Starting phenix.real_space_refine on Sun Jan 26 11:58:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ukd_42352/01_2025/8ukd_42352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ukd_42352/01_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_42352/01_2025/8ukd_42352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ukd_42352/01_2025/8ukd_42352.map" model { file = "/net/cci-nas-00/data/ceres_data/8ukd_42352/01_2025/8ukd_42352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ukd_42352/01_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-5571/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: 13.61, per 1000 atoms: 0.55 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: 6.52 Conformation dependent library (CDL) restraints added in 3.4 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: 3.51 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: 10.69 Time building geometry restraints manager: 7.26 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 55.900 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.530 ------------------------------------------------------------------------------- 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 25338 Z= 0.358 Angle : 0.833 27.021 34470 Z= 0.447 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 *********************** 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 : 3.083 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: 1.2109 time to fit residues: 399.5844 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 : 3.262 ------------------------------------------------------------------------------- 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 25338 Z= 0.161 Angle : 0.530 12.725 34470 Z= 0.278 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 *********************** 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 : 2.665 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: 1.1744 time to fit residues: 359.4071 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 : 3.325 ------------------------------------------------------------------------------- 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: 0.0980 chunk 253 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 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 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 = 0.3916 r_free = 0.3916 target = 0.176368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137417 restraints weight = 26931.014| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.56 r_work: 0.3080 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25338 Z= 0.264 Angle : 0.563 10.685 34470 Z= 0.294 Chirality : 0.046 0.299 3996 Planarity : 0.004 0.054 4425 Dihedral : 5.862 52.749 3909 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 1.84 % Allowed : 9.28 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3081 helix: 1.43 (0.19), residues: 726 sheet: 0.12 (0.20), residues: 639 loop : -1.37 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.006 0.001 HIS B1048 PHE 0.021 0.002 PHE B 168 TYR 0.022 0.001 TYR A1067 ARG 0.005 0.000 ARG B 190 *********************** 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 275 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8233 (m-30) cc_final: 0.7838 (m-30) REVERT: A 661 GLU cc_start: 0.8228 (tt0) cc_final: 0.7946 (tt0) REVERT: A 869 MET cc_start: 0.9301 (mtt) cc_final: 0.9076 (mtt) REVERT: A 1010 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 226 LEU cc_start: 0.7079 (pp) cc_final: 0.6656 (pp) REVERT: B 236 THR cc_start: 0.7936 (m) cc_final: 0.7415 (p) REVERT: B 1113 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: C 450 ASN cc_start: 0.7667 (m-40) cc_final: 0.7460 (m-40) REVERT: C 646 ARG cc_start: 0.7849 (tpt90) cc_final: 0.7270 (mtp180) REVERT: C 690 GLN cc_start: 0.7866 (mm110) cc_final: 0.7529 (mp10) REVERT: C 740 MET cc_start: 0.8862 (tpp) cc_final: 0.8613 (tpt) REVERT: C 869 MET cc_start: 0.9034 (mtt) cc_final: 0.8683 (mtt) REVERT: C 1005 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8194 (tp40) outliers start: 50 outliers final: 32 residues processed: 253 average time/residue: 1.1502 time to fit residues: 347.2330 Evaluate side-chains 243 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 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 697 MET 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: 8.9990 chunk 283 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 265 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 277 optimal weight: 0.0050 chunk 38 optimal weight: 6.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 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** C 394 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.177334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128862 restraints weight = 27265.831| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.79 r_work: 0.3078 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25338 Z= 0.167 Angle : 0.513 9.115 34470 Z= 0.268 Chirality : 0.044 0.264 3996 Planarity : 0.004 0.054 4425 Dihedral : 5.478 52.698 3909 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 1.95 % Allowed : 10.31 % Favored : 87.73 % 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: -0.28 (0.15), residues: 3081 helix: 1.80 (0.19), residues: 723 sheet: 0.24 (0.20), residues: 618 loop : -1.27 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.018 0.001 PHE B 168 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG B 357 *********************** 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 272 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 219 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 655 TYR cc_start: 0.8397 (t80) cc_final: 0.8149 (t80) REVERT: A 661 GLU cc_start: 0.8135 (tt0) cc_final: 0.7860 (tt0) REVERT: A 869 MET cc_start: 0.9314 (mtt) cc_final: 0.9038 (mtt) REVERT: A 1010 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: B 200 TYR cc_start: 0.7497 (m-80) cc_final: 0.7275 (m-80) REVERT: B 226 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6632 (pp) REVERT: B 236 THR cc_start: 0.7793 (m) cc_final: 0.7257 (p) REVERT: B 1113 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: C 690 GLN cc_start: 0.7848 (mm110) cc_final: 0.7554 (mp10) REVERT: C 740 MET cc_start: 0.8874 (tpp) cc_final: 0.8653 (tpt) REVERT: C 869 MET cc_start: 0.8987 (mtt) cc_final: 0.8688 (mtt) REVERT: C 1005 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8154 (tp40) outliers start: 53 outliers final: 31 residues processed: 249 average time/residue: 1.1146 time to fit residues: 332.6555 Evaluate side-chains 246 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 3.017 ------------------------------------------------------------------------------- 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 859 THR Chi-restraints excluded: chain A residue 957 GLN 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 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 227 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 302 optimal weight: 0.0980 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 272 optimal weight: 0.1980 chunk 13 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 965 GLN A1010 GLN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 556 ASN B1002 GLN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124396 restraints weight = 27226.273| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.01 r_work: 0.3001 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25338 Z= 0.300 Angle : 0.583 7.953 34470 Z= 0.303 Chirality : 0.047 0.292 3996 Planarity : 0.004 0.053 4425 Dihedral : 5.613 54.911 3909 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.54 % Allowed : 10.53 % Favored : 86.92 % 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: -0.41 (0.15), residues: 3081 helix: 1.62 (0.19), residues: 732 sheet: 0.12 (0.20), residues: 645 loop : -1.33 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.007 0.001 HIS B1048 PHE 0.020 0.002 PHE B 168 TYR 0.023 0.002 TYR A 170 ARG 0.005 0.000 ARG B1039 *********************** 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 281 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8292 (m-30) cc_final: 0.8005 (m-30) REVERT: A 661 GLU cc_start: 0.8376 (tt0) cc_final: 0.8054 (tt0) REVERT: A 787 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: A 1010 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: B 52 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: B 218 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7649 (mm110) REVERT: B 226 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6785 (pp) REVERT: B 827 THR cc_start: 0.7514 (t) cc_final: 0.7304 (p) REVERT: B 1113 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 309 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7423 (mm-30) REVERT: C 646 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7303 (mtp180) REVERT: C 690 GLN cc_start: 0.7897 (mm110) cc_final: 0.7539 (mp10) REVERT: C 869 MET cc_start: 0.9083 (mtt) cc_final: 0.8736 (mtt) outliers start: 69 outliers final: 37 residues processed: 254 average time/residue: 1.0788 time to fit residues: 330.4396 Evaluate side-chains 250 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 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 957 GLN Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 108 THR 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 1113 GLN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 59 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 935 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.172874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133277 restraints weight = 27069.626| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.59 r_work: 0.3024 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1887 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: