Starting phenix.real_space_refine on Sun May 25 00:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyh_38773/05_2025/8xyh_38773.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyh_38773/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyh_38773/05_2025/8xyh_38773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyh_38773/05_2025/8xyh_38773.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyh_38773/05_2025/8xyh_38773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyh_38773/05_2025/8xyh_38773.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.53, per 1000 atoms: 0.60 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: 5.97 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4.03 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: 12.99 Time building geometry restraints manager: 7.12 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1110 or resid 1301 through 1314)) selection = (chain 'B' and (resid 16 through 1110 or resid 1301 through 1314)) selection = (chain 'C' and (resid 16 through 1110 or resid 1301 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 60.760 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP C 64 HIS 0.003 0.001 HIS C 66 PHE 0.028 0.002 PHE B 902 TYR 0.024 0.002 TYR B 505 ARG 0.004 0.000 ARG A 901 Details of bonding type rmsd link_NAG-ASN : bond 0.01186 ( 48) link_NAG-ASN : angle 5.56403 ( 144) link_BETA1-4 : bond 0.03208 ( 3) link_BETA1-4 : angle 6.64574 ( 9) hydrogen bonds : bond 0.21318 ( 988) hydrogen bonds : angle 7.26504 ( 2742) SS BOND : bond 0.00525 ( 39) SS BOND : angle 2.69400 ( 78) covalent geometry : bond 0.00462 (26469) covalent geometry : angle 0.73787 (36009) *********************** 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 : 3.023 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: 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: 0.8160 (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: 1.3739 time to fit residues: 458.2669 Evaluate side-chains 125 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 2.804 ------------------------------------------------------------------------------- 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 271 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 187 optimal weight: 0.0570 chunk 291 optimal weight: 5.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- 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 317 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.078827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060669 restraints weight = 75314.606| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.27 r_work: 0.3016 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26559 Z= 0.161 Angle : 0.687 19.938 36240 Z= 0.348 Chirality : 0.049 0.659 4203 Planarity : 0.004 0.056 4614 Dihedral : 7.241 115.303 4583 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.19 % Rotamer: Outliers : 1.11 % Allowed : 7.17 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3201 helix: 1.64 (0.20), residues: 684 sheet: 0.43 (0.20), residues: 690 loop : -1.87 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS C 146 PHE 0.022 0.001 PHE B 884 TYR 0.018 0.001 TYR B1063 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00769 ( 48) link_NAG-ASN : angle 4.06190 ( 144) link_BETA1-4 : bond 0.00996 ( 3) link_BETA1-4 : angle 3.69327 ( 9) hydrogen bonds : bond 0.06799 ( 988) hydrogen bonds : angle 5.56513 ( 2742) SS BOND : bond 0.00291 ( 39) SS BOND : angle 1.57359 ( 78) covalent geometry : bond 0.00361 (26469) covalent geometry : angle 0.63213 (36009) *********************** 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 159 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.6331 (p90) REVERT: A 891 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: B 258 TRP cc_start: 0.7880 (p-90) cc_final: 0.7446 (p-90) REVERT: B 865 MET cc_start: 0.9103 (mtt) cc_final: 0.8895 (mtt) REVERT: B 883 THR cc_start: 0.8811 (p) cc_final: 0.8549 (t) REVERT: C 1103 ARG cc_start: 0.7837 (mtt90) cc_final: 0.7525 (mmt-90) REVERT: C 1107 GLU cc_start: 0.7546 (mp0) cc_final: 0.7245 (mp0) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 1.3260 time to fit residues: 235.3499 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 : 2.882 ------------------------------------------------------------------------------- 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 267 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 245 HIS ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 HIS C 146 HIS C 493 GLN C1109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058758 restraints weight = 75620.629| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.27 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26559 Z= 0.186 Angle : 0.666 19.739 36240 Z= 0.339 Chirality : 0.048 0.580 4203 Planarity : 0.004 0.046 4614 Dihedral : 6.551 59.803 4577 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 1.57 % Allowed : 8.82 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3201 helix: 1.71 (0.20), residues: 681 sheet: 0.35 (0.20), residues: 759 loop : -1.90 (0.12), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 152 HIS 0.003 0.001 HIS B 66 PHE 0.017 0.001 PHE B 884 TYR 0.016 0.001 TYR C 248 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 48) link_NAG-ASN : angle 3.76306 ( 144) link_BETA1-4 : bond 0.00737 ( 3) link_BETA1-4 : angle 3.34874 ( 9) hydrogen bonds : bond 0.06652 ( 988) hydrogen bonds : angle 5.25494 ( 2742) SS BOND : bond 0.00381 ( 39) SS BOND : angle 1.61481 ( 78) covalent geometry : bond 0.00440 (26469) covalent geometry : angle 0.61762 (36009) *********************** 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 146 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8289 (mtp) cc_final: 0.7795 (mtt) REVERT: A 565 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6628 (p90) REVERT: A 571 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8617 (t0) REVERT: B 169 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8557 (mm-30) REVERT: B 258 TRP cc_start: 0.7974 (p-90) cc_final: 0.7335 (p-90) REVERT: B 646 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8764 (ttp80) REVERT: B 865 MET cc_start: 0.9102 (mtt) cc_final: 0.8889 (mtt) REVERT: B 883 THR cc_start: 0.8749 (p) cc_final: 0.8484 (t) REVERT: B 984 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8344 (mt-10) REVERT: C 565 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7510 (p90) REVERT: C 984 GLU cc_start: 0.8536 (tp30) cc_final: 0.8198 (tp30) REVERT: C 1103 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7523 (mmt-90) REVERT: C 1107 GLU cc_start: 0.7614 (mp0) cc_final: 0.7400 (mp0) outliers start: 44 outliers final: 18 residues processed: 136 average time/residue: 1.1709 time to fit residues: 192.6468 Evaluate side-chains 114 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 2.814 ------------------------------------------------------------------------------- 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 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 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 975 ASP 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 234 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 275 optimal weight: 0.0770 chunk 263 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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** A 317 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 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 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055861 restraints weight = 77014.586| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.27 r_work: 0.2904 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 26559 Z= 0.286 Angle : 0.760 19.878 36240 Z= 0.390 Chirality : 0.051 0.602 4203 Planarity : 0.005 0.052 4614 Dihedral : 6.979 57.282 4577 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 2.32 % Allowed : 9.28 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3201 helix: 1.10 (0.20), residues: 717 sheet: 0.25 (0.19), residues: 792 loop : -2.14 (0.12), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 152 HIS 0.007 0.001 HIS C 146 PHE 0.024 0.002 PHE A1085 TYR 0.021 0.002 TYR C 380 ARG 0.006 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00743 ( 48) link_NAG-ASN : angle 3.84418 ( 144) link_BETA1-4 : bond 0.00322 ( 3) link_BETA1-4 : angle 3.29236 ( 9) hydrogen bonds : bond 0.07929 ( 988) hydrogen bonds : angle 5.44623 ( 2742) SS BOND : bond 0.00491 ( 39) SS BOND : angle 2.07428 ( 78) covalent geometry : bond 0.00694 (26469) covalent geometry : angle 0.71374 (36009) *********************** 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 163 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 98 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8210 (mtp) cc_final: 0.7710 (mtt) REVERT: A 565 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.6827 (p90) REVERT: A 571 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (t0) REVERT: A 891 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: A 896 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6936 (mtp) REVERT: A 1104 ASN cc_start: 0.7432 (m-40) cc_final: 0.7145 (m-40) REVERT: B 52 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8122 (tp40) REVERT: B 565 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7198 (p90) REVERT: B 646 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8799 (ttp80) REVERT: B 883 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8481 (t) REVERT: B 984 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8393 (mt-10) REVERT: C 565 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7347 (p90) REVERT: C 868 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8608 (mt0) REVERT: C 984 GLU cc_start: 0.8652 (tp30) cc_final: 0.8398 (tp30) REVERT: C 1104 ASN cc_start: 0.7392 (m-40) cc_final: 0.6584 (p0) REVERT: C 1107 GLU cc_start: 0.7604 (mp0) cc_final: 0.7354 (mp0) outliers start: 65 outliers final: 25 residues processed: 152 average time/residue: 1.1210 time to fit residues: 205.4392 Evaluate side-chains 126 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 