Starting phenix.real_space_refine on Fri Sep 19 08:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmg_38476/09_2025/8xmg_38476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmg_38476/09_2025/8xmg_38476.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/8xmg_38476/09_2025/8xmg_38476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmg_38476/09_2025/8xmg_38476.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmg_38476/09_2025/8xmg_38476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmg_38476/09_2025/8xmg_38476.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 107 5.16 5 C 15602 2.51 5 N 4043 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24476 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 55, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7942 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 55, 'TRANS': 960} Chain breaks: 7 Chain: "C" Number of atoms: 8002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8002 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 55, 'TRANS': 967} Chain breaks: 7 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.23, per 1000 atoms: 0.25 Number of scatterers: 24476 At special positions: 0 Unit cell: (135.744, 135.744, 164.832, 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 107 16.00 O 4724 8.00 N 4043 7.00 C 15602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 61 " " NAG B1314 " - " ASN B1098 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 61 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 42 sheets defined 25.1% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.741A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.366A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.506A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.000A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.072A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.746A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.520A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.504A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.584A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.268A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.170A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.236A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.840A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.507A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.738A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.559A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.503A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.521A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.885A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.747A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 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 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.998A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.740A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.813A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 3.641A pdb=" N THR A 23 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.501A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.322A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.083A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.898A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.144A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 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 654 through 655 removed outlier: 5.906A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.660A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.517A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.603A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.731A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 23 through 30 removed outlier: 7.708A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.624A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.875A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.931A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.615A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.379A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.995A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.494A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD5, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.832A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.067A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.815A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1121 1044 hydrogen bonds defined for protein. 2895 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7282 1.33 - 1.46: 6302 1.46 - 1.59: 11316 1.59 - 1.71: 1 1.71 - 1.84: 133 Bond restraints: 25034 Sorted by residual: bond pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.40e+00 bond pdb=" N ASN A1135 " pdb=" CA ASN A1135 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 bond pdb=" N SER C1097 " pdb=" CA SER C1097 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.02e+00 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.26e-02 6.30e+03 6.73e+00 bond pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.22e-02 6.72e+03 6.68e+00 ... (remaining 25029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 32969 1.55 - 3.11: 945 3.11 - 4.66: 134 4.66 - 6.21: 16 6.21 - 7.77: 4 Bond angle restraints: 34068 Sorted by residual: angle pdb=" C PRO B 527 " pdb=" CA PRO B 527 " pdb=" CB PRO B 527 " ideal model delta sigma weight residual 111.64 105.55 6.09 1.26e+00 6.30e-01 2.34e+01 angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 121.02 113.92 7.10 1.48e+00 4.57e-01 2.30e+01 angle pdb=" C PRO A 527 " pdb=" CA PRO A 527 " pdb=" CB PRO A 527 " ideal model delta sigma weight residual 111.56 104.88 6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 122.09 128.00 -5.91 1.48e+00 4.57e-01 1.59e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.48 3.14 7.90e-01 1.60e+00 1.58e+01 ... (remaining 34063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14159 17.97 - 35.93: 1037 35.93 - 53.90: 180 53.90 - 71.86: 50 71.86 - 89.83: 19 Dihedral angle restraints: 15445 sinusoidal: 6517 harmonic: 8928 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -3.20 -82.80 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 14.12 78.88 1 1.00e+01 1.00e-02 7.75e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -9.03 -76.97 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 15442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 3977 0.331 - 0.661: 4 0.661 - 0.992: 1 0.992 - 1.323: 1 1.323 - 1.654: 1 Chirality restraints: 3984 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3981 not shown) Planarity restraints: 4394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.322 2.00e-02 2.50e+03 2.80e-01 9.80e+02 pdb=" C7 NAG C1311 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.495 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1313 " -0.249 2.00e-02 2.50e+03 2.13e-01 5.69e+02 pdb=" C7 NAG B1313 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1313 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B1313 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG B1313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.243 2.00e-02 2.50e+03 2.08e-01 5.41e+02 pdb=" C7 NAG B1305 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.182 2.00e-02 2.50e+03 ... (remaining 4391 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3011 2.75 - 3.29: 23349 3.29 - 3.83: 39892 3.83 - 4.36: 46428 4.36 - 4.90: 81760 Nonbonded interactions: 194440 Sorted by model distance: nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.216 3.040 nonbonded pdb=" OG SER C 112 " pdb=" OE1 GLN C 134 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 94 " pdb=" OE1 GLU B 96 " model vdw 2.237 3.040 nonbonded pdb=" O GLN C 580 " pdb=" O6 NAG C1303 " model vdw 2.246 3.040 ... (remaining 194435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 143 or resid 159 through 176 or resid 187 throu \ gh 676 or resid 689 through 826 or resid 855 through 1312)) selection = (chain 'B' and (resid 20 through 826 or resid 855 through 1312)) selection = (chain 'C' and (resid 20 through 143 or resid 159 through 176 or resid 187 throu \ gh 676 or resid 689 through 826 or resid 855 through 1312)) } 