Starting phenix.real_space_refine on Fri May 23 23:29:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukd_42352/05_2025/8ukd_42352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukd_42352/05_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_42352/05_2025/8ukd_42352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukd_42352/05_2025/8ukd_42352.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukd_42352/05_2025/8ukd_42352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukd_42352/05_2025/8ukd_42352.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.40, per 1000 atoms: 0.58 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: 5.88 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.58 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: 10.51 Time building geometry restraints manager: 6.88 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: 0.08 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.920 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (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 TRP 0.030 0.002 TRP B 886 HIS 0.008 0.001 HIS A 519 PHE 0.035 0.002 PHE B 168 TYR 0.028 0.002 TYR B 453 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 2.92354 ( 81) hydrogen bonds : bond 0.20961 ( 976) hydrogen bonds : angle 7.59217 ( 2691) SS BOND : bond 0.00617 ( 42) SS BOND : angle 2.08503 ( 84) covalent geometry : bond 0.00553 (25338) covalent geometry : angle 0.83322 (34470) *********************** 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 : 2.665 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: 1.1315 time to fit residues: 377.9467 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 : 2.967 ------------------------------------------------------------------------------- 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 263 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 244 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 321 GLN A 439 ASN A 544 ASN A1010 GLN A1011 GLN B 196 ASN B 207 HIS B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN C 66 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 907 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.182917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.145035 restraints weight = 26936.492| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.55 r_work: 0.3161 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25407 Z= 0.111 Angle : 0.541 12.725 34635 Z= 0.281 Chirality : 0.044 0.290 3996 Planarity : 0.004 0.056 4425 Dihedral : 6.119 53.497 3911 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.25 % Allowed : 6.81 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3081 helix: 0.98 (0.19), residues: 735 sheet: 0.38 (0.20), residues: 648 loop : -1.44 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.001 PHE B 168 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 27) link_NAG-ASN : angle 1.87183 ( 81) hydrogen bonds : bond 0.04796 ( 976) hydrogen bonds : angle 5.37523 ( 2691) SS BOND : bond 0.00418 ( 42) SS BOND : angle 1.42965 ( 84) covalent geometry : bond 0.00243 (25338) covalent geometry : angle 0.52980 (34470) *********************** 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 275 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 655 TYR cc_start: 0.8352 (t80) cc_final: 0.8128 (t80) REVERT: A 661 GLU cc_start: 0.8071 (tt0) cc_final: 0.7807 (tt0) REVERT: B 226 LEU cc_start: 0.6776 (pp) cc_final: 0.6391 (pp) REVERT: B 236 THR cc_start: 0.7813 (m) cc_final: 0.7258 (p) REVERT: C 450 ASN cc_start: 0.7632 (m-40) cc_final: 0.7412 (m-40) REVERT: C 558 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7571 (mptt) REVERT: C 740 MET cc_start: 0.8709 (tpp) cc_final: 0.8431 (tpt) REVERT: C 1005 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8151 (tp40) outliers start: 34 outliers final: 16 residues processed: 257 average time/residue: 1.0959 time to fit residues: 336.5779 Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 2.579 ------------------------------------------------------------------------------- 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 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 571 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 189 LEU 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 814 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 230 optimal weight: 0.0170 chunk 253 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 519 HIS A 901 GLN A 965 GLN A1010 GLN B 66 HIS B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C1011 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.176176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137087 restraints weight = 26921.498| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.58 r_work: 0.3072 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25407 Z= 0.164 Angle : 0.580 10.636 34635 Z= 0.299 Chirality : 0.046 0.300 3996 Planarity : 0.004 0.054 4425 Dihedral : 5.848 52.917 