2.828 ------------------------------------------------------------------------------- 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 891 GLN 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 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1062 THR 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 868 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 911 VAL 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 235 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 317 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058921 restraints weight = 76195.280| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.27 r_work: 0.2980 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2609 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= 0.123 Angle : 0.609 19.730 36240 Z= 0.309 Chirality : 0.046 0.553 4203 Planarity : 0.004 0.044 4614 Dihedral : 6.285 59.962 4577 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.38 % Rotamer: Outliers : 1.64 % Allowed : 10.92 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3201 helix: 1.59 (0.20), residues: 702 sheet: 0.87 (0.21), residues: 672 loop : -1.96 (0.12), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 152 HIS 0.007 0.001 HIS B 146 PHE 0.015 0.001 PHE B 884 TYR 0.016 0.001 TYR C 145 ARG 0.008 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 48) link_NAG-ASN : angle 3.48088 ( 144) link_BETA1-4 : bond 0.00638 ( 3) link_BETA1-4 : angle 3.00888 ( 9) hydrogen bonds : bond 0.05628 ( 988) hydrogen bonds : angle 4.96361 ( 2742) SS BOND : bond 0.00309 ( 39) SS BOND : angle 1.38557 ( 78) covalent geometry : bond 0.00267 (26469) covalent geometry : angle 0.56380 (36009) *********************** 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 146 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8131 (mtp) cc_final: 0.7650 (mtt) REVERT: A 565 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.6940 (p90) REVERT: A 571 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8618 (t0) REVERT: A 1104 ASN cc_start: 0.7398 (m-40) cc_final: 0.7066 (m-40) REVERT: B 52 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: B 169 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8618 (mm-30) REVERT: B 883 THR cc_start: 0.8726 (p) cc_final: 0.8429 (t) REVERT: B 984 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 565 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7543 (p90) REVERT: C 984 GLU cc_start: 0.8691 (tp30) cc_final: 0.8378 (tp30) REVERT: C 1103 ARG cc_start: 0.7404 (mmt-90) cc_final: 0.6684 (mmm-85) REVERT: C 1107 GLU cc_start: 0.7548 (mp0) cc_final: 0.7344 (mp0) outliers start: 46 outliers final: 18 residues processed: 137 average time/residue: 1.1540 time to fit residues: 190.5793 Evaluate side-chains 115 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 1062 THR 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 336 CYS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 645 THR 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 1101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 91 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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** A1032 GLN B 164 ASN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 ASN C 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059699 restraints weight = 75839.431| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.25 r_work: 0.2998 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26559 Z= 0.116 Angle : 0.587 19.389 36240 Z= 0.296 Chirality : 0.046 0.533 4203 Planarity : 0.004 0.042 4614 Dihedral : 5.992 58.734 4577 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 1.78 % Allowed : 10.99 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3201 helix: 1.87 (0.21), residues: 684 sheet: 0.81 (0.20), residues: 711 loop : -1.89 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 882 HIS 0.003 0.001 HIS B 146 PHE 0.017 0.001 PHE B1071 TYR 0.020 0.001 TYR B1063 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 48) link_NAG-ASN : angle 3.32315 ( 144) link_BETA1-4 : bond 0.00645 ( 3) link_BETA1-4 : angle 2.71051 ( 9) hydrogen bonds : bond 0.05191 ( 988) hydrogen bonds : angle 4.76335 ( 2742) SS BOND : bond 0.00230 ( 39) SS BOND : angle 1.26750 ( 78) covalent geometry : bond 0.00259 (26469) covalent geometry : angle 0.54547 (36009) *********************** 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 150 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8094 (mtp) cc_final: 0.7599 (mtt) REVERT: A 565 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7008 (p90) REVERT: A 571 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8625 (t0) REVERT: A 727 MET cc_start: 0.8932 (ptp) cc_final: 0.8708 (ptm) REVERT: A 800 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8693 (mm110) REVERT: A 984 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8304 (mp0) REVERT: A 1104 ASN cc_start: 0.7381 (m-40) cc_final: 0.7073 (m-40) REVERT: B 169 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8612 (mm-30) REVERT: B 565 