Starting phenix.real_space_refine on Mon Aug 25 02:52:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukd_42352/08_2025/8ukd_42352.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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 15822 2.51 5 N 4089 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24777 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "B" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "C" Number of atoms: 8133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8133 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.99, per 1000 atoms: 0.20 Number of scatterers: 24777 At special positions: 0 Unit cell: (141.48, 132.84, 173.88, 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 4752 8.00 N 4089 7.00 C 15822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5862 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 47 sheets defined 25.6% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.943A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.690A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.595A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.552A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.558A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.522A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.665A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.729A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.562A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.597A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.507A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.590A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.517A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.689A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.722A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.938A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.447A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.697A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.535A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.568A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.541A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.794A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.583A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.524A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.620A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.526A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 142 removed outlier: 5.412A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.216A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.558A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.969A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.888A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.317A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.605A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.725A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.813A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 201 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.931A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AC5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.816A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.215A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.507A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.203A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.738A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.915A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.421A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.852A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.434A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.129A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.053A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.914A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.971A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.446A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 976 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 1552 1.23 - 1.39: 8663 1.39 - 1.54: 14826 1.54 - 1.70: 156 1.70 - 1.85: 141 Bond restraints: 25338 Sorted by residual: bond pdb=" CG PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 1.503 1.079 0.424 3.40e-02 8.65e+02 1.56e+02 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.332 1.385 -0.054 1.32e-02 5.74e+03 1.66e+01 bond pdb=" N PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" CB PRO B 82 " pdb=" CG PRO B 82 " ideal model delta sigma weight residual 1.492 1.365 0.127 5.00e-02 4.00e+02 6.43e+00 bond pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.75e+00 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 34394 5.40 - 10.81: 66 10.81 - 16.21: 7 16.21 - 21.62: 1 21.62 - 27.02: 2 Bond angle restraints: 34470 Sorted by residual: angle pdb=" N PRO B 82 " pdb=" CD PRO B 82 " pdb=" CG PRO B 82 " ideal model delta sigma weight residual 103.20 76.18 27.02 1.50e+00 4.44e-01 3.25e+02 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 113.10 101.52 11.58 9.70e-01 