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: 11.080 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 : 0.004 0.050 25108 Z= 0.212 Angle : 0.655 15.311 34254 Z= 0.351 Chirality : 0.059 1.654 3984 Planarity : 0.009 0.280 4356 Dihedral : 12.814 89.830 9585 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3014 helix: 2.20 (0.21), residues: 641 sheet: 0.56 (0.18), residues: 710 loop : -0.88 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.001 PHE C 823 TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00412 (25034) covalent geometry : angle 0.61385 (34068) SS BOND : bond 0.00565 ( 36) SS BOND : angle 1.49962 ( 72) hydrogen bonds : bond 0.12867 ( 1020) hydrogen bonds : angle 6.62761 ( 2895) link_NAG-ASN : bond 0.00470 ( 38) link_NAG-ASN : angle 3.84720 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 771 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7399 (pt0) cc_final: 0.7182 (pt0) REVERT: A 32 PHE cc_start: 0.8735 (m-80) cc_final: 0.8451 (m-80) REVERT: A 43 PHE cc_start: 0.8810 (t80) cc_final: 0.8505 (t80) REVERT: A 130 VAL cc_start: 0.7535 (t) cc_final: 0.7233 (p) REVERT: A 305 SER cc_start: 0.8462 (t) cc_final: 0.8205 (p) REVERT: A 306 PHE cc_start: 0.8803 (m-80) cc_final: 0.8427 (m-80) REVERT: A 391 CYS cc_start: 0.7070 (m) cc_final: 0.6677 (m) REVERT: A 422 ASN cc_start: 0.6442 (m110) cc_final: 0.6206 (m110) REVERT: A 505 HIS cc_start: 0.7230 (m-70) cc_final: 0.6761 (m-70) REVERT: A 574 ASP cc_start: 0.7700 (t70) cc_final: 0.7429 (t0) REVERT: A 576 VAL cc_start: 0.9127 (t) cc_final: 0.8896 (p) REVERT: A 581 THR cc_start: 0.7876 (m) cc_final: 0.7571 (p) REVERT: A 660 TYR cc_start: 0.8398 (m-80) cc_final: 0.8139 (m-80) REVERT: A 723 THR cc_start: 0.8467 (p) cc_final: 0.8250 (m) REVERT: A 725 GLU cc_start: 0.7905 (tt0) cc_final: 0.7622 (tt0) REVERT: A 737 ASP cc_start: 0.7965 (t0) cc_final: 0.7671 (t70) REVERT: A 814 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8205 (mmtt) REVERT: A 950 ASP cc_start: 0.7244 (m-30) cc_final: 0.6684 (m-30) REVERT: A 1038 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8084 (mmtm) REVERT: A 1045 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7431 (mmtm) REVERT: A 1096 VAL cc_start: 0.8428 (t) cc_final: 0.8198 (m) REVERT: B 53 ASP cc_start: 0.7294 (t0) cc_final: 0.7072 (t0) REVERT: B 127 VAL cc_start: 0.8305 (t) cc_final: 0.7982 (m) REVERT: B 221 SER cc_start: 0.8471 (m) cc_final: 0.8270 (m) REVERT: B 309 GLU cc_start: 0.7602 (mp0) cc_final: 0.7285 (mp0) REVERT: B 328 ARG cc_start: 0.7461 (mmm160) cc_final: 0.7236 (mtp180) REVERT: B 436 TRP cc_start: 0.6457 (p90) cc_final: 0.6192 (p90) REVERT: B 557 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8152 (mttp) REVERT: B 574 ASP cc_start: 0.7346 (t70) cc_final: 0.7027 (t0) REVERT: B 619 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 658 ASN cc_start: 0.7705 (p0) cc_final: 0.7490 (p0) REVERT: B 723 THR cc_start: 0.8431 (p) cc_final: 0.8090 (t) REVERT: B 731 MET cc_start: 0.8923 (ptt) cc_final: 0.8699 (ptm) REVERT: B 735 SER cc_start: 0.8551 (m) cc_final: 0.8324 (t) REVERT: B 736 VAL cc_start: 0.8886 (m) cc_final: 0.8602 (t) REVERT: B 776 LYS cc_start: 0.8361 (tttm) cc_final: 0.7980 (tttm) REVERT: B 780 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 790 LYS cc_start: 0.7962 (mppt) cc_final: 0.7713 (mppt) REVERT: B 823 PHE cc_start: 0.7185 (m-80) cc_final: 0.6952 (m-80) REVERT: B 867 ASP cc_start: 0.7760 (m-30) cc_final: 0.7559 (m-30) REVERT: B 868 GLU cc_start: 0.7674 (mp0) cc_final: 0.7388 (mp0) REVERT: B 952 VAL cc_start: 0.8587 (t) cc_final: 0.8384 (m) REVERT: B 979 ASP cc_start: 0.7756 (t70) cc_final: 0.7445 (t70) REVERT: B 1002 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7861 (tp-100) REVERT: B 1038 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7947 (mmtm) REVERT: B 1096 VAL cc_start: 0.8571 (t) cc_final: 0.8241 (m) REVERT: B 1107 ARG cc_start: 0.7818 (mtt-85) cc_final: 0.7511 (mmt90) REVERT: C 24 ARG cc_start: 0.5154 (mtm-85) cc_final: 0.3953 (ttp80) REVERT: C 100 ILE cc_start: 0.8426 (tp) cc_final: 0.8187 (pp) REVERT: C 155 SER cc_start: 0.8692 (m) cc_final: 0.8273 (t) REVERT: C 156 GLU cc_start: 0.7180 (pm20) cc_final: 0.6787 (pp20) REVERT: C 224 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 305 SER cc_start: 0.8655 (t) cc_final: 0.8330 (p) REVERT: C 308 VAL cc_start: 0.8665 (t) cc_final: 0.8461 (p) REVERT: C 317 ASN cc_start: 0.8305 (m-40) cc_final: 0.7912 (m-40) REVERT: C 515 PHE cc_start: 0.6823 (m-80) cc_final: 0.6337 (m-80) REVERT: C 555 SER cc_start: 0.8591 (t) cc_final: 0.7212 (p) REVERT: C 556 ASN cc_start: 0.8040 (m110) cc_final: 0.7759 (p0) REVERT: C 576 VAL cc_start: 0.8979 (t) cc_final: 0.8575 (p) REVERT: C 578 ASP cc_start: 0.7880 (t0) cc_final: 0.7486 (t70) REVERT: C 581 THR cc_start: 0.7955 (m) cc_final: 0.7178 (t) REVERT: C 584 ILE cc_start: 0.8240 (mm) cc_final: 0.7789 (mm) REVERT: C 651 ILE cc_start: 0.8590 (pt) cc_final: 0.8310 (mt) REVERT: C 661 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6717 (tm-30) REVERT: C 790 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7822 (mtmm) REVERT: C 805 ILE cc_start: 0.8281 (mm) cc_final: 0.8069 (pt) REVERT: C 811 LYS cc_start: 0.8130 (tttm) cc_final: 0.7666 (tttm) REVERT: C 990 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 1041 ASP cc_start: 0.7756 (m-30) cc_final: 0.7410 (m-30) REVERT: C 1073 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7844 (mmmm) outliers start: 3 outliers final: 5 residues processed: 773 average time/residue: 0.6113 time to fit residues: 546.9935 Evaluate side-chains 615 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 610 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 805 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 196 ASN A 207 HIS A 354 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 710 ASN A 751 ASN A 784 GLN A 913 GLN A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 239 GLN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 613 GLN B 710 ASN B 804 GLN B 935 GLN B 957 GLN B1010 GLN C 26 GLN C 196 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 784 GLN C 960 ASN C 978 ASN C1088 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129189 restraints weight = 35930.976| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.41 r_work: 0.3485 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 25108 Z= 0.223 Angle : 0.648 12.552 34254 Z= 0.329 Chirality : 0.049 0.427 3984 Planarity : 0.004 0.059 4356 Dihedral : 6.381 99.278 4088 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 11.86 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.15), residues: 3014 helix: 2.31 (0.20), residues: 633 sheet: 0.60 (0.18), residues: 695 loop : -0.89 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 466 TYR 0.023 0.002 TYR B 279 PHE 0.023 0.002 PHE C 541 TRP 0.009 0.002 TRP B 353 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00521 (25034) covalent geometry : angle 0.61570 (34068) SS BOND : bond 0.00509 ( 36) SS BOND : angle 2.22934 ( 72) hydrogen bonds : bond 0.05101 ( 1020) hydrogen bonds : angle 5.66539 ( 2895) link_NAG-ASN : bond 0.00614 ( 38) link_NAG-ASN : angle 3.13569 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 612 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7663 (pt0) cc_final: 0.7416 (pt0) REVERT: A 32 PHE cc_start: 0.8987 (m-80) cc_final: 0.8715 (m-80) REVERT: A 41 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8628 (mttm) REVERT: A 45 SER cc_start: 0.8185 (t) cc_final: 0.7936 (p) REVERT: A 46 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 53 ASP cc_start: 0.7321 (t0) cc_final: 0.7085 (t0) REVERT: A 130 VAL cc_start: 0.7660 (t) cc_final: 0.7443 (p) REVERT: A 205 SER cc_start: 0.8659 (m) cc_final: 0.8441 (p) REVERT: A 235 ILE cc_start: 0.7143 (tp) cc_final: 0.6870 (tp) REVERT: A 305 SER cc_start: 0.8486 (t) cc_final: 0.8204 (p) REVERT: A 505 HIS cc_start: 0.7450 (m-70) cc_final: 0.6862 (m-70) REVERT: A 574 ASP cc_start: 0.8057 (t70) cc_final: 0.7669 (t0) REVERT: A 645 THR cc_start: 0.8260 (m) cc_final: 0.7851 (p) REVERT: A 660 TYR cc_start: 0.8585 (m-80) cc_final: 0.8273 (m-80) REVERT: A 714 ILE cc_start: 0.8676 (mm) cc_final: 0.8446 (mp) REVERT: A 723 THR cc_start: 0.8484 (p) cc_final: 0.8279 (m) REVERT: A 725 GLU cc_start: 0.8231 (tt0) cc_final: 0.7971 (tt0) REVERT: A 