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6984 (p90) REVERT: B 883 THR cc_start: 0.8707 (p) cc_final: 0.8419 (t) REVERT: B 984 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8306 (mt-10) REVERT: C 565 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7444 (p90) REVERT: C 984 GLU cc_start: 0.8669 (tp30) cc_final: 0.8335 (tp30) REVERT: C 1103 ARG cc_start: 0.7386 (mmt-90) cc_final: 0.6628 (mmm-85) outliers start: 50 outliers final: 24 residues processed: 140 average time/residue: 1.2421 time to fit residues: 209.2289 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 : 2.602 ------------------------------------------------------------------------------- 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 597 VAL Chi-restraints excluded: chain A residue 800 GLN Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR 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 336 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 645 THR 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 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 Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 286 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 99 optimal weight: 0.0030 chunk 299 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 overall best weight: 1.3190 ------------------------------------------------------------------------------- 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 931 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 = 0.3529 r_free = 0.3529 target = 0.077449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059410 restraints weight = 76314.351| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.26 r_work: 0.2992 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26559 Z= 0.124 Angle : 0.585 19.273 36240 Z= 0.296 Chirality : 0.045 0.525 4203 Planarity : 0.004 0.043 4614 Dihedral : 5.930 58.521 4577 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 2.07 % Allowed : 11.42 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3201 helix: 1.72 (0.20), residues: 702 sheet: 0.78 (0.20), residues: 732 loop : -1.83 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 882 HIS 0.003 0.001 HIS B 146 PHE 0.012 0.001 PHE B 884 TYR 0.013 0.001 TYR B 265 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 48) link_NAG-ASN : angle 3.27715 ( 144) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 2.55829 ( 9) hydrogen bonds : bond 0.05226 ( 988) hydrogen bonds : angle 4.71338 ( 2742) SS BOND : bond 0.00241 ( 39) SS BOND : angle 1.28251 ( 78) covalent geometry : bond 0.00283 (26469) covalent geometry : angle 0.54405 (36009) *********************** 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 154 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 96 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8070 (mtp) cc_final: 0.7595 (mtt) REVERT: A 565 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.6983 (p90) REVERT: A 571 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8619 (t0) REVERT: A 984 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8302 (mp0) REVERT: A 1104 ASN cc_start: 0.7355 (m-40) cc_final: 0.7087 (m-40) REVERT: B 24 LEU cc_start: 0.9102 (mp) cc_final: 0.8900 (mp) REVERT: B 52 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8137 (tp40) REVERT: B 169 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8605 (mm-30) REVERT: B 565 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6960 (p90) REVERT: B 883 THR cc_start: 0.8742 (p) cc_final: 0.8446 (t) REVERT: B 984 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 271 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: C 565 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7439 (p90) REVERT: C 984 GLU cc_start: 0.8673 (tp30) cc_final: 0.8338 (tp30) REVERT: C 1103 ARG cc_start: 0.7347 (mmt-90) cc_final: 0.6523 (mmm-85) outliers start: 58 outliers final: 29 residues processed: 143 average time/residue: 1.2009 time to fit residues: 210.3304 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 : 2.599 ------------------------------------------------------------------------------- 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 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 701 VAL 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 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 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR 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 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 907 VAL Chi-restraints excluded: chain C residue 1101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 157 optimal weight: 0.0370 chunk 236 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- 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 897 GLN 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 = 0.3537 r_free = 0.3537 target = 0.077829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059838 restraints weight = 75899.187| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.27 r_work: 0.3002 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26559 Z= 0.118 Angle : 0.584 19.190 36240 Z= 0.295 Chirality : 0.045 0.516 4203 Planarity : 0.004 0.043 4614 Dihedral : 5.901 58.592 4577 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.25 % Rotamer: Outliers : 1.75 % Allowed : 11.