1.06e+00 1.43e+02 angle pdb=" CA PRO B 82 " pdb=" CB PRO B 82 " pdb=" CG PRO B 82 " ideal model delta sigma weight residual 104.50 84.24 20.26 1.90e+00 2.77e-01 1.14e+02 angle pdb=" CA PRO B 82 " pdb=" N PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CB PRO B 82 " pdb=" CG PRO B 82 " pdb=" CD PRO B 82 " ideal model delta sigma weight residual 106.10 128.47 -22.37 3.20e+00 9.77e-02 4.89e+01 ... (remaining 34465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13993 17.95 - 35.90: 1216 35.90 - 53.86: 189 53.86 - 71.81: 61 71.81 - 89.76: 27 Dihedral angle restraints: 15486 sinusoidal: 6381 harmonic: 9105 Sorted by residual: dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 147.32 -54.32 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -36.07 -49.93 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 15483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3516 0.087 - 0.174: 446 0.174 - 0.261: 25 0.261 - 0.348: 6 0.348 - 0.435: 3 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CG LEU B 117 " pdb=" CB LEU B 117 " pdb=" CD1 LEU B 117 " pdb=" CD2 LEU B 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 3993 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.03e+01 pdb=" N PRO B 521 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 198 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" CG ASP C 198 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP C 198 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP C 198 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " 0.028 2.00e-02 2.50e+03 2.69e-02 9.02e+00 pdb=" CG ASN C 801 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG C1309 " 0.030 2.00e-02 2.50e+03 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6273 2.80 - 3.33: 19763 3.33 - 3.85: 39926 3.85 - 4.38: 45368 4.38 - 4.90: 81735 Nonbonded interactions: 193065 Sorted by model distance: nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.280 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.300 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.304 3.040 nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.308 3.040 ... (remaining 193060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.520 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.006 0.424 25407 Z= 0.236 Angle : 0.849 27.021 34635 Z= 0.451 Chirality : 0.056 0.435 3996 Planarity : 0.006 0.080 4425 Dihedral : 14.071 89.762 9498 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.14), residues: 3081 helix: -0.47 (0.17), residues: 690 sheet: -0.24 (0.19), residues: 663 loop : -1.57 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.028 0.002 TYR B 453 PHE 0.035 0.002 PHE B 168 TRP 0.030 0.002 TRP B 886 HIS 0.008 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00553 (25338) covalent geometry : angle 0.83322 (34470) SS BOND : bond 0.00617 ( 42) SS BOND : angle 2.08503 ( 84) hydrogen bonds : bond 0.20961 ( 976) hydrogen bonds : angle 7.59217 ( 2691) link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 2.92354 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8487 (m-80) cc_final: 0.8268 (m-80) REVERT: A 661 GLU cc_start: 0.7557 (tt0) cc_final: 0.7318 (tt0) REVERT: B 51 THR cc_start: 0.8917 (p) cc_final: 0.8647 (p) REVERT: B 420 ASP cc_start: 0.7499 (m-30) cc_final: 0.6997 (m-30) REVERT: C 450 ASN cc_start: 0.7595 (m-40) cc_final: 0.7340 (m-40) REVERT: C 1005 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7584 (tp40) outliers start: 1 outliers final: 1 residues processed: 279 average time/residue: 0.4894 time to fit residues: 161.3200 Evaluate side-chains 207 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 439 ASN A 544 ASN A 901 GLN A1010 GLN A1011 GLN B 196 ASN B 207 HIS B 394 ASN B 532 ASN B 556 ASN B1002 GLN B1010 GLN C 66 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 907 ASN C1011 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.178292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130530 restraints weight = 27215.080| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.70 r_work: 0.3104 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25407 Z= 0.130 Angle : 0.565 12.664 34635 Z= 0.294 Chirality : 0.045 0.300 3996 Planarity : 0.004 0.056 4425 Dihedral : 6.236 52.584 3911 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.22 % Allowed : 7.11 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3081 helix: 1.04 (0.19), residues: 714 sheet: 0.37 (0.20), residues: 654 loop : -1.47 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.021 0.001 TYR A1067 PHE 0.021 0.001 PHE B 168 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00297 (25338) covalent geometry : angle 0.55254 (34470) SS BOND : bond 0.00434 ( 42) SS BOND : angle 1.54953 ( 84) hydrogen bonds : bond 0.05155 ( 976) hydrogen bonds : angle 5.40287 ( 2691) link_NAG-ASN : bond 0.00363 ( 27) link_NAG-ASN : angle 1.99657 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8121 (m-30) cc_final: 0.7670 (m-30) REVERT: A 655 TYR cc_start: 0.8392 (t80) cc_final: 0.8147 (t80) REVERT: A 661 GLU cc_start: 0.8106 (tt0) cc_final: 