3909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 1.88 % Allowed : 9.36 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3081 helix: 1.41 (0.19), residues: 729 sheet: 0.18 (0.20), residues: 648 loop : -1.37 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.006 0.001 HIS B1048 PHE 0.022 0.002 PHE B 168 TYR 0.022 0.001 TYR A1067 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 27) link_NAG-ASN : angle 2.04738 ( 81) hydrogen bonds : bond 0.05555 ( 976) hydrogen bonds : angle 5.10922 ( 2691) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.62274 ( 84) covalent geometry : bond 0.00400 (25338) covalent geometry : angle 0.56701 (34470) *********************** 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 278 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8244 (m-30) cc_final: 0.7857 (m-30) REVERT: A 661 GLU cc_start: 0.8254 (tt0) cc_final: 0.7970 (tt0) REVERT: A 869 MET cc_start: 0.9287 (mtt) cc_final: 0.9067 (mtt) REVERT: A 1010 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 226 LEU cc_start: 0.7026 (pp) cc_final: 0.6613 (pp) REVERT: B 236 THR cc_start: 0.7947 (m) cc_final: 0.7417 (p) REVERT: B 1113 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: C 269 TYR cc_start: 0.8213 (m-10) cc_final: 0.7895 (m-10) REVERT: C 450 ASN cc_start: 0.7664 (m-40) cc_final: 0.7458 (m-40) REVERT: C 646 ARG cc_start: 0.7881 (tpt90) cc_final: 0.7298 (mtp180) REVERT: C 690 GLN cc_start: 0.7867 (mm110) cc_final: 0.7540 (mp10) REVERT: C 740 MET cc_start: 0.8881 (tpp) cc_final: 0.8631 (tpt) REVERT: C 869 MET cc_start: 0.9035 (mtt) cc_final: 0.8669 (mtt) REVERT: C 1005 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8191 (tp40) outliers start: 51 outliers final: 32 residues processed: 257 average time/residue: 1.0631 time to fit residues: 328.4892 Evaluate side-chains 242 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 277 LEU 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 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 B residue 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU 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 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 128 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 277 optimal weight: 0.0370 chunk 38 optimal weight: 6.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 66 HIS B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN B1088 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.179705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142678 restraints weight = 27148.082| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.53 r_work: 0.3104 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25407 Z= 0.123 Angle : 0.535 8.950 34635 Z= 0.277 Chirality : 0.044 0.271 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.534 52.193 3909 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.14 % Allowed : 10.28 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3081 helix: 1.91 (0.20), residues: 705 sheet: 0.20 (0.20), residues: 621 loop : -1.29 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1048 PHE 0.019 0.001 PHE B 168 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 27) link_NAG-ASN : angle 1.84217 ( 81) hydrogen bonds : bond 0.04834 ( 976) hydrogen bonds : angle 4.94013 ( 2691) SS BOND : bond 0.00523 ( 42) SS BOND : angle 1.49209 ( 84) covalent geometry : bond 0.00287 (25338) covalent geometry : angle 0.52321 (34470) *********************** 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 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 221 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8218 (m-30) cc_final: 0.7854 (m-30) REVERT: A 655 TYR cc_start: 0.8400 (t80) cc_final: 0.8200 (t80) REVERT: A 661 GLU cc_start: 0.8176 (tt0) cc_final: 0.7884 (tt0) REVERT: A 869 MET cc_start: 0.9304 (mtt) cc_final: 0.9039 (mtt) REVERT: B 226 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6641 (pp) REVERT: B 236 THR cc_start: 0.7831 (m) cc_final: 0.7315 (p) REVERT: B 506 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: B 1113 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: C 269 TYR cc_start: 0.8218 (m-10) cc_final: 0.7872 (m-10) REVERT: C 450 ASN cc_start: 0.7667 (m-40) cc_final: 0.7457 (m-40) REVERT: C 646 ARG cc_start: 0.7892 (tpt90) cc_final: 0.7278 (mtp180) REVERT: C 690 GLN cc_start: 0.7861 (mm110) cc_final: 0.7515 (mp10) REVERT: C 740 MET cc_start: 0.8878 (tpp) cc_final: 0.8677 (tpt) REVERT: C 869 MET cc_start: 0.9012 (mtt) cc_final: 0.8644 (mtt) REVERT: C 1005 GLN cc_start: 0.8522 (tp-100) cc_final: 0.8208 (tp40) REVERT: C 1029 MET cc_start: 0.9046 (tpp) cc_final: 0.8736 (tpp) outliers start: 58 outliers final: 34 residues processed: 256 average time/residue: 1.0348 time to fit residues: 319.7839 Evaluate side-chains 250 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 2.601 ------------------------------------------------------------------------------- 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 