8165 (ptp) cc_final: 0.7905 (ptt) REVERT: C 565 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7587 (p90) REVERT: C 984 GLU cc_start: 0.8661 (tp30) cc_final: 0.8378 (tp30) REVERT: C 1034 LYS cc_start: 0.8818 (mppt) cc_final: 0.8605 (ttpt) REVERT: C 1103 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7187 (tpp80) outliers start: 51 outliers final: 22 residues processed: 140 average time/residue: 0.5007 time to fit residues: 84.2269 Evaluate side-chains 126 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 616 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 146 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 897 GLN A1032 GLN B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.076304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058101 restraints weight = 76108.716| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.26 r_work: 0.2958 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26559 Z= 0.176 Angle : 0.636 19.241 36240 Z= 0.324 Chirality : 0.047 0.545 4203 Planarity : 0.004 0.045 4614 Dihedral : 6.154 59.654 4577 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.63 % Rotamer: Outliers : 1.86 % Allowed : 10.74 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.14), residues: 3201 helix: 1.60 (0.20), residues: 702 sheet: 0.53 (0.20), residues: 753 loop : -1.88 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.014 0.001 TYR C 265 PHE 0.028 0.001 PHE B 923 TRP 0.024 0.002 TRP A 882 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00420 (26469) covalent geometry : angle 0.59420 (36009) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.67483 ( 78) hydrogen bonds : bond 0.06202 ( 988) hydrogen bonds : angle 4.92787 ( 2742) link_BETA1-4 : bond 0.00445 ( 3) link_BETA1-4 : angle 2.67148 ( 9) link_NAG-ASN : bond 0.00562 ( 48) link_NAG-ASN : angle 3.39922 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.6888 (p90) REVERT: A 571 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8657 (t0) REVERT: A 843 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7568 (mmp-170) REVERT: A 896 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7020 (mtp) REVERT: A 1104 ASN cc_start: 0.7363 (m-40) cc_final: 0.7044 (m-40) REVERT: B 52 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: B 169 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8660 (mm-30) REVERT: B 258 TRP cc_start: 0.7989 (p-90) cc_final: 0.6969 (p-90) REVERT: B 565 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6976 (p90) REVERT: B 883 THR cc_start: 0.8730 (p) cc_final: 0.8442 (t) REVERT: B 984 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8312 (mt-10) REVERT: B 1101 THR cc_start: 0.8089 (t) cc_final: 0.7808 (m) REVERT: C 153 MET cc_start: 0.8168 (ptp) cc_final: 0.7872 (ptt) REVERT: C 565 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7514 (p90) REVERT: C 984 GLU cc_start: 0.8681 (tp30) cc_final: 0.8410 (tp30) REVERT: C 1034 LYS cc_start: 0.8846 (mppt) cc_final: 0.8425 (mmtm) REVERT: C 1103 ARG cc_start: 0.7531 (mtt90) cc_final: 0.7181 (tpp80) REVERT: C 1104 ASN cc_start: 0.7320 (m-40) cc_final: 0.6558 (p0) REVERT: C 1107 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: C 1109 GLN cc_start: 0.7706 (mp10) cc_final: 0.7250 (mp10) outliers start: 52 outliers final: 27 residues processed: 136 average time/residue: 0.4368 time to fit residues: 72.0462 Evaluate side-chains 129 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1101 THR Chi-restraints excluded: chain C residue 1107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 285 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.076550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058429 restraints weight = 76154.538| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.26 r_work: 0.2967 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26559 Z= 0.154 Angle : 0.616 19.217 36240 Z= 0.313 Chirality : 0.046 0.539 4203 Planarity : 0.004 0.045 4614 Dihedral : 6.064 59.934 4577 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 1.61 % Allowed : 11.31 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3201 helix: 1.62 (0.20), residues: 702 sheet: 0.67 (0.20), residues: 717 loop : -1.87 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.020 0.001 TYR B1063 PHE 0.026 0.001 PHE C1105 TRP 0.026 0.002 TRP A 882 