0.7832 (tt0) REVERT: B 226 LEU cc_start: 0.6858 (pp) cc_final: 0.6459 (pp) REVERT: B 236 THR cc_start: 0.7844 (m) cc_final: 0.7324 (p) REVERT: C 450 ASN cc_start: 0.7606 (m-40) cc_final: 0.7398 (m-40) REVERT: C 740 MET cc_start: 0.8773 (tpp) cc_final: 0.8492 (tpt) REVERT: C 1005 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8110 (tp40) outliers start: 33 outliers final: 19 residues processed: 255 average time/residue: 0.5080 time to fit residues: 152.6967 Evaluate side-chains 228 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 248 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 215 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 519 HIS A 965 GLN A1010 GLN B 66 HIS B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 532 ASN B 556 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 907 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.176970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136898 restraints weight = 27261.766| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.61 r_work: 0.3082 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25407 Z= 0.141 Angle : 0.554 10.087 34635 Z= 0.286 Chirality : 0.045 0.281 3996 Planarity : 0.004 0.055 4425 Dihedral : 5.750 51.847 3909 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 9.10 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.14), residues: 3081 helix: 1.70 (0.19), residues: 702 sheet: 0.15 (0.20), residues: 633 loop : -1.33 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.024 0.001 TYR A 170 PHE 0.022 0.001 PHE B 168 TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00338 (25338) covalent geometry : angle 0.54205 (34470) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.49813 ( 84) hydrogen bonds : bond 0.05184 ( 976) hydrogen bonds : angle 5.03571 ( 2691) link_NAG-ASN : bond 0.00353 ( 27) link_NAG-ASN : angle 1.93997 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8235 (m-30) cc_final: 0.7799 (m-30) REVERT: A 655 TYR cc_start: 0.8434 (t80) cc_final: 0.8183 (t80) REVERT: A 661 GLU cc_start: 0.8166 (tt0) cc_final: 0.7876 (tt0) REVERT: A 869 MET cc_start: 0.9303 (mtt) cc_final: 0.9046 (mtt) REVERT: A 1010 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 226 LEU cc_start: 0.7047 (pp) cc_final: 0.6628 (pp) REVERT: B 236 THR cc_start: 0.7913 (m) cc_final: 0.7392 (p) REVERT: C 269 TYR cc_start: 0.8196 (m-10) cc_final: 0.7832 (m-10) REVERT: C 450 ASN cc_start: 0.7671 (m-40) cc_final: 0.7460 (m-40) REVERT: C 646 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7225 (mtp180) REVERT: C 690 GLN cc_start: 0.7859 (mm110) cc_final: 0.7525 (mp10) REVERT: C 740 MET cc_start: 0.8830 (tpp) cc_final: 0.8585 (tpt) REVERT: C 869 MET cc_start: 0.9028 (mtt) cc_final: 0.8807 (mtt) REVERT: C 1005 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8216 (tp40) outliers start: 51 outliers final: 31 residues processed: 254 average time/residue: 0.4787 time to fit residues: 144.8896 Evaluate side-chains 242 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 965 GLN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 824 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.175497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.136679 restraints weight = 27101.178| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.54 r_work: 0.3073 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25407 Z= 0.167 Angle : 0.576 8.853 34635 Z= 0.297 Chirality : 0.046 0.284 3996 Planarity : 0.004 0.054 4425 Dihedral : 5.650 53.301 3909 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 2.36 % Allowed : 10.24 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 3081 helix: 1.60 (0.19), residues: 729 sheet: 0.18 (0.20), residues: 642 loop : -1.35 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.002 PHE B 168 TRP 0.013 0.001 TRP A 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00408 (25338) covalent geometry : angle 0.56265 (34470) SS BOND : bond 0.00466 ( 42) SS BOND : angle 1.69630 ( 84) hydrogen bonds : bond 0.05375 ( 976) hydrogen bonds : angle 5.00828 ( 2691) link_NAG-ASN : bond 0.00356 ( 27) link_NAG-ASN : angle 1.98067 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8183 (m-30) cc_final: 0.7707 (m-30) REVERT: A 661 GLU cc_start: 0.8296 (tt0) cc_final: 0.8010 (tt0) REVERT: A 787 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: A 869 MET cc_start: 0.9285 (mtt) cc_final: 0.9082 (mtt) REVERT: B 226 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6763 (pp) REVERT: B 506 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: C 269 TYR cc_start: 0.8258 (m-10) cc_final: 0.7866 (m-10) REVERT: C 450 ASN cc_start: 0.7739 (m-40) cc_final: 0.7534 (m-40) REVERT: C 646 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7309 (mtp180) REVERT: C 690 GLN cc_start: 0.7875 (mm110) cc_final: 0.7528 (mp10) REVERT: C 869 MET cc_start: 0.9056 (mtt) cc_final: 0.8842 (mtt) outliers start: 64 outliers final: 36 residues processed: 250 average time/residue: 0.4681 time to fit residues: 140.5648 Evaluate side-chains 246 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 187 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 965 GLN A1010 GLN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.179326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141714 restraints weight = 27048.222| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.55 r_work: 0.3083 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25407 Z= 0.120 Angle : 0.528 10.872 34635 Z= 0.273 Chirality : 0.044 0.264 3996 Planarity : 0.004 0.060 4425 Dihedral : 5.393 52.433 3909 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.06 % Allowed : 11.