547 THR 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 226 LEU Chi-restraints excluded: chain B residue 235 ILE 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 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 B residue 1092 GLU Chi-restraints excluded: chain B residue 1113 GLN 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 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.172872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133087 restraints weight = 27195.203| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.60 r_work: 0.3008 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 25407 Z= 0.243 Angle : 0.655 8.185 34635 Z= 0.337 Chirality : 0.050 0.318 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.892 57.764 3909 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 2.58 % Allowed : 10.64 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3081 helix: 1.39 (0.19), residues: 720 sheet: -0.13 (0.19), residues: 675 loop : -1.33 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.009 0.001 HIS B1048 PHE 0.021 0.002 PHE B 168 TYR 0.023 0.002 TYR A1067 ARG 0.006 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 27) link_NAG-ASN : angle 2.27660 ( 81) hydrogen bonds : bond 0.06321 ( 976) hydrogen bonds : angle 5.17555 ( 2691) SS BOND : bond 0.00514 ( 42) SS BOND : angle 2.10424 ( 84) covalent geometry : bond 0.00605 (25338) covalent geometry : angle 0.63904 (34470) *********************** 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 288 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8271 (m-30) cc_final: 0.8027 (m-30) REVERT: A 661 GLU cc_start: 0.8401 (tt0) cc_final: 0.8088 (tt0) REVERT: A 787 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8459 (mt0) REVERT: B 118 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6746 (mt) REVERT: B 218 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7637 (mm110) REVERT: B 226 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6668 (pp) REVERT: B 814 LYS cc_start: 0.7683 (mptt) cc_final: 0.7365 (mppt) REVERT: B 827 THR cc_start: 0.7608 (t) cc_final: 0.7407 (p) REVERT: B 1113 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: C 53 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.6894 (t0) REVERT: C 269 TYR cc_start: 0.8332 (m-10) cc_final: 0.7953 (m-10) REVERT: C 309 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 646 ARG cc_start: 0.8081 (tpt90) cc_final: 0.7449 (mtp180) REVERT: C 690 GLN cc_start: 0.7884 (mm110) cc_final: 0.7521 (mp10) REVERT: C 869 MET cc_start: 0.9102 (mtt) cc_final: 0.8758 (mtt) outliers start: 70 outliers final: 38 residues processed: 264 average time/residue: 1.0489 time to fit residues: 333.3182 Evaluate side-chains 252 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 66 HIS 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 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 118 LEU 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 307 THR Chi-restraints excluded: chain B residue 332 ILE 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 645 THR 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 B residue 1113 GLN Chi-restraints excluded: chain C residue 53 ASP 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 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 59 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 276 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 935 GLN A 965 GLN B 66 HIS B 207 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.174266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135117 restraints weight = 27045.733| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.57 r_work: 0.3049 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25407 Z= 0.160 Angle : 0.576 9.386 34635 Z= 0.297 Chirality : 0.046 0.289 3996 Planarity : 0.004 0.062 4425 Dihedral : 5.636 55.761 3909 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.58 % Allowed : 11.38 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3081 helix: 1.57 (0.20), residues: 720 sheet: 0.03 (0.19), residues: 708 loop : -1.33 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.018 0.001 PHE B 168 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 27) link_NAG-ASN : angle 1.99602 ( 81) hydrogen bonds : bond 0.05326 ( 976) hydrogen bonds : angle 4.98034 ( 2691) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.69618 ( 84) covalent geometry : bond 0.00389 (25338) covalent geometry : angle 0.56310 (34470) *********************** 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 286 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8247 (m-30) cc_final: 0.7883 (m-30) REVERT: A 586 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: A 661 GLU cc_start: 0.8325 (tt0) cc_final: 0.8018 (tt0) REVERT: A 787 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: B 218 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7694 (mm110) REVERT: B 226 