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3201 helix: 1.76 (0.21), residues: 702 sheet: 0.87 (0.20), residues: 711 loop : -1.84 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 882 HIS 0.003 0.001 HIS B 146 PHE 0.018 0.001 PHE B1071 TYR 0.021 0.001 TYR B1063 ARG 0.006 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 48) link_NAG-ASN : angle 3.21725 ( 144) link_BETA1-4 : bond 0.00713 ( 3) link_BETA1-4 : angle 2.42480 ( 9) hydrogen bonds : bond 0.05029 ( 988) hydrogen bonds : angle 4.65810 ( 2742) SS BOND : bond 0.00230 ( 39) SS BOND : angle 1.60282 ( 78) covalent geometry : bond 0.00268 (26469) covalent geometry : angle 0.54337 (36009) *********************** 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 149 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8045 (mtp) cc_final: 0.7560 (mtt) REVERT: A 565 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.6970 (p90) REVERT: A 571 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8621 (t0) REVERT: A 1104 ASN cc_start: 0.7333 (m-40) cc_final: 0.7085 (m-40) REVERT: B 52 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8089 (tp40) REVERT: B 169 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: B 565 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6951 (p90) REVERT: B 883 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8406 (t) REVERT: B 984 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8293 (mt-10) REVERT: C 271 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: C 565 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7410 (p90) REVERT: C 984 GLU cc_start: 0.8658 (tp30) cc_final: 0.8317 (tp30) REVERT: C 1103 ARG cc_start: 0.7330 (mmt-90) cc_final: 0.6518 (mmm-85) outliers start: 49 outliers final: 26 residues processed: 139 average time/residue: 1.1004 time to fit residues: 184.6118 Evaluate side-chains 125 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1062 THR 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 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 883 THR 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 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 907 VAL Chi-restraints excluded: chain C residue 1024 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 105 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 146 optimal weight: 0.0570 chunk 113 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- 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 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 = 0.3518 r_free = 0.3518 target = 0.076861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058735 restraints weight = 76534.922| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.28 r_work: 0.2975 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26559 Z= 0.146 Angle : 0.608 19.148 36240 Z= 0.308 Chirality : 0.046 0.519 4203 Planarity : 0.004 0.044 4614 Dihedral : 6.008 59.826 4577 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.09 % Favored : 93.81 % Rotamer: Outliers : 1.64 % Allowed : 11.96 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3201 helix: 1.70 (0.21), residues: 702 sheet: 0.81 (0.20), residues: 726 loop : -1.87 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 882 HIS 0.005 0.001 HIS A1097 PHE 0.017 0.001 PHE B 796 TYR 0.013 0.001 TYR B 248 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 48) link_NAG-ASN : angle 3.24545 ( 144) link_BETA1-4 : bond 0.00494 ( 3) link_BETA1-4 : angle 2.42186 ( 9) hydrogen bonds : bond 0.05540 ( 988) hydrogen bonds : angle 4.72555 ( 2742) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.64063 ( 78) covalent geometry : bond 0.00346 (26469) covalent geometry : angle 0.56818 (36009) *********************** 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 141 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8049 (mtp) cc_final: 0.7558 (mtt) REVERT: A 565 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.6919 (p90) REVERT: A 571 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8638 (t0) REVERT: A 896 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7117 (mtp) REVERT: B 52 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: B 169 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8603 (mm-30) REVERT: B 565 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.6942 (p90) REVERT: B 883 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8440 (t) REVERT: B 984 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 1104 ASN cc_start: 0.7316 (m-40) cc_final: 0.6956 (p0) REVERT: C 271 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: C 565 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7450 (p90) REVERT: C 882 TRP cc_start: 0.7177 (p90) cc_final: 0.6896 (p90) REVERT: C 984 GLU cc_start: 0.8691 (tp30) cc_final: 0.8364 (tp30) REVERT: C 1103 ARG cc_start: 0.7204 (mmt-90) cc_final: 0.6846 (mmt-90) outliers start: 46 outliers final: 26 residues processed: 129 average time/residue: 1.2367 time to fit residues: 189.3251 Evaluate side-chains 123 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 701 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 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 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1046 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 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 907 VAL Chi-restraints excluded: chain C residue 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 158 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 252 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.076230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058109 restraints weight = 76171.569| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.28 r_work: 0.2961 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26559 Z= 0.159 Angle : 0.624 19.191 36240 Z= 0.318 Chirality : 0.046 0.525 4203 Planarity : 0.004 0.056 4614 Dihedral : 6.141 61.732 4577 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 1.68 % Allowed : 12.03 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3201 helix: 1.63 (0.20), residues: 702 sheet: 0.61 (0.20), residues: 729 loop : -1.88 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 882 HIS 0.004 0.001 HIS B 146 PHE 0.040 0.001 PHE C1105 TYR 0.021 0.001 TYR B1063 ARG 0.005 0.000 ARG C1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 48) link_NAG-ASN : angle 3.25383 ( 144) link_BETA1-4 : bond 0.00535 ( 3) link_BETA1-4 : angle 2.42295 ( 9) hydrogen bonds : bond 0.05861 ( 988) hydrogen bonds : angle 4.80083 ( 2742) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.65719 ( 78) covalent geometry : bond 0.00377 (26469) covalent geometry : angle 0.58491 (36009) ********************** 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: 47 poor density : 86 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8056 (mtp) cc_final: 0.7562 (mtt) REVERT: A 565 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.6978 (p90) REVERT: A 571 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8656 (t0) REVERT: A 843 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7331 (mmp-170) REVERT: A 896 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: B 52 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: B 169 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: B 565 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6958 (p90) REVERT: B 883 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 984 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 1104 ASN cc_start: 0.7334 (m-40) cc_final: 0.6938 (p0) REVERT: C 271 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: C 565 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7440 (p90) REVERT: C 984 GLU cc_start: 0.8714 (tp30) cc_final: 0.8391 (tp30) REVERT: C 1073 THR cc_start: 0.7753 (p) cc_final: 0.7463 (p) REVERT: C 1103 ARG cc_start: 0.7192 (mmt-90) cc_final: 0.6444 (mmm-85) outliers start: 47 outliers final: 26 residues processed: 119 average time/residue: 1.1822 time to fit residues: 169.5212 Evaluate side-chains 119 residues out of total 2802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 701 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 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 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 638 THR 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 B residue 1046 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 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 1077 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 171 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.076636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058607 restraints weight = 76208.156| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.27 r_work: 0.2974 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3066 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= 0.140 Angle : 0.605 19.146 36240 Z= 0.307 Chirality : 0.046 0.518 4203 Planarity : 0.004 0.048 4614 Dihedral : 6.048 63.360 4577 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 1.46 % Allowed : 12.35 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3201 helix: 1.66 (0.21), residues: 702 sheet: 0.64 (0.20), residues: 732 loop : -1.87 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 882 HIS 0.002 0.000 HIS A1044 PHE 0.040 0.001 PHE C1105 TYR 0.019 0.001 TYR B1063 ARG 0.009 0.000 ARG B 147 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 48) link_NAG-ASN : angle 3.20437 ( 144) link_BETA1-4 : bond 0.00578 ( 3) link_BETA1-4 : angle 2.42227 ( 9) hydrogen bonds : bond 0.05548 ( 988) hydrogen bonds : angle 4.73681 ( 2742) SS BOND : bond 0.00259 ( 39) SS BOND : angle 1.54721 ( 78) covalent geometry : bond 0.00328 (26469) covalent geometry : angle 0.56679 (36009) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16643.59 seconds wall clock time: 287 minutes 59.59 seconds (17279.59 seconds total)