737 ASP cc_start: 0.8122 (t0) cc_final: 0.7749 (t0) REVERT: A 814 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8195 (mmmm) REVERT: A 904 TYR cc_start: 0.7260 (m-10) cc_final: 0.7030 (m-10) REVERT: A 933 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8272 (mtpp) REVERT: A 950 ASP cc_start: 0.7516 (m-30) cc_final: 0.7041 (m-30) REVERT: A 968 SER cc_start: 0.8536 (t) cc_final: 0.8333 (m) REVERT: A 984 LEU cc_start: 0.7303 (mt) cc_final: 0.7076 (tp) REVERT: A 1045 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7723 (mmtm) REVERT: A 1096 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8108 (m) REVERT: A 1122 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 28 TYR cc_start: 0.7636 (m-10) cc_final: 0.7391 (m-10) REVERT: B 41 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6391 (mmtm) REVERT: B 53 ASP cc_start: 0.7626 (t0) cc_final: 0.7407 (t0) REVERT: B 190 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7899 (tpp80) REVERT: B 436 TRP cc_start: 0.6640 (p90) cc_final: 0.6425 (p90) REVERT: B 557 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8139 (mttt) REVERT: B 574 ASP cc_start: 0.7730 (t70) cc_final: 0.7183 (t0) REVERT: B 619 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 646 ARG cc_start: 0.8328 (mtm180) cc_final: 0.8087 (mtm110) REVERT: B 657 ASN cc_start: 0.7293 (m110) cc_final: 0.7092 (m-40) REVERT: B 702 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 723 THR cc_start: 0.8412 (p) cc_final: 0.8088 (t) REVERT: B 735 SER cc_start: 0.8621 (m) cc_final: 0.8372 (t) REVERT: B 736 VAL cc_start: 0.8919 (m) cc_final: 0.8598 (t) REVERT: B 740 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8280 (tmm) REVERT: B 776 LYS cc_start: 0.8509 (tttm) cc_final: 0.8124 (tttp) REVERT: B 811 LYS cc_start: 0.7274 (tttm) cc_final: 0.6763 (tptp) REVERT: B 814 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7784 (mmtt) REVERT: B 868 GLU cc_start: 0.7942 (mp0) cc_final: 0.7675 (mp0) REVERT: B 952 VAL cc_start: 0.8624 (t) cc_final: 0.8390 (m) REVERT: B 979 ASP cc_start: 0.7941 (t70) cc_final: 0.7628 (t70) REVERT: B 1031 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 1038 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8125 (mmtm) REVERT: B 1072 GLU cc_start: 0.8524 (pm20) cc_final: 0.7826 (pm20) REVERT: B 1096 VAL cc_start: 0.8435 (t) cc_final: 0.8096 (m) REVERT: C 24 ARG cc_start: 0.5146 (mtm-85) cc_final: 0.3675 (ttp80) REVERT: C 41 LYS cc_start: 0.6883 (mmpt) cc_final: 0.5848 (mtpp) REVERT: C 100 ILE cc_start: 0.8563 (tp) cc_final: 0.8296 (pp) REVERT: C 155 SER cc_start: 0.8780 (m) cc_final: 0.8417 (t) REVERT: C 156 GLU cc_start: 0.7307 (pm20) cc_final: 0.6976 (pp20) REVERT: C 304 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8181 (mmmm) REVERT: C 305 SER cc_start: 0.8630 (t) cc_final: 0.8292 (p) REVERT: C 308 VAL cc_start: 0.8701 (t) cc_final: 0.8453 (p) REVERT: C 317 ASN cc_start: 0.8574 (m-40) cc_final: 0.8307 (m-40) REVERT: C 364 ASP cc_start: 0.7348 (t0) cc_final: 0.6511 (p0) REVERT: C 515 PHE cc_start: 0.6820 (m-80) cc_final: 0.6350 (m-80) REVERT: C 577 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8501 (ttm-80) REVERT: C 578 ASP cc_start: 0.8119 (t0) cc_final: 0.7805 (t70) REVERT: C 581 THR cc_start: 0.8113 (m) cc_final: 0.7420 (t) REVERT: C 586 ASP cc_start: 0.7893 (m-30) cc_final: 0.7622 (m-30) REVERT: C 606 ASN cc_start: 0.8928 (m-40) cc_final: 0.8648 (m110) REVERT: C 651 ILE cc_start: 0.8455 (pt) cc_final: 0.8209 (mt) REVERT: C 661 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7008 (tm-30) REVERT: C 748 GLU cc_start: 0.6603 (pp20) cc_final: 0.6206 (pp20) REVERT: C 776 LYS cc_start: 0.8474 (tttm) cc_final: 0.8219 (ttmm) REVERT: C 790 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7784 (mtpp) REVERT: C 811 LYS cc_start: 0.8221 (tttm) cc_final: 0.7825 (tttm) REVERT: C 1073 LYS cc_start: 0.8391 (mmmm) cc_final: 0.8151 (mmmm) REVERT: C 1105 THR cc_start: 0.8501 (p) cc_final: 0.8149 (t) outliers start: 89 outliers final: 43 residues processed: 643 average time/residue: 0.5926 time to fit residues: 443.3097 Evaluate side-chains 627 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 578 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 33 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B1002 GLN C 26 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN C 957 GLN C 960 ASN C 978 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128577 restraints weight = 35806.518| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.43 r_work: 0.3481 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25108 Z= 0.204 Angle : 0.616 11.939 34254 Z= 0.314 Chirality : 0.048 0.453 3984 Planarity : 0.004 0.042 4356 Dihedral : 5.939 58.618 4082 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 3.62 % Allowed : 14.32 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3014 helix: 2.33 (0.20), residues: 634 sheet: 0.59 (0.18), residues: 694 loop : -0.90 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 466 TYR 0.028 0.002 TYR B 170 PHE 0.026 0.002 PHE C 541 TRP 0.007 0.002 TRP A 353 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00474 (25034) covalent geometry : angle 0.58398 (34068) SS BOND : bond 0.00411 ( 36) SS BOND : angle 2.13250 ( 72) hydrogen bonds : bond 0.04942 ( 1020) hydrogen bonds : angle 5.54624 ( 2895) link_NAG-ASN : bond 0.00605 ( 38) link_NAG-ASN : angle 3.01729 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 595 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7693 (pt0) cc_final: 0.7473 (pt0) REVERT: A 32 PHE cc_start: 0.9001 (m-80) cc_final: 0.8724 (m-80) REVERT: A 41 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (mttm) REVERT: A 45 SER cc_start: 0.8207 (t) cc_final: 0.7963 (p) REVERT: A 53 ASP cc_start: 0.7335 (t0) cc_final: 0.7072 (t0) REVERT: A 130 VAL cc_start: 0.7711 (t) cc_final: 0.7509 (p) REVERT: A 205 SER cc_start: 0.8648 (m) cc_final: 0.8426 (p) REVERT: A 305 SER cc_start: 0.8479 (t) cc_final: 0.8201 (p) REVERT: A 505 HIS cc_start: 0.7483 (m-70) cc_final: 0.6861 (m-70) REVERT: A 554 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 564 GLN cc_start: 0.8153 (mp10) cc_final: 0.7798 (mp10) REVERT: A 574 ASP cc_start: 0.8026 (t70) cc_final: 0.7600 (t0) REVERT: A 617 CYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5847 (p) REVERT: A 645 THR cc_start: 0.8254 (m) cc_final: 0.7822 (p) REVERT: A 660 TYR cc_start: 0.8591 (m-80) cc_final: 0.8296 (m-80) REVERT: A 723 THR cc_start: 0.8490 (p) cc_final: 0.8255 (m) REVERT: A 725 GLU cc_start: 0.8201 (tt0) cc_final: 0.7903 (tt0) REVERT: A 737 ASP cc_start: 0.8160 (t0) cc_final: 0.7802 (t0) REVERT: A 804 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8320 (mm-40) REVERT: A 814 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8144 (mmmm) REVERT: A 823 PHE cc_start: 0.7202 (m-80) cc_final: 0.6979 (t80) REVERT: A 904 TYR cc_start: 0.7455 (m-10) cc_final: 0.6976 (m-10) REVERT: A 933 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8232 (mtpp) REVERT: A 950 ASP cc_start: 0.7514 (m-30) cc_final: 0.7019 (m-30) REVERT: A 957 GLN cc_start: 0.8022 (tp40) cc_final: 0.7791 (tp40) REVERT: A 1045 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7790 (mmtm) REVERT: A 1122 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7822 (t) REVERT: B 28 TYR cc_start: 0.7660 (m-10) cc_final: 0.7422 (m-80) REVERT: B 41 LYS cc_start: 0.7342 (mmtt) cc_final: 0.6493 (mmtm) REVERT: B 53 ASP cc_start: 0.7628 (t0) cc_final: 0.7411 (t0) REVERT: B 190 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7736 (tpp80) REVERT: B 215 ASP cc_start: 0.5149 (OUTLIER) cc_final: 0.4938 (t70) REVERT: B 281 GLU cc_start: 0.8088 (pp20) cc_final: 0.7853 (pp20) REVERT: B 436 TRP cc_start: 0.6668 (p90) cc_final: 0.6396 (p90) REVERT: B 557 LYS cc_start: 0.8440 (ptpt) cc_final: 0.8184 (mttp) REVERT: B 574 ASP cc_start: 0.7729 (t70) cc_final: 0.7248 (t0) REVERT: B 578 ASP cc_start: 0.7621 (t0) cc_final: 0.7390 (t0) REVERT: B 619 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7349 (mm-30) REVERT: B 646 ARG cc_start: 0.8323 (mtm180) cc_final: 0.8101 (mtm110) REVERT: B 702 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7552 (mm-30) REVERT: B 723 THR cc_start: 0.8437 (p) cc_final: 0.8102 (t) REVERT: B 735 SER cc_start: 0.8686 (m) cc_final: 0.8410 (t) REVERT: B 736 VAL