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6788 (pp) REVERT: B 696 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8659 (m) REVERT: B 814 LYS cc_start: 0.7651 (mptt) cc_final: 0.7403 (mppt) REVERT: B 827 THR cc_start: 0.7537 (t) cc_final: 0.7333 (p) REVERT: B 1113 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: C 53 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6856 (t0) REVERT: C 269 TYR cc_start: 0.8293 (m-10) cc_final: 0.7936 (m-10) REVERT: C 309 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 646 ARG cc_start: 0.8053 (tpt90) cc_final: 0.7478 (mtp180) REVERT: C 690 GLN cc_start: 0.7868 (mm110) cc_final: 0.7497 (mp10) REVERT: C 869 MET cc_start: 0.9073 (mtt) cc_final: 0.8780 (mtt) outliers start: 70 outliers final: 42 residues processed: 261 average time/residue: 1.0666 time to fit residues: 335.5566 Evaluate side-chains 250 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 2.664 ------------------------------------------------------------------------------- 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 66 HIS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR 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 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU 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 205 SER 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 350 VAL 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 649 CYS Chi-restraints excluded: chain B residue 696 THR 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 53 ASP 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL 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 Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 220 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 448 ASN A 493 GLN A 965 GLN B 66 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B 804 GLN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.173966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134817 restraints weight = 27165.943| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.57 r_work: 0.3043 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25407 Z= 0.166 Angle : 0.578 8.325 34635 Z= 0.298 Chirality : 0.046 0.286 3996 Planarity : 0.004 0.060 4425 Dihedral : 5.583 56.185 3909 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.54 % Allowed : 11.86 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3081 helix: 1.61 (0.20), residues: 720 sheet: 0.04 (0.19), residues: 702 loop : -1.33 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.012 0.001 HIS A 66 PHE 0.018 0.001 PHE B 168 TYR 0.025 0.001 TYR A 170 ARG 0.004 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 27) link_NAG-ASN : angle 2.00448 ( 81) hydrogen bonds : bond 0.05372 ( 976) hydrogen bonds : angle 4.95957 ( 2691) SS BOND : bond 0.00433 ( 42) SS BOND : angle 1.69689 ( 84) covalent geometry : bond 0.00405 (25338) covalent geometry : angle 0.56490 (34470) *********************** 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 277 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8250 (m-30) cc_final: 0.7955 (m-30) REVERT: A 586 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: A 661 GLU cc_start: 0.8319 (tt0) cc_final: 0.8009 (tt0) REVERT: A 787 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: A 869 MET cc_start: 0.9328 (mtt) cc_final: 0.9093 (mtt) REVERT: B 218 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7669 (mm110) REVERT: B 226 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6798 (pp) REVERT: B 506 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 696 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8661 (m) REVERT: B 814 LYS cc_start: 0.7679 (mptt) cc_final: 0.7389 (mppt) REVERT: B 827 THR cc_start: 0.7646 (t) cc_final: 0.7441 (p) REVERT: B 1113 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: C 53 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6866 (t0) REVERT: C 269 TYR cc_start: 0.8310 (m-10) cc_final: 0.7942 (m-10) REVERT: C 309 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 646 ARG cc_start: 0.8096 (tpt90) cc_final: 0.7482 (mtp180) REVERT: C 690 GLN cc_start: 0.7874 (mm110) cc_final: 0.7513 (mp10) REVERT: C 869 MET cc_start: 0.9072 (mtt) cc_final: 0.8771 (mtt) outliers start: 69 outliers final: 43 residues processed: 253 average time/residue: 1.0409 time to fit residues: 315.8994 Evaluate side-chains 254 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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 132 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR 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 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU 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 205 SER 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 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 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR 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 53 ASP 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.7980 