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.15), residues: 3081 helix: 2.05 (0.20), residues: 705 sheet: 0.18 (0.20), residues: 624 loop : -1.25 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.024 0.001 TYR A 170 PHE 0.018 0.001 PHE B 168 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00282 (25338) covalent geometry : angle 0.51740 (34470) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.51821 ( 84) hydrogen bonds : bond 0.04704 ( 976) hydrogen bonds : angle 4.86524 ( 2691) link_NAG-ASN : bond 0.00336 ( 27) link_NAG-ASN : angle 1.76556 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8178 (m-30) cc_final: 0.7679 (m-30) REVERT: A 661 GLU cc_start: 0.8182 (tt0) cc_final: 0.7880 (tt0) REVERT: A 1010 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: B 218 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7623 (mm110) REVERT: B 226 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6732 (pp) REVERT: B 236 THR cc_start: 0.7871 (m) cc_final: 0.7349 (p) REVERT: B 506 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: B 934 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7917 (mp) REVERT: C 269 TYR cc_start: 0.8236 (m-10) cc_final: 0.7875 (m-10) REVERT: C 646 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7321 (mtp180) REVERT: C 690 GLN cc_start: 0.7857 (mm110) cc_final: 0.7507 (mp10) REVERT: C 869 MET cc_start: 0.9024 (mtt) cc_final: 0.8766 (mtt) outliers start: 56 outliers final: 32 residues processed: 251 average time/residue: 0.4688 time to fit residues: 140.1643 Evaluate side-chains 245 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 257 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 218 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 156 optimal weight: 0.0670 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 935 GLN A 965 GLN A1010 GLN B 66 HIS B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.184456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150291 restraints weight = 26882.816| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.35 r_work: 0.3142 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25407 Z= 0.098 Angle : 0.502 9.476 34635 Z= 0.259 Chirality : 0.043 0.249 3996 Planarity : 0.003 0.053 4425 Dihedral : 5.154 53.358 3909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 12.08 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3081 helix: 2.10 (0.20), residues: 723 sheet: 0.28 (0.20), residues: 624 loop : -1.16 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.001 PHE B 168 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00219 (25338) covalent geometry : angle 0.49328 (34470) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.21401 ( 84) hydrogen bonds : bond 0.04185 ( 976) hydrogen bonds : angle 4.72311 ( 2691) link_NAG-ASN : bond 0.00331 ( 27) link_NAG-ASN : angle 1.62754 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8153 (m-30) cc_final: 0.7588 (m-30) REVERT: A 661 GLU cc_start: 0.8058 (tt0) cc_final: 0.7760 (tt0) REVERT: A 787 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: A 1010 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7747 (tp-100) REVERT: B 118 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6223 (mt) REVERT: B 218 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7555 (mm110) REVERT: B 226 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6660 (pp) REVERT: B 236 THR cc_start: 0.7782 (m) cc_final: 0.7229 (p) REVERT: B 506 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: C 269 TYR cc_start: 0.8197 (m-10) cc_final: 0.7993 (m-10) REVERT: C 646 ARG cc_start: 0.7878 (tpt90) cc_final: 0.7202 (mtp180) REVERT: C 690 GLN cc_start: 0.7772 (mm110) cc_final: 0.7427 (mp10) REVERT: C 1029 MET cc_start: 0.8995 (tpp) cc_final: 0.8607 (tpp) outliers start: 48 outliers final: 26 residues processed: 251 average time/residue: 0.4596 time to fit residues: 137.5196 Evaluate side-chains 239 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 7 optimal weight: 0.0040 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 339 HIS A 493 GLN A 965 GLN A1010 GLN B 66 HIS B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.185223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151235 restraints weight = 26888.006| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.36 r_work: 0.3154 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25407 Z= 0.094 Angle : 0.487 8.524 34635 Z= 0.252 Chirality : 0.043 0.243 3996 Planarity : 0.003 0.053 