cc_start: 0.8890 (m) cc_final: 0.8575 (t) REVERT: B 740 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8247 (tmm) REVERT: B 776 LYS cc_start: 0.8433 (tttm) cc_final: 0.8230 (tttm) REVERT: B 811 LYS cc_start: 0.7237 (tttm) cc_final: 0.6864 (tppp) REVERT: B 814 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7795 (mmtt) REVERT: B 868 GLU cc_start: 0.7911 (mp0) cc_final: 0.7613 (mp0) REVERT: B 952 VAL cc_start: 0.8627 (t) cc_final: 0.8396 (m) REVERT: B 1038 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8125 (mmtm) REVERT: B 1072 GLU cc_start: 0.8557 (pm20) cc_final: 0.7944 (pm20) REVERT: B 1096 VAL cc_start: 0.8459 (t) cc_final: 0.8155 (m) REVERT: C 24 ARG cc_start: 0.5079 (mtm-85) cc_final: 0.3544 (ttp-170) REVERT: C 33 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8280 (p) REVERT: C 41 LYS cc_start: 0.6982 (mmpt) cc_final: 0.5636 (mtpp) REVERT: C 100 ILE cc_start: 0.8590 (tp) cc_final: 0.8317 (pp) REVERT: C 155 SER cc_start: 0.8783 (m) cc_final: 0.8431 (t) REVERT: C 156 GLU cc_start: 0.7293 (pm20) cc_final: 0.6941 (pp20) REVERT: C 189 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 304 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8178 (mmmm) REVERT: C 305 SER cc_start: 0.8615 (t) cc_final: 0.8284 (p) REVERT: C 308 VAL cc_start: 0.8722 (t) cc_final: 0.8470 (p) REVERT: C 317 ASN cc_start: 0.8598 (m-40) cc_final: 0.8339 (m-40) REVERT: C 515 PHE cc_start: 0.6853 (m-80) cc_final: 0.6426 (m-80) REVERT: C 578 ASP cc_start: 0.8094 (t0) cc_final: 0.7761 (t70) REVERT: C 581 THR cc_start: 0.8111 (m) cc_final: 0.7480 (t) REVERT: C 586 ASP cc_start: 0.7932 (m-30) cc_final: 0.7714 (m-30) REVERT: C 606 ASN cc_start: 0.8935 (m-40) cc_final: 0.8681 (m110) REVERT: C 619 GLU cc_start: 0.7531 (pm20) cc_final: 0.7324 (pm20) REVERT: C 651 ILE cc_start: 0.8398 (pt) cc_final: 0.8187 (mt) REVERT: C 661 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6997 (tm-30) REVERT: C 748 GLU cc_start: 0.6724 (pp20) cc_final: 0.6286 (pp20) REVERT: C 776 LYS cc_start: 0.8506 (tttm) cc_final: 0.8261 (ttmm) REVERT: C 790 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7908 (mtpp) REVERT: C 811 LYS cc_start: 0.8253 (tttm) cc_final: 0.7843 (tttm) REVERT: C 904 TYR cc_start: 0.7148 (m-10) cc_final: 0.6845 (m-10) REVERT: C 957 GLN cc_start: 0.8412 (tt0) cc_final: 0.8144 (tt0) REVERT: C 1073 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8146 (mmmm) outliers start: 97 outliers final: 52 residues processed: 629 average time/residue: 0.6188 time to fit residues: 450.8988 Evaluate side-chains 631 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 570 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 161 optimal weight: 0.8980 chunk 147 optimal weight: 0.0470 chunk 123 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 217 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 193 optimal weight: 0.0370 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 710 ASN C 121 ASN C 188 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 955 ASN C 960 ASN C 978 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129830 restraints weight = 35758.497| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.41 r_work: 0.3515 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25108 Z= 0.134 Angle : 0.578 11.379 34254 Z= 0.292 Chirality : 0.047 0.427 3984 Planarity : 0.004 0.083 4356 Dihedral : 5.807 58.955 4082 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 3.21 % Allowed : 15.96 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 3014 helix: 2.53 (0.20), residues: 633 sheet: 0.56 (0.18), residues: 709 loop : -0.84 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 466 TYR 0.028 0.001 TYR B 170 PHE 0.026 0.001 PHE C 168 TRP 0.018 0.001 TRP C 353 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00305 (25034) covalent geometry : angle 0.54948 (34068) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.62332 ( 72) hydrogen bonds : bond 0.04393 ( 1020) hydrogen bonds : angle 5.38794 ( 2895) link_NAG-ASN : bond 0.00632 ( 38) link_NAG-ASN : angle 2.93490 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 582 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7682 (pt0) cc_final: 0.7465 (pt0) REVERT: A 32 PHE cc_start: 0.9002 (m-80) cc_final: 0.8704 (m-80) REVERT: A 41 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: A 53 ASP cc_start: 0.7382 (t0) cc_final: 0.7060 (t70) REVERT: A 205 SER cc_start: 0.8647 (m) cc_final: 0.8429 (p) REVERT: A 305 SER cc_start: 0.8436 (t) cc_final: 0.8145 (p) REVERT: A 554 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 564 GLN cc_start: 0.8164 (mp10) cc_final: 0.7843 (mp10) REVERT: A 574 ASP cc_start: 0.8013 (t70) cc_final: 0.7585 (t0) REVERT: A 645 THR cc_start: 0.8230 (m) cc_final: 0.7773 (p) REVERT: A 660 TYR cc_start: 0.8609 (m-80) cc_final: 0.8356 (m-80) REVERT: A 725 GLU cc_start: 0.8206 (tt0) cc_final: 0.7916 (tt0) REVERT: A 737 ASP cc_start: 0.8089 (t0) cc_final: 0.7728 (t0) REVERT: A 804 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8320 (mm-40) REVERT: A 814 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8175 (mmmm) REVERT: A 823 PHE cc_start: 0.7161 (m-80) cc_final: 0.6958 (t80) REVERT: A 904 TYR cc_start: 0.7520 (m-10) cc_final: 0.6958 (m-10) REVERT: A 933 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8242 (mtpp) REVERT: A 950 ASP cc_start: 0.7441 (m-30) cc_final: 0.6965 (m-30) REVERT: A 957 GLN cc_start: 0.7983 (tp40) cc_final: 0.7767 (tp40) REVERT: A 1031 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7466 (tt0) REVERT: A 1045 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7765 (mmtm) REVERT: A 1122 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7794 (t) REVERT: B 28 TYR cc_start: 0.7663 (m-10) cc_final: 0.7401 (m-80) REVERT: B 41 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6172 (mmtp) REVERT: B 53 ASP cc_start: 0.7574 (t0) cc_final: 0.7355 (t0) REVERT: B 127 VAL cc_start: 0.8338 (t) cc_final: 0.8126 (m) REVERT: B 215 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4892 (t70) REVERT: B 436 TRP cc_start: 0.6692 (p90) cc_final: 0.6434 (p90) REVERT: B 557 LYS cc_start: 0.8390 (ptpt) cc_final: 0.8177 (mtmt) REVERT: B 574 ASP cc_start: 0.7730 (t70) cc_final: 0.7171 (t0) REVERT: B 619 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 658 ASN cc_start: 0.8085 (p0) cc_final: 0.7459 (p0) REVERT: B 702 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 723 THR cc_start: 0.8446 (p) cc_final: 0.8115 (t) REVERT: B 735 SER cc_start: 0.8646 (m) cc_final: 0.8364 (t) REVERT: B 736 VAL cc_start: 0.8855 (m) cc_final: 0.8563 (t) REVERT: B 740 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: B 811 LYS cc_start: 0.7213 (tttm) cc_final: 0.6691 (tttm) REVERT: B 814 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7843 (mmtt) REVERT: B 868 GLU cc_start: 0.7915 (mp0) cc_final: 0.7558 (mp0) REVERT: B 902 MET cc_start: 0.8345 (tpp) cc_final: 0.8144 (mmp) REVERT: B 1031 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 1038 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8107 (mmtm) REVERT: B 1072 GLU cc_start: 0.8532 (pm20) cc_final: 0.8039 (pm20) REVERT: B 1096 VAL cc_start: 0.8406 (t) cc_final: 0.8108 (m) REVERT: B 1122 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8392 (t) REVERT: C 24 ARG cc_start: 0.5060 (mtm-85) cc_final: 0.3575 (ttp-170) REVERT: C 33 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8238 (p) REVERT: C 41 LYS cc_start: 0.6918 (mmpt) cc_final: 0.5761 (mtpp) REVERT: C 100 ILE cc_start: 0.8590 (tp) cc_final: 0.8326 (pp) REVERT: C 155 SER cc_start: 0.8799 (m) cc_final: 0.8461 (t) REVERT: C 156 GLU cc_start: 0.7308 (pm20) cc_final: 0.6974 (pp20) REVERT: C 189 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 305 SER cc_start: 0.8627 (t) cc_final: 0.8286 (p) REVERT: C 308 VAL cc_start: 0.8696 (t) cc_final: 0.8432 (p) REVERT: C 317 ASN cc_start: 0.8554 (m-40) cc_final: 0.8279 (m-40) REVERT: C 541 PHE cc_start: 0.7887 (p90) cc_final: 0.7479 (p90) REVERT: C 577 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8549 (ttm110) REVERT: C 578 ASP cc_start: 0.8047 (t0) cc_final: 0.7791 (t70) REVERT: C 581 THR cc_start: 0.8133 (m) cc_final: 0.7540 (t) REVERT: C 606 ASN cc_start: 0.8906 (m-40) cc_final: 0.8693 (m-40) REVERT: C 619 GLU cc_start: 0.7418 (pm20) cc_final: 0.7202 (pm20) REVERT: C 651 ILE cc_start: 0.8382 (pt) cc_final: 0.8103 (mt) REVERT: C 661 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 776 LYS cc_start: 0.8524 (tttm) cc_final: 0.8254 (ttmm) REVERT: C 790 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7857 (mtpp) REVERT: C 811 LYS cc_start: 0.8238 (tttm) cc_final: 0.7822 (tttm) REVERT: C 904 TYR cc_start: 0.7099 (m-10) cc_final: 0.6768 (m-10) REVERT: C 957 GLN cc_start: 0.8462 (tt0) cc_final: 0.8253 (tt0) REVERT: C 1073 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8162 (mmmm) outliers start: 86 outliers final: 44 residues processed: 611 average time/residue: 0.6313 time to fit residues: 446.8397 Evaluate side-chains 623 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 571 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 120 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN A 965 GLN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 710 ASN B1010 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128782 restraints weight = 35658.475| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.40 r_work: 0.3502 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25108 Z= 0.186 Angle : 0.608 12.056 34254 Z= 0.308 Chirality : 0.047 0.380 3984 Planarity : 0.004 0.043 4356 Dihedral : 5.676 59.865 4080 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 3.54 % Allowed : 17.53 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 3014 helix: 2.41 (0.20), residues: 635 sheet: 0.58 (0.18), residues: 699 loop : -0.85 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.022 0.002 TYR C 91 PHE 0.027 0.001 PHE C 168 TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00437 (25034) covalent geometry : angle 0.58120 (34068) SS BOND : bond 0.00456 ( 36) SS BOND : angle 1.61880 ( 72) hydrogen bonds : bond 0.04701 ( 1020) hydrogen bonds : angle 5.41421 ( 2895) link_NAG-ASN : bond 0.00646 ( 38) link_NAG-ASN : angle 2.90998 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 584 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7705 (pt0) cc_final: 0.7491 (pt0) REVERT: A 32 PHE cc_start: 0.8995 (m-80) cc_final: 0.8740 (m-80) REVERT: A 41 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8693 (mttm) REVERT: A 205 SER cc_start: 0.8667 (m) cc_final: 0.8453 (p) REVERT: A 305 SER cc_start: 0.8444 (t) cc_final: 0.8157 (p) REVERT: A 554 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 564 GLN cc_start: 0.8236 (mp10) cc_final: 0.7912 (mp10) REVERT: A 574 ASP cc_start: 0.8011 (t70) cc_final: 0.7582 (t0) REVERT: A 645 THR cc_start: 0.8409 (m) cc_final: 0.7962 (p) REVERT: A 660 TYR cc_start: 0.8630 (m-80) cc_final: 0.8346 (m-80) REVERT: A 725 GLU cc_start: 0.8227 (tt0) cc_final: 0.7927 (tt0) REVERT: A 737 ASP cc_start: 0.8115 (t0) cc_final: 0.7905 (t0) REVERT: A 804 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8353 (mm-40) REVERT: A 814 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8195 (mmmm) REVERT: A 823 PHE cc_start: 0.7161 (m-80) cc_final: 0.6946 (t80) REVERT: A 868 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 904 TYR cc_start: 0.7703 (m-10) cc_final: 0.7067 (m-10) REVERT: A 933 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8244 (mtpp) REVERT: A 950 ASP cc_start: 0.7498 (m-30) cc_final: 0.7028 (m-30) REVERT: A 957 GLN cc_start: 0.8002 (tp40) cc_final: 0.7779 (tp40) REVERT: A 1045 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7810 (mmtm) REVERT: A 1100 THR cc_start: 0.8272 (m) cc_final: 0.8047 (p) REVERT: A 1111 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7870 (tt0) REVERT: A 1122 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7861 (t) REVERT: B 28 TYR cc_start: 0.7660 (m-10) cc_final: 0.7432 (m-80) REVERT: B 41 LYS cc_start: 0.7367 (mmtt) cc_final: 0.6221 (mmtp) REVERT: B 53 ASP cc_start: 0.7614 (t0) cc_final: 0.7397 (t0) REVERT: B 127 VAL cc_start: 0.8343 (t) cc_final: 0.8104 (m) REVERT: B 190 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: B 215 ASP cc_start: 0.5164 (OUTLIER) cc_final: 0.4957 (t70) REVERT: B 436 TRP cc_start: 0.6695 (p90) cc_final: 0.6452 (p90) REVERT: B 557 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8210 (mtmt) REVERT: B 574 ASP cc_start: 0.7744 (t70) cc_final: 0.7156 (t0) REVERT: B 619 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 702 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 723 THR cc_start: 0.8446 (p) cc_final: 0.8118 (t) REVERT: B 735 SER cc_start: 0.8665 (m) cc_final: 0.8375 (t) REVERT: B 736 VAL cc_start: 0.8861 (m) cc_final: 0.8544 (t) REVERT: B 740 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8235 (tmm) REVERT: B 811 LYS cc_start: 0.7223 (tttm) cc_final: 0.6699 (tttm) REVERT: B 814 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7836 (mmtt) REVERT: B 868 GLU cc_start: 0.7913 (mp0) cc_final: 0.7549 (mp0) REVERT: B 902 MET cc_start: 0.8398 (tpp) cc_final: 0.8181 (mmp) REVERT: B 1038 LYS cc_start: 0.8383 (mmtm) cc_final: 0.8101 (mmtm) REVERT: B 1096 VAL cc_start: 0.8446 (t) cc_final: 0.8152 (m) REVERT: B 1116 THR cc_start: 0.8144 (p) cc_final: 0.7793 (t) REVERT: B 1122 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 24 ARG cc_start: 0.5172 (mtm-85) cc_final: 0.3601 (ttp-170) REVERT: C 33 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 41 LYS cc_start: 0.6887 (mmpt) cc_final: 0.5530 (mtpp) REVERT: C 100 ILE cc_start: 0.8602 (tp) cc_final: 0.8344 (pp) REVERT: C 155 SER cc_start: 0.8795 (m) cc_final: 0.8478 (t) REVERT: C 156 GLU cc_start: 0.7312 (pm20) cc_final: 0.7020 (pp20) REVERT: C 189 LEU cc_start: 0.8663 (tt) cc_final: 0.8390 (tp) REVERT: C 305 SER cc_start: 0.8632 (t) cc_final: 0.8297 (p) REVERT: C 308 VAL cc_start: 0.8702 (t) cc_final: 0.8445 (p) REVERT: C 541 PHE cc_start: 0.7923 (p90) cc_final: 0.7641 (p90) REVERT: C 577 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8504 (ttm-80) REVERT: C 578 ASP cc_start: 0.8089 (t0) cc_final: 0.7777 (t70) REVERT: C 581 THR cc_start: 0.8156 (m) cc_final: 0.7579 (t) REVERT: C 606 ASN cc_start: 0.8917 (m-40) cc_final: 0.8693 (m-40) REVERT: C 619 GLU cc_start: 0.7516 (pm20) cc_final: 0.7273 (pm20) REVERT: C 651 ILE cc_start: 0.8395 (pt) cc_final: 0.8163 (mt) REVERT: C 661 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7004 (tm-30) REVERT: C 748 GLU cc_start: 0.6589 (pp20) cc_final: 0.6213 (pp20) REVERT: C 752 LEU cc_start: 0.7448 (tt) cc_final: 0.7219 (tt) REVERT: C 776 LYS cc_start: 0.8544 (tttm) cc_final: 0.8292 (ttmm) REVERT: C 790 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7979 (mtmm) REVERT: C 904 TYR cc_start: 0.7097 (m-10) cc_final: 0.6792 (m-10) REVERT: C 990 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7006 (mm-30) REVERT: C 1073 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8156 (mmmm) outliers start: 95 outliers final: 58 residues processed: 619 average time/residue: 0.6548 time to fit residues: 471.0903 Evaluate side-chains 631 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 565 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 89 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 134 optimal weight: 0.9980 chunk 46 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 291 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 239 GLN B 606 ASN B 710 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129223 restraints weight = 35965.178| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.41 r_work: 0.3514 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25108 Z= 0.150 Angle : 0.578 10.207 34254 Z= 0.294 Chirality : 0.046 0.380 3984 Planarity : 0.004 0.040 4356 Dihedral : 5.425 58.720 4080 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 3.17 % Allowed : 18.61 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3014 helix: 2.45 (0.20), residues: 640 sheet: 0.57 (0.18), residues: 694 loop : -0.83 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1091 TYR 0.028 0.001 TYR B 170 PHE 0.027 0.001 PHE B 429 TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00347 (25034) covalent geometry : angle 0.55267 (34068) SS BOND : bond 0.00508 ( 36) SS BOND : angle 1.52120 ( 72) hydrogen bonds : bond 0.04435 ( 1020) hydrogen bonds : angle 5.34499 ( 2895) link_NAG-ASN : bond 0.00637 ( 38) link_NAG-ASN : angle 2.74376 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 570 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7688 (pt0) cc_final: 0.7464 (pt0) REVERT: A 32 PHE cc_start: 0.8990 (m-80) cc_final: 0.8699 (m-80) REVERT: A 41 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8670 (mttm) REVERT: A 205 SER cc_start: 0.8685 (m) cc_final: 0.8450 (p) REVERT: A 235 ILE cc_start: 0.6712 (tp) cc_final: 0.6472 (tp) REVERT: A 305 SER cc_start: 0.8419 (t) cc_final: 0.8131 (p) REVERT: A 554 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 571 ASP cc_start: 0.7565 (t0) cc_final: 0.7147 (t0) REVERT: A 574 ASP cc_start: 0.8026 (t70) cc_final: 0.7598 (t0) REVERT: A 645 THR cc_start: 0.8490 (m) cc_final: 0.8143 (p) REVERT: A 725 GLU cc_start: 0.8220 (tt0) cc_final: 0.7920 (tt0) REVERT: A 804 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8359 (mm-40) REVERT: A 814 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8244 (mppt) REVERT: A 868 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 933 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8225 (mtpp) REVERT: A 950 ASP cc_start: 0.7450 (m-30) cc_final: 0.6979 (m-30) REVERT: A 1031 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7447 (tt0) REVERT: A 1045 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7767 (mmtm) REVERT: A 1105 THR cc_start: 0.8581 (p) cc_final: 0.8236 (t) REVERT: A 1111 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7741 (tt0) REVERT: A 1122 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.7850 (t) REVERT: B 28 TYR cc_start: 0.7668 (m-10) cc_final: 0.7442 (m-80) REVERT: B 41 LYS cc_start: 0.7379 (mmtt) cc_final: 0.6328 (mmtm) REVERT: B 53 ASP cc_start: 0.7602 (t0) cc_final: 0.7381 (t0) REVERT: B 127 VAL cc_start: 0.8318 (t) cc_final: 0.8114 (m) REVERT: B 171 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8492 (m) REVERT: B 190 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.8000 (tpp80) REVERT: B 215 ASP cc_start: 0.5160 (OUTLIER) cc_final: 0.4956 (t70) REVERT: B 436 TRP cc_start: 0.6696 (p90) cc_final: 0.6427 (p90) REVERT: B 524 VAL cc_start: 0.7986 (t) cc_final: 0.7757 (t) REVERT: B 557 LYS cc_start: 0.8392 (ptpt) cc_final: 0.8189 (mtmt) REVERT: B 574 ASP cc_start: 0.7705 (t70) cc_final: 0.7128 (t0) REVERT: B 619 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 702 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 723 THR cc_start: 0.8442 (p) cc_final: 0.8106 (t) REVERT: B 735 SER cc_start: 0.8617 (m) cc_final: 0.8332 (t) REVERT: B 736 VAL cc_start: 0.8850 (m) cc_final: 0.8536 (t) REVERT: B 740 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8203 (tmm) REVERT: B 776 LYS cc_start: 0.8319 (tttm) cc_final: 0.8052 (tttm) REVERT: B 811 LYS cc_start: 0.7200 (tttm) cc_final: 0.6690 (tttm) REVERT: B 814 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7826 (mmtt) REVERT: B 868 GLU cc_start: 0.7913 (mp0) cc_final: 0.7504 (mp0) REVERT: B 1038 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8096 (mmtm) REVERT: B 1096 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8110 (m) REVERT: B 1116 THR cc_start: 0.8103 (p) cc_final: 0.7758 (t) REVERT: B 1122 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8409 (t) REVERT: C 24 ARG cc_start: 0.5127 (mtm-85) cc_final: 0.3574 (ttp-170) REVERT: C 33 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8177 (p) REVERT: C 41 LYS cc_start: 0.6869 (mmpt) cc_final: 0.5685 (mtpp) REVERT: C 100 ILE cc_start: 0.8603 (tp) cc_final: 0.8341 (pp) REVERT: C 155 SER cc_start: 0.8792 (m) cc_final: 0.8469 (t) REVERT: C 156 GLU cc_start: 0.7323 (pm20) cc_final: 0.7009 (pp20) REVERT: C 189 LEU cc_start: 0.8696 (tt) cc_final: 0.8437 (tp) REVERT: C 200 TYR cc_start: 0.8275 (m-10) cc_final: 0.7926 (m-80) REVERT: C 304 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8279 (mmtp) REVERT: C 305 SER cc_start: 0.8641 (t) cc_final: 0.8297 (p) REVERT: C 308 VAL cc_start: 0.8703 (t) cc_final: 0.8444 (p) REVERT: C 541 PHE cc_start: 0.7903 (p90) cc_final: 0.7637 (p90) REVERT: C 578 ASP cc_start: 0.8088 (t0) cc_final: 0.7805 (t70) REVERT: C 580 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: C 581 THR cc_start: 0.8166 (m) cc_final: 0.7576 (t) REVERT: C 606 ASN cc_start: 0.8919 (m-40) cc_final: 0.8685 (m-40) REVERT: C 619 GLU cc_start: 0.7427 (pm20) cc_final: 0.7167 (pm20) REVERT: C 651 ILE cc_start: 0.8384 (pt) cc_final: 0.8127 (mt) REVERT: C 661 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6962 (tm-30) REVERT: C 725 GLU cc_start: 0.8224 (tt0) cc_final: 0.8008 (tt0) REVERT: C 748 GLU cc_start: 0.6554 (pp20) cc_final: 0.6147 (pp20) REVERT: C 776 LYS cc_start: 0.8502 (tttm) cc_final: 0.8239 (ttmm) REVERT: C 790 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7822 (mtpp) REVERT: C 904 TYR cc_start: 0.7012 (m-10) cc_final: 0.6747 (m-10) REVERT: C 990 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6969 (mm-30) REVERT: C 1031 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7680 (mp0) REVERT: C 1073 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8149 (mmmm) outliers start: 85 outliers final: 50 residues processed: 601 average time/residue: 0.6269 time to fit residues: 436.1482 Evaluate side-chains 618 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 557 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 268 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 710 ASN A 751 ASN B 196 ASN B 239 GLN B 710 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN C1036 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128573 restraints weight = 35860.080| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.43 r_work: 0.3506 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25108 Z= 0.164 Angle : 0.584 10.176 34254 Z= 0.298 Chirality : 0.046 0.360 3984 Planarity : 0.004 0.039 4356 Dihedral : 5.357 58.878 4080 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 3.32 % Allowed : 18.99 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3014 helix: 2.46 (0.20), residues: 642 sheet: 0.57 (0.18), residues: 695 loop : -0.84 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.021 0.001 TYR C 28 PHE 0.024 0.001 PHE B 168 TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00382 (25034) covalent geometry : angle 0.56000 (34068) SS BOND : bond 0.00476 ( 36) SS BOND : angle 1.56322 ( 72) hydrogen bonds : bond 0.04506 ( 1020) hydrogen bonds : angle 5.34593 ( 2895) link_NAG-ASN : bond 0.00583 ( 38) link_NAG-ASN : angle 2.71078 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 567 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7691 (pt0) cc_final: 0.7464 (pt0) REVERT: A 32 PHE cc_start: 0.8987 (m-80) cc_final: 0.8705 (m-80) REVERT: A 41 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (mttm) REVERT: A 205 SER cc_start: 0.8673 (m) cc_final: 0.8434 (p) REVERT: A 305 SER cc_start: 0.8425 (t) cc_final: 0.8138 (p) REVERT: A 554 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7662 (mm-30) REVERT: A 571 ASP cc_start: 0.7579 (t0) cc_final: 0.7182 (t0) REVERT: A 574 ASP cc_start: 0.8022 (t70) cc_final: 0.7595 (t0) REVERT: A 645 THR cc_start: 0.8508 (m) cc_final: 0.8140 (p) REVERT: A 660 TYR cc_start: 0.8654 (m-80) cc_final: 0.8289 (m-80) REVERT: A 725 GLU cc_start: 0.8228 (tt0) cc_final: 0.7931 (tt0) REVERT: A 804 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8363 (mm-40) REVERT: A 814 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8236 (mppt) REVERT: A 823 PHE cc_start: 0.7231 (t80) cc_final: 0.6866 (m-80) REVERT: A 933 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8223 (mtpp) REVERT: A 950 ASP cc_start: 0.7448 (m-30) cc_final: 0.6977 (m-30) REVERT: A 998 THR cc_start: 0.8298 (t) cc_final: 0.8082 (p) REVERT: A 1045 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7765 (mmtm) REVERT: A 1105 THR cc_start: 0.8606 (p) cc_final: 0.8265 (t) REVERT: A 1111 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7807 (tt0) REVERT: A 1122 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.7878 (t) REVERT: B 28 TYR cc_start: 0.7677 (m-10) cc_final: 0.7460 (m-80) REVERT: B 41 LYS cc_start: 0.7386 (mmtt) cc_final: 0.6231 (mmtp) REVERT: B 53 ASP cc_start: 0.7612 (t0) cc_final: 0.7393 (t0) REVERT: B 171 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8466 (m) REVERT: B 436 TRP cc_start: 0.6706 (p90) cc_final: 0.6405 (p90) REVERT: B 574 ASP cc_start: 0.7726 (t70) cc_final: 0.7148 (t0) REVERT: B 619 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 