chunk 58 optimal weight: 0.0050 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 246 optimal weight: 7.9990 chunk 308 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 965 GLN B 66 HIS B 207 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 907 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.176826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132445 restraints weight = 27185.233| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.69 r_work: 0.3066 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25407 Z= 0.105 Angle : 0.513 8.585 34635 Z= 0.266 Chirality : 0.044 0.261 3996 Planarity : 0.004 0.061 4425 Dihedral : 5.254 53.420 3909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.32 % Allowed : 12.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3081 helix: 1.98 (0.20), residues: 729 sheet: 0.36 (0.20), residues: 648 loop : -1.24 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS A 66 PHE 0.017 0.001 PHE C 592 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 27) link_NAG-ASN : angle 1.72535 ( 81) hydrogen bonds : bond 0.04320 ( 976) hydrogen bonds : angle 4.74854 ( 2691) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.30686 ( 84) covalent geometry : bond 0.00238 (25338) covalent geometry : angle 0.50340 (34470) *********************** 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 279 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: A 661 GLU cc_start: 0.8095 (tt0) cc_final: 0.7789 (tt0) REVERT: A 787 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: A 869 MET cc_start: 0.9291 (mtt) cc_final: 0.8953 (mtt) REVERT: A 878 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 226 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6648 (pp) REVERT: B 236 THR cc_start: 0.7923 (m) cc_final: 0.7459 (p) REVERT: B 1113 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: C 269 TYR cc_start: 0.8261 (m-10) cc_final: 0.7861 (m-10) REVERT: C 646 ARG cc_start: 0.8070 (tpt90) cc_final: 0.7356 (mtp180) REVERT: C 690 GLN cc_start: 0.7804 (mm110) cc_final: 0.7457 (mp10) REVERT: C 869 MET cc_start: 0.8940 (mtt) cc_final: 0.8679 (mtt) REVERT: C 1029 MET cc_start: 0.9055 (tpp) cc_final: 0.8648 (tpp) outliers start: 63 outliers final: 35 residues processed: 255 average time/residue: 1.0615 time to fit residues: 327.1261 Evaluate side-chains 243 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 3.022 ------------------------------------------------------------------------------- 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 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 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 135 PHE 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 350 VAL Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 645 THR 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 274 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 278 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN B 66 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 804 GLN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 394 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.175901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130593 restraints weight = 27325.288| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.79 r_work: 0.3035 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25407 Z= 0.124 Angle : 0.534 8.317 34635 Z= 0.275 Chirality : 0.044 0.260 3996 Planarity : 0.004 0.061 4425 Dihedral : 5.214 52.849 3909 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 1.80 % Allowed : 13.52 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3081 helix: 1.87 (0.20), residues: 750 sheet: 0.21 (0.19), residues: 687 loop : -1.17 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.015 0.001 PHE B 168 TYR 0.027 0.001 TYR A 170 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 27) link_NAG-ASN : angle 1.77069 ( 81) hydrogen bonds : bond 0.04631 ( 976) hydrogen bonds : angle 4.74398 ( 2691) SS BOND : bond 0.00364 ( 42) SS BOND : angle 1.47997 ( 84) covalent geometry : bond 0.00294 (25338) covalent geometry : angle 0.52338 (34470) *********************** 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 257 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 GLU cc_start: 0.8161 (tt0) cc_final: 0.7871 (tt0) REVERT: A 787 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: A 869 MET cc_start: 0.9314 (mtt) cc_final: 0.9022 (mtt) REVERT: B 226 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6785 (pp) REVERT: B 1113 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: C 269 TYR cc_start: 0.8252 (m-10) cc_final: 0.7873 (m-10) REVERT: C 403 ARG cc_start: 0.7297 (ptm160) cc_final: 0.6952 (ptp-170) REVERT: C 646 ARG cc_start: 0.8141 (tpt90) cc_final: 0.7393 (mtp180) REVERT: C 690 GLN cc_start: 0.7798 (mm110) cc_final: 0.7456 (mp10) REVERT: C 869 MET cc_start: 0.8993 (mtt) cc_final: 0.8686 (mtt) REVERT: C 1029 MET cc_start: 0.9072 (tpp) cc_final: 