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00362 (26469) covalent geometry : angle 0.57552 (36009) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.51133 ( 78) hydrogen bonds : bond 0.05866 ( 988) hydrogen bonds : angle 4.85417 ( 2742) link_BETA1-4 : bond 0.00487 ( 3) link_BETA1-4 : angle 2.66633 ( 9) link_NAG-ASN : bond 0.00544 ( 48) link_NAG-ASN : angle 3.33120 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.6915 (p90) REVERT: A 571 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8643 (t0) REVERT: A 843 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7474 (mmp-170) REVERT: A 896 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: A 1104 ASN cc_start: 0.7349 (m-40) cc_final: 0.7093 (m-40) REVERT: B 52 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8123 (tp40) REVERT: B 169 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: B 258 TRP cc_start: 0.7976 (p-90) cc_final: 0.6938 (p-90) REVERT: B 565 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6971 (p90) REVERT: B 883 THR cc_start: 0.8728 (p) cc_final: 0.8442 (t) REVERT: B 984 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 1101 THR cc_start: 0.8045 (t) cc_final: 0.7748 (m) REVERT: C 153 MET cc_start: 0.8177 (ptp) cc_final: 0.7901 (ptt) REVERT: C 271 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: C 565 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7458 (p90) REVERT: C 984 GLU cc_start: 0.8679 (tp30) cc_final: 0.8407 (tp30) REVERT: C 1034 LYS cc_start: 0.8852 (mppt) cc_final: 0.8433 (mmtm) REVERT: C 1103 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7100 (tpp80) REVERT: C 1104 ASN cc_start: 0.7285 (m-40) cc_final: 0.6559 (p0) outliers start: 45 outliers final: 26 residues processed: 134 average time/residue: 0.5364 time to fit residues: 85.7299 Evaluate side-chains 128 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 1087 ARG Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 36 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 310 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059220 restraints weight = 76431.848| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.28 r_work: 0.2986 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26559 Z= 0.128 Angle : 0.595 19.065 36240 Z= 0.301 Chirality : 0.046 0.526 4203 Planarity : 0.004 0.051 4614 Dihedral : 5.887 58.992 4577 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 1.61 % Allowed : 11.63 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3201 helix: 1.69 (0.21), residues: 702 sheet: 0.80 (0.20), residues: 729 loop : -1.87 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.012 0.001 TYR B 265 PHE 0.040 0.001 PHE B 923 TRP 0.029 0.002 TRP A 882 HIS 0.002 0.000 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00294 (26469) covalent geometry : angle 0.55539 (36009) SS BOND : bond 0.00253 ( 39) SS BOND : angle 1.39208 ( 78) hydrogen bonds : bond 0.05373 ( 988) hydrogen bonds : angle 4.74118 ( 2742) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 2.58158 ( 9) link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 3.24114 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.6908 (p90) REVERT: A 571 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8635 (t0) REVERT: A 843 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7413 (mmp-170) REVERT: A 896 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7073 (mtp) REVERT: A 1104 ASN cc_start: 0.7309 (m-40) cc_final: 0.7078 (m-40) REVERT: B 52 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8101 (tp40) REVERT: B 169 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: B 258 TRP cc_start: 0.7921 (p-90) cc_final: 0.6654 (p-90) REVERT: B 565 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.6953 (p90) REVERT: B 883 THR cc_start: 0.8711 (p) cc_final: 0.8435 (t) REVERT: B 984 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 1101 THR cc_start: 0.7996 (t) cc_final: 0.7672 (m) REVERT: C 153 MET cc_start: 0.8148 (ptp) cc_final: 0.7885 (ptt) REVERT: C 565 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7528 (p90) REVERT: C 892 ILE cc_start: 0.7756 (mm) cc_final: 0.7343 (tp) REVERT: C 984 GLU cc_start: 0.8663 (tp30) cc_final: 0.8388 (tp30) REVERT: C 1034 LYS cc_start: 0.8839 (mppt) cc_final: 0.8621 (ttpt) REVERT: C 1103 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7038 (mmt-90) REVERT: C 1104 ASN cc_start: 0.7129 (m-40) cc_final: 0.6427 (p0) outliers start: 45 outliers final: 25 residues processed: 129 average time/residue: 0.5459 time to fit residues: 84.7122 Evaluate side-chains 119 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 616 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 297 optimal weight: 10.0000 chunk 262 optimal weight: 0.3980 chunk 203 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 301 optimal weight: 0.4980 chunk 286 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.075515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057350 restraints weight = 76369.569| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.27 r_work: 0.2942 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 26559 Z= 0.197 Angle : 0.653 19.096 36240 Z= 0.333 Chirality : 0.048 0.544 4203 Planarity : 0.004 0.046 4614 Dihedral : 6.169 59.467 4577 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.31 % Rotamer: Outliers : 1.57 % Allowed : 11.74 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.14), residues: 3201 helix: 1.38 (0.20), residues: 720 sheet: 0.56 (0.20), residues: 729 loop : -1.92 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.018 0.001 TYR B1063 PHE 0.037 0.001 PHE B 923 TRP 0.038 0.002 TRP A 882 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00476 (26469) covalent geometry : angle 0.61410 (36009) SS BOND : bond 0.00354 ( 39) SS BOND : angle 1.65839 ( 78) hydrogen bonds : bond 0.06427 ( 988) hydrogen bonds : angle 4.93483 ( 2742) link_BETA1-4 : bond 0.00436 ( 3) link_BETA1-4 : angle 2.68528 ( 9) link_NAG-ASN : bond 0.00536 ( 48) link_NAG-ASN : angle 3.34497 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.6922 (p90) REVERT: A 571 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8680 (t0) REVERT: A 843 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7381 (mmp-170) REVERT: A 896 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7098 (mtp) REVERT: B 52 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: B 565 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.6948 (p90) REVERT: B 883 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 984 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8316 (mt-10) REVERT: B 1104 ASN cc_start: 0.7265 (m-40) cc_final: 0.6849 (p0) REVERT: C 271 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: C 565 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7441 (p90) REVERT: C 882 TRP cc_start: 0.7198 (p90) cc_final: 0.6883 (p90) REVERT: C 984 GLU cc_start: 0.8686 (tp30) cc_final: 0.8365 (tp30) REVERT: C 1034 LYS cc_start: 0.8852 (mppt) cc_final: 0.8429 (mmtm) REVERT: C 1073 THR cc_start: 0.7723 (p) cc_final: 0.7426 (p) outliers start: 44 outliers final: 26 residues processed: 124 average time/residue: 0.5487 time to fit residues: 81.6933 Evaluate side-chains 118 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1078 CYS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 1024 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 254 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058311 restraints weight = 75763.237| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.26 r_work: 0.2966 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26559 Z= 0.146 Angle : 0.612 19.100 36240 Z= 0.311 Chirality : 0.046 0.534 4203 Planarity : 0.004 0.048 4614 Dihedral : 6.055 60.783 4577 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 1.46 % Allowed : 11.96 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.14), residues: 3201 helix: 1.65 (0.21), residues: 702 sheet: 0.90 (0.21), residues: 678 loop : -1.92 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 843 TYR 0.018 0.001 TYR B1063 PHE 0.036 0.001 PHE B 923 TRP 0.037 0.002 TRP A 882 HIS 0.002 0.000 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00341 (26469) covalent geometry : angle 0.57249 (36009) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.45860 ( 78) hydrogen bonds : bond 0.05765 ( 988) hydrogen bonds : angle 4.81281 ( 2742) link_BETA1-4 : bond 0.00566 ( 3) link_BETA1-4 : angle 2.58624 ( 9) link_NAG-ASN : bond 0.00528 ( 48) link_NAG-ASN : angle 3.26979 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7827.98 seconds wall clock time: 134 minutes 16.43 seconds (8056.43 seconds total)