4425 Dihedral : 4.975 53.324 3909 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.77 % Allowed : 12.67 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.15), residues: 3081 helix: 2.24 (0.20), residues: 723 sheet: 0.35 (0.20), residues: 624 loop : -1.10 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.025 0.001 TYR A 170 PHE 0.015 0.001 PHE C 592 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.000 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00207 (25338) covalent geometry : angle 0.47914 (34470) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.14233 ( 84) hydrogen bonds : bond 0.03974 ( 976) hydrogen bonds : angle 4.62351 ( 2691) link_NAG-ASN : bond 0.00332 ( 27) link_NAG-ASN : angle 1.55705 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8155 (m-30) cc_final: 0.7698 (m-30) REVERT: A 661 GLU cc_start: 0.8065 (tt0) cc_final: 0.7795 (tt0) REVERT: A 787 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: A 1010 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7795 (tp-100) REVERT: B 118 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.6179 (mt) REVERT: B 226 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6722 (pp) REVERT: B 236 THR cc_start: 0.7747 (m) cc_final: 0.7191 (p) REVERT: B 506 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: B 1113 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: C 403 ARG cc_start: 0.7294 (ptm160) cc_final: 0.6945 (ptp-170) REVERT: C 646 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7176 (mtp180) REVERT: C 690 GLN cc_start: 0.7770 (mm110) cc_final: 0.7450 (mp10) REVERT: C 1029 MET cc_start: 0.8984 (tpp) cc_final: 0.8631 (tpp) outliers start: 48 outliers final: 27 residues processed: 255 average time/residue: 0.4365 time to fit residues: 133.3907 Evaluate side-chains 241 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 135 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 187 optimal weight: 0.0670 chunk 301 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 935 GLN A 965 GLN A1010 GLN B 66 HIS B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1010 GLN B1088 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.184545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150539 restraints weight = 26935.849| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.36 r_work: 0.3153 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25407 Z= 0.104 Angle : 0.505 13.632 34635 Z= 0.257 Chirality : 0.043 0.236 3996 Planarity : 0.003 0.052 4425 Dihedral : 4.957 52.782 3909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 1.92 % Allowed : 12.97 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.15), residues: 3081 helix: 2.25 (0.20), residues: 723 sheet: 0.32 (0.20), residues: 624 loop : -1.09 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.017 0.001 TYR B1067 PHE 0.014 0.001 PHE B 168 TRP 0.007 0.001 TRP C 436 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00238 (25338) covalent geometry : angle 0.49672 (34470) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.20225 ( 84) hydrogen bonds : bond 0.04139 ( 976) hydrogen bonds : angle 4.61265 ( 2691) link_NAG-ASN : bond 0.00322 ( 27) link_NAG-ASN : angle 1.56621 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8167 (m-30) cc_final: 0.7719 (m-30) REVERT: A 661 GLU cc_start: 0.8096 (tt0) cc_final: 0.7820 (tt0) REVERT: A 787 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: B 118 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6192 (mt) REVERT: B 226 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6762 (pp) REVERT: B 236 THR cc_start: 0.7776 (m) cc_final: 0.7223 (p) REVERT: B 382 VAL cc_start: 0.8468 (m) cc_final: 0.8208 (p) REVERT: B 506 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: B 1113 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: C 403 ARG cc_start: 0.7239 (ptm160) cc_final: 0.6914 (ptp-170) REVERT: C 646 ARG cc_start: 0.7907 (tpt90) cc_final: 0.7218 (mtp180) REVERT: C 690 GLN cc_start: 0.7773 (mm110) cc_final: 0.7457 (mp10) REVERT: C 1029 MET cc_start: 0.8973 (tpp) cc_final: 0.8611 (tpp) outliers start: 52 outliers final: 35 residues processed: 248 average time/residue: 0.4585 time to fit residues: 135.3999 Evaluate side-chains 245 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 247 optimal weight: 0.2980 chunk 194 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 127 optimal weight: 0.0050 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 965 GLN A1010 GLN B 314 GLN B 405 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.185890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151179 restraints weight = 26875.435| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.46 r_work: 0.3147 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25407 Z= 0.092 Angle : 0.486 12.941 34635 Z= 0.248 Chirality : 0.043 0.231 3996 Planarity : 0.003 0.052 4425 Dihedral : 4.810 53.377 3909 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 1.73 % Allowed : 13.48 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 3081 helix: 2.39 (0.20), residues: 723 sheet: 0.36 (0.20), residues: 630 loop : -1.03 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.025 0.001 TYR A 170 PHE 0.013 0.001 PHE B 168 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00203 (25338) covalent geometry : angle 0.47875 (34470) SS BOND : bond 0.00279 ( 42) SS BOND : angle 1.06581 ( 84) hydrogen bonds : bond 0.03820 ( 976) hydrogen bonds : angle 4.51171 ( 2691) link_NAG-ASN : bond 0.00325 ( 27) link_NAG-ASN : angle 1.49239 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8146 (m-30) cc_final: 0.7677 (m-30) REVERT: A 661 GLU cc_start: 0.8054 (tt0) cc_final: 0.7778 (tt0) REVERT: A 787 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8365 (mt0) REVERT: A 900 MET cc_start: 0.8712 (mtp) cc_final: 0.8342 (mmm) REVERT: B 118 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6087 (mt) REVERT: B 226 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6778 (pp) REVERT: B 236 THR cc_start: 0.7863 (m) cc_final: 0.7272 (p) REVERT: B 382 VAL cc_start: 0.8480 (m) cc_final: 0.8247 (p) REVERT: B 506 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 1113 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: C 403 ARG cc_start: 0.7203 (ptm160) cc_final: 0.6863 (ptp-170) REVERT: C 505 HIS cc_start: 0.6516 (m170) cc_final: 0.6236 (m-70) REVERT: C 558 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7773 (mttt) REVERT: C 646 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7306 (mtp180) REVERT: C 690 GLN cc_start: 0.7810 (mm110) cc_final: 0.7517 (mp10) outliers start: 47 outliers final: 35 residues processed: 245 average time/residue: 0.5017 time to fit residues: 146.2773 Evaluate side-chains 248 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 308 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 965 GLN A1010 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.176156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131128 restraints weight = 27202.649| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.71 r_work: 0.3054 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25407 Z= 0.127 Angle : 0.529 12.751 34635 Z= 0.270 Chirality : 0.044 0.248 3996 Planarity : 0.003 0.052 4425 Dihedral : 4.989 51.525 3909 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 1.77 % Allowed : 13.44 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 3081 helix: 2.06 (0.20), residues: 747 sheet: 0.31 (0.20), residues: 630 loop : -1.11 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE C 592 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00303 (25338) covalent geometry : angle 0.51966 (34470) SS BOND : bond 0.00384 ( 42) SS BOND : angle 1.41421 ( 84) hydrogen bonds : bond 0.04600 ( 976) hydrogen bonds : angle 4.65278 ( 2691) link_NAG-ASN : bond 0.00320 ( 27) link_NAG-ASN : angle 1.66930 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8121 (m-30) cc_final: 0.7647 (m-30) REVERT: A 661 GLU cc_start: 0.8168 (tt0) cc_final: 0.7845 (tt0) REVERT: A 787 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: B 118 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6160 (mt) REVERT: B 226 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6845 (pp) REVERT: B 236 THR cc_start: 0.7814 (m) cc_final: 0.7268 (p) REVERT: B 506 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: B 646 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7582 (mtm180) REVERT: B 1113 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: C 403 ARG cc_start: 0.7138 (ptm160) cc_final: 0.6800 (ptp-170) REVERT: C 646 ARG cc_start: 0.8055 (tpt90) cc_final: 0.7338 (mtp180) REVERT: C 690 GLN cc_start: 0.7784 (mm110) cc_final: 0.7501 (mp10) outliers start: 48 outliers final: 37 residues processed: 251 average time/residue: 0.5358 time to fit residues: 160.3261 Evaluate side-chains 251 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 965 GLN A1010 GLN B 207 HIS B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.173923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128615 restraints weight = 27061.529| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.70 r_work: 0.3016 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25407 Z= 0.168 Angle : 0.579 12.928 34635 Z= 0.296 Chirality : 0.046 0.276 3996 Planarity : 0.004 0.065 4425 Dihedral : 5.283 53.419 3909 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 1.88 % Allowed : 13.48 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.15), residues: 3081 helix: 1.82 (0.19), residues: 750 sheet: 0.13 (0.19), residues: 669 loop : -1.14 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.024 0.001 TYR A 170 PHE 0.016 0.002 PHE B 168 TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00412 (25338) covalent geometry : angle 0.56750 (34470) SS BOND : bond 0.00429 ( 42) SS BOND : angle 1.65638 ( 84) hydrogen bonds : bond 0.05295 ( 976) hydrogen bonds : angle 4.82006 ( 2691) link_NAG-ASN : bond 0.00346 ( 27) link_NAG-ASN : angle 1.91909 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7711.35 seconds wall clock time: 131 minutes 54.89 seconds (7914.89 seconds total)