641 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7306 (t0) REVERT: B 702 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 723 THR cc_start: 0.8455 (p) cc_final: 0.8119 (t) REVERT: B 735 SER cc_start: 0.8640 (m) cc_final: 0.8352 (t) REVERT: B 736 VAL cc_start: 0.8863 (m) cc_final: 0.8547 (t) REVERT: B 776 LYS cc_start: 0.8314 (tttm) cc_final: 0.8087 (tttm) REVERT: B 811 LYS cc_start: 0.7198 (tttm) cc_final: 0.6704 (tttm) REVERT: B 814 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7837 (mmtt) REVERT: B 868 GLU cc_start: 0.7907 (mp0) cc_final: 0.7492 (mp0) REVERT: B 1038 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8104 (mmtm) REVERT: B 1096 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 1116 THR cc_start: 0.8120 (p) cc_final: 0.7774 (t) REVERT: B 1122 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 24 ARG cc_start: 0.5110 (mtm-85) cc_final: 0.3549 (ttp-170) REVERT: C 33 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8190 (p) REVERT: C 41 LYS cc_start: 0.6871 (mmpt) cc_final: 0.5577 (mtpp) REVERT: C 100 ILE cc_start: 0.8596 (tp) cc_final: 0.8351 (pp) REVERT: C 155 SER cc_start: 0.8805 (m) cc_final: 0.8503 (t) REVERT: C 156 GLU cc_start: 0.7345 (pm20) cc_final: 0.7087 (pp20) REVERT: C 189 LEU cc_start: 0.8687 (tt) cc_final: 0.8454 (tp) REVERT: C 200 TYR cc_start: 0.8251 (m-10) cc_final: 0.7954 (m-80) REVERT: C 218 GLN cc_start: 0.7884 (mp10) cc_final: 0.7610 (mp-120) REVERT: C 237 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7935 (mtp85) REVERT: C 305 SER cc_start: 0.8659 (t) cc_final: 0.8324 (p) REVERT: C 308 VAL cc_start: 0.8704 (t) cc_final: 0.8444 (p) REVERT: C 541 PHE cc_start: 0.7913 (p90) cc_final: 0.7656 (p90) REVERT: C 578 ASP cc_start: 0.8088 (t0) cc_final: 0.7819 (t70) REVERT: C 580 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: C 581 THR cc_start: 0.8171 (m) cc_final: 0.7588 (t) REVERT: C 606 ASN cc_start: 0.8916 (m-40) cc_final: 0.8686 (m-40) REVERT: C 651 ILE cc_start: 0.8394 (pt) cc_final: 0.8141 (mt) REVERT: C 661 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 748 GLU cc_start: 0.6487 (pp20) cc_final: 0.6031 (pp20) REVERT: C 776 LYS cc_start: 0.8497 (tttm) cc_final: 0.8236 (ttmm) REVERT: C 790 LYS cc_start: 0.8259 (mtmm) cc_final: 0.8008 (mtmm) REVERT: C 904 TYR cc_start: 0.7013 (m-10) cc_final: 0.6779 (m-10) REVERT: C 1031 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 1073 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8161 (mmmm) outliers start: 89 outliers final: 54 residues processed: 606 average time/residue: 0.6406 time to fit residues: 449.8549 Evaluate side-chains 623 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 559 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 191 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 290 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 751 ASN B 239 GLN B 710 ASN C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN C1036 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.154198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128644 restraints weight = 35822.119| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.41 r_work: 0.3506 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25108 Z= 0.162 Angle : 0.598 10.180 34254 Z= 0.304 Chirality : 0.046 0.358 3984 Planarity : 0.004 0.039 4356 Dihedral : 5.343 58.772 4080 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 3.06 % Allowed : 19.77 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.15), residues: 3014 helix: 2.45 (0.20), residues: 642 sheet: 0.56 (0.19), residues: 698 loop : -0.83 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1019 TYR 0.027 0.001 TYR B 170 PHE 0.028 0.001 PHE B 429 TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00379 (25034) covalent geometry : angle 0.57439 (34068) SS BOND : bond 0.00521 ( 36) SS BOND : angle 1.54471 ( 72) hydrogen bonds : bond 0.04492 ( 1020) hydrogen bonds : angle 5.32541 ( 2895) link_NAG-ASN : bond 0.00586 ( 38) link_NAG-ASN : angle 2.70172 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 560 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7700 (pt0) cc_final: 0.7474 (pt0) REVERT: A 32 PHE cc_start: 0.9003 (m-80) cc_final: 0.8748 (m-80) REVERT: A 41 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: A 205 SER cc_start: 0.8684 (m) cc_final: 0.8442 (p) REVERT: A 305 SER cc_start: 0.8450 (t) cc_final: 0.8161 (p) REVERT: A 554 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 571 ASP cc_start: 0.7577 (t0) cc_final: 0.7174 (t0) REVERT: A 574 ASP cc_start: 0.8012 (t70) cc_final: 0.7590 (t0) REVERT: A 645 THR cc_start: 0.8529 (m) cc_final: 0.8169 (p) REVERT: A 660 TYR cc_start: 0.8655 (m-80) cc_final: 0.8268 (m-80) REVERT: A 725 GLU cc_start: 0.8193 (tt0) cc_final: 0.7902 (tt0) REVERT: A 735 SER cc_start: 0.8848 (m) cc_final: 0.8592 (t) REVERT: A 804 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8369 (mm-40) REVERT: A 814 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8361 (tppt) REVERT: A 823 PHE cc_start: 0.7221 (t80) cc_final: 0.6838 (m-80) REVERT: A 933 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8210 (mtpp) REVERT: A 950 ASP cc_start: 0.7433 (m-30) cc_final: 0.6960 (m-30) REVERT: A 998 THR cc_start: 0.8317 (t) cc_final: 0.8096 (p) REVERT: A 1045 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7760 (mmtm) REVERT: A 1122 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7886 (t) REVERT: B 28 TYR cc_start: 0.7707 (m-10) cc_final: 0.7494 (m-80) REVERT: B 36 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 41 LYS cc_start: 0.7388 (mmtt) cc_final: 0.6345 (mmtm) REVERT: B 53 ASP cc_start: 0.7627 (t0) cc_final: 0.7401 (t0) REVERT: B 171 VAL cc_start: 0.8705 (t) cc_final: 0.8495 (m) REVERT: B 436 TRP cc_start: 0.6698 (p90) cc_final: 0.6411 (p90) REVERT: B 574 ASP cc_start: 0.7703 (t70) cc_final: 0.7159 (t0) REVERT: B 619 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 641 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7287 (t0) REVERT: B 702 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 723 THR cc_start: 0.8457 (p) cc_final: 0.8120 (t) REVERT: B 735 SER cc_start: 0.8639 (m) cc_final: 0.8349 (t) REVERT: B 736 VAL cc_start: 0.8862 (m) cc_final: 0.8541 (t) REVERT: B 740 MET cc_start: 0.8537 (tpt) cc_final: 0.8235 (tmm) REVERT: B 814 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7841 (mmtt) REVERT: B 868 GLU cc_start: 0.7909 (mp0) cc_final: 0.7498 (mp0) REVERT: B 1038 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8092 (mmtm) REVERT: B 1096 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8121 (m) REVERT: B 1116 THR cc_start: 0.8102 (p) cc_final: 0.7755 (t) REVERT: B 1122 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8420 (t) REVERT: B 1128 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (t) REVERT: C 24 ARG cc_start: 0.5130 (mtm-85) cc_final: 0.3553 (ttp-170) REVERT: C 33 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 41 LYS cc_start: 0.6866 (mmpt) cc_final: 0.5564 (mtpp) REVERT: C 100 ILE cc_start: 0.8587 (tp) cc_final: 0.8339 (pp) REVERT: C 155 SER cc_start: 0.8806 (m) cc_final: 0.8504 (t) REVERT: C 156 GLU cc_start: 0.7332 (pm20) cc_final: 0.7069 (pp20) REVERT: C 189 LEU cc_start: 0.8704 (tt) cc_final: 0.8479 (tp) REVERT: C 200 TYR cc_start: 0.8238 (m-10) cc_final: 0.7931 (m-80) REVERT: C 218 GLN cc_start: 0.7952 (mp10) cc_final: 0.7649 (mp-120) REVERT: C 237 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7946 (mtp85) REVERT: C 304 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8286 (mmtp) REVERT: C 305 SER cc_start: 0.8669 (t) cc_final: 0.8326 (p) REVERT: C 308 VAL cc_start: 0.8700 (t) cc_final: 0.8442 (p) REVERT: C 541 PHE cc_start: 0.7906 (p90) cc_final: 0.7661 (p90) REVERT: C 578 ASP cc_start: 0.8101 (t0) cc_final: 0.7826 (t70) REVERT: C 580 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: C 581 THR cc_start: 0.8162 (m) cc_final: 0.7564 (t) REVERT: C 583 GLU cc_start: 0.7769 (pm20) cc_final: 0.7415 (pm20) REVERT: C 606 ASN cc_start: 0.8912 (m-40) cc_final: 0.8685 (m-40) REVERT: C 651 ILE cc_start: 0.8383 (pt) cc_final: 0.8134 (mt) REVERT: C 661 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6934 (tm-30) REVERT: C 776 LYS cc_start: 0.8503 (tttm) cc_final: 0.8240 (ttmm) REVERT: C 790 