0.8650 (tpp) outliers start: 49 outliers final: 38 residues processed: 241 average time/residue: 1.0097 time to fit residues: 294.2558 Evaluate side-chains 241 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 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 787 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE 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 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 645 THR 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 780 GLU 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 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 130 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 242 optimal weight: 0.0870 chunk 56 optimal weight: 0.4980 chunk 279 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 448 ASN A 935 GLN A 965 GLN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3921 r_free = 0.3921 target = 0.176362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133458 restraints weight = 27022.960| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.64 r_work: 0.3104 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2077 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= 0.104 Angle : 0.509 8.322 34635 Z= 0.263 Chirality : 0.044 0.249 3996 Planarity : 0.004 0.063 4425 Dihedral : 5.081 53.040 3909 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 1.62 % Allowed : 13.78 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3081 helix: 2.00 (0.20), residues: 750 sheet: 0.24 (0.19), residues: 690 loop : -1.14 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS B 519 PHE 0.014 0.001 PHE B 168 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 27) link_NAG-ASN : angle 1.65972 ( 81) hydrogen bonds : bond 0.04201 ( 976) hydrogen bonds : angle 4.65078 ( 2691) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.27847 ( 84) covalent geometry : bond 0.00237 (25338) covalent geometry : angle 0.49968 (34470) ********************** 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 257 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 GLU cc_start: 0.8217 (tt0) cc_final: 0.7915 (tt0) REVERT: A 869 MET cc_start: 0.9292 (mtt) cc_final: 0.8935 (mtt) REVERT: B 226 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6743 (pp) REVERT: B 236 THR cc_start: 0.7956 (m) cc_final: 0.7535 (p) REVERT: B 382 VAL cc_start: 0.8603 (m) cc_final: 0.8334 (p) REVERT: B 506 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: B 1113 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: C 269 TYR cc_start: 0.8256 (m-10) cc_final: 0.7875 (m-10) REVERT: C 403 ARG cc_start: 0.7481 (ptm160) cc_final: 0.7136 (ptp-170) REVERT: C 646 ARG cc_start: 0.8235 (tpt90) cc_final: 0.7532 (mtp180) REVERT: C 690 GLN cc_start: 0.7856 (mm110) cc_final: 0.7537 (mp10) REVERT: C 869 MET cc_start: 0.8970 (mtt) cc_final: 0.8698 (mtt) REVERT: C 1029 MET cc_start: 0.8976 (tpp) cc_final: 0.8613 (tpp) outliers start: 44 outliers final: 38 residues processed: 242 average time/residue: 1.1601 time to fit residues: 343.4618 Evaluate side-chains 247 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 66 HIS 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 828 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU 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 571 ASP Chi-restraints excluded: chain B residue 645 THR 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 780 GLU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 198 ASP 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 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 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 62 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 207 HIS B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 675 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.175113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132035 restraints weight = 27069.409| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.71 r_work: 0.3076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25407 Z= 0.131 Angle : 0.529 8.239 34635 Z= 0.273 Chirality : 0.044 0.254 3996 Planarity : 0.004 0.062 4425 Dihedral : 5.121 52.174 3909 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 1.80 % Allowed : 13.85 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3081 helix: 1.94 (0.19), residues: 750 sheet: 0.25 (0.19), residues: 687 loop : -1.14 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.006 0.001 HIS A 66 PHE 0.017 0.001 PHE C 592 TYR 0.027 0.001 TYR A 170 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 27) link_NAG-ASN : angle 1.70752 ( 81) hydrogen bonds : bond 0.04551 ( 976) hydrogen bonds : angle 4.67591 ( 2691) SS BOND : bond 0.00357 ( 42) SS BOND : angle 1.39653 ( 84) covalent geometry : bond 0.00314 (25338) covalent geometry : angle 0.51951 (34470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17134.39 seconds wall clock time: 295 minutes 32.01 seconds (17732.01 seconds total)