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7821 (mtpp) REVERT: C 904 TYR cc_start: 0.7024 (m-10) cc_final: 0.6787 (m-10) REVERT: C 1031 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7718 (tt0) REVERT: C 1073 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8159 (mmmm) outliers start: 82 outliers final: 55 residues processed: 594 average time/residue: 0.6458 time to fit residues: 445.4608 Evaluate side-chains 618 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 552 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 228 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 205 optimal weight: 0.1980 chunk 238 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 196 ASN B 239 GLN B 710 ASN B 755 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN C1036 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128233 restraints weight = 35779.638| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.41 r_work: 0.3498 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25108 Z= 0.186 Angle : 0.620 11.821 34254 Z= 0.315 Chirality : 0.047 0.358 3984 Planarity : 0.004 0.050 4356 Dihedral : 5.395 59.586 4080 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.28 % Rotamer: Outliers : 2.91 % Allowed : 20.37 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3014 helix: 2.40 (0.20), residues: 649 sheet: 0.57 (0.18), residues: 704 loop : -0.88 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 577 TYR 0.020 0.001 TYR C 28 PHE 0.032 0.002 PHE C 592 TRP 0.010 0.001 TRP B 353 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00439 (25034) covalent geometry : angle 0.59820 (34068) SS BOND : bond 0.00496 ( 36) SS BOND : angle 1.59175 ( 72) hydrogen bonds : bond 0.04673 ( 1020) hydrogen bonds : angle 5.35250 ( 2895) link_NAG-ASN : bond 0.00517 ( 38) link_NAG-ASN : angle 2.67098 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 563 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7704 (pt0) cc_final: 0.7487 (pt0) REVERT: A 32 PHE cc_start: 0.8993 (m-80) cc_final: 0.8746 (m-80) REVERT: A 41 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8677 (mttm) REVERT: A 205 SER cc_start: 0.8694 (m) cc_final: 0.8458 (p) REVERT: A 305 SER cc_start: 0.8445 (t) cc_final: 0.8158 (p) REVERT: A 554 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7650 (mm-30) REVERT: A 574 ASP cc_start: 0.8023 (t70) cc_final: 0.7598 (t0) REVERT: A 645 THR cc_start: 0.8518 (m) cc_final: 0.8160 (p) REVERT: A 660 TYR cc_start: 0.8653 (m-80) cc_final: 0.8303 (m-80) REVERT: A 725 GLU cc_start: 0.8216 (tt0) cc_final: 0.7912 (tt0) REVERT: A 735 SER cc_start: 0.8856 (m) cc_final: 0.8589 (t) REVERT: A 804 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8372 (mm-40) REVERT: A 814 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8270 (mppt) REVERT: A 933 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8213 (mtpp) REVERT: A 950 ASP cc_start: 0.7469 (m-30) cc_final: 0.6987 (m-30) REVERT: A 998 THR cc_start: 0.8324 (t) cc_final: 0.8102 (p) REVERT: A 1045 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7775 (mmtm) REVERT: A 1105 THR cc_start: 0.8626 (p) cc_final: 0.8294 (t) REVERT: A 1122 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7931 (t) REVERT: B 41 LYS cc_start: 0.7351 (mmtt) cc_final: 0.6190 (mmtp) REVERT: B 53 ASP cc_start: 0.7640 (t0) cc_final: 0.7418 (t0) REVERT: B 171 VAL cc_start: 0.8690 (t) cc_final: 0.8461 (m) REVERT: B 436 TRP cc_start: 0.6704 (p90) cc_final: 0.6363 (p90) REVERT: B 574 ASP cc_start: 0.7703 (t70) cc_final: 0.7167 (t0) REVERT: B 619 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 641 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7264 (t0) REVERT: B 702 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 723 THR cc_start: 0.8465 (p) cc_final: 0.8126 (t) REVERT: B 735 SER cc_start: 0.8682 (m) cc_final: 0.8391 (t) REVERT: B 736 VAL cc_start: 0.8875 (m) cc_final: 0.8547 (t) REVERT: B 787 GLN cc_start: 0.8283 (mt0) cc_final: 0.7893 (mt0) REVERT: B 814 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7892 (mmtt) REVERT: B 868 GLU cc_start: 0.7880 (mp0) cc_final: 0.7463 (mp0) REVERT: B 1038 LYS cc_start: 0.8394 (mmtm) cc_final: 0.8123 (mmtm) REVERT: B 1096 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (m) REVERT: B 1116 THR cc_start: 0.8112 (p) cc_final: 0.7769 (t) REVERT: B 1122 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 41 LYS cc_start: 0.6880 (mmpt) cc_final: 0.5551 (mtpp) REVERT: C 100 ILE cc_start: 0.8595 (tp) cc_final: 0.8360 (pp) REVERT: C 155 SER cc_start: 0.8809 (m) cc_final: 0.8505 (t) REVERT: C 156 GLU cc_start: 0.7339 (pm20) cc_final: 0.7035 (pp20) REVERT: C 189 LEU cc_start: 0.8714 (tt) cc_final: 0.8492 (tp) REVERT: C 200 TYR cc_start: 0.8269 (m-10) cc_final: 0.8064 (m-10) REVERT: C 237 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7939 (mtp85) REVERT: C 304 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8311 (mmtp) REVERT: C 305 SER cc_start: 0.8674 (t) cc_final: 0.8326 (p) REVERT: C 308 VAL cc_start: 0.8698 (t) cc_final: 0.8439 (p) REVERT: C 541 PHE cc_start: 0.7894 (p90) cc_final: 0.7661 (p90) REVERT: C 574 ASP cc_start: 0.8050 (t0) cc_final: 0.7686 (t0) REVERT: C 578 ASP cc_start: 0.8126 (t0) cc_final: 0.7843 (t70) REVERT: C 580 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: C 581 THR cc_start: 0.8136 (m) cc_final: 0.7530 (t) REVERT: C 583 GLU cc_start: 0.7785 (pm20) cc_final: 0.7420 (pm20) REVERT: C 606 ASN cc_start: 0.8919 (m-40) cc_final: 0.8693 (m-40) REVERT: C 651 ILE cc_start: 0.8382 (pt) cc_final: 0.8153 (mt) REVERT: C 661 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6962 (tm-30) REVERT: C 748 GLU cc_start: 0.6416 (pp20) cc_final: 0.5935 (pp20) REVERT: C 776 LYS cc_start: 0.8502 (tttm) cc_final: 0.8249 (ttmm) REVERT: C 790 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7796 (mtpp) REVERT: C 904 TYR cc_start: 0.7046 (m-10) cc_final: 0.6809 (m-10) REVERT: C 1031 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 1073 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8154 (mmmm) outliers start: 78 outliers final: 54 residues processed: 597 average time/residue: 0.6129 time to fit residues: 425.8649 Evaluate side-chains 615 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 553 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 290 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN B 196 ASN B 239 GLN B 710 ASN B 755 GLN C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1036 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127769 restraints weight = 35781.013| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.43 r_work: 0.3496 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25108 Z= 0.200 Angle : 0.646 12.153 34254 Z= 0.325 Chirality : 0.048 0.391 3984 Planarity : 0.004 0.040 4356 Dihedral : 5.502 59.979 4080 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.76 % Allowed : 20.66 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3014 helix: 2.34 (0.20), residues: 649 sheet: 0.59 (0.19), residues: 692 loop : -0.89 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 577 TYR 0.035 0.002 TYR B 904 PHE 0.034 0.002 PHE C 592 TRP 0.009 0.002 TRP B 353 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00473 (25034) covalent geometry : angle 0.61932 (34068) SS BOND : bond 0.00555 ( 36) SS BOND : angle 1.66873 ( 72) hydrogen bonds : bond 0.04731 ( 1020) hydrogen bonds : angle 5.36848 ( 2895) link_NAG-ASN : bond 0.00638 ( 38) link_NAG-ASN : angle 2.98028 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6028 Ramachandran restraints generated. 3014 Oldfield, 0 Emsley, 3014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 553 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.7712 (pt0) cc_final: 0.7501 (pt0) REVERT: A 32 PHE cc_start: 0.8989 (m-80) cc_final: 0.8764 (m-80) REVERT: A 41 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: A 117 LEU cc_start: 0.7971 (mp) cc_final: 0.7725 (mp) REVERT: A 205 SER cc_start: 0.8687 (m) cc_final: 0.8453 (p) REVERT: A 305 SER cc_start: 0.8442 (t) cc_final: 0.8153 (p) REVERT: A 433 VAL cc_start: 0.9006 (t) cc_final: 0.8641 (m) REVERT: A 554 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 574 ASP cc_start: 0.8004 (t70) cc_final: 0.7582 (t0) REVERT: A 645 THR cc_start: 0.8536 (m) cc_final: 0.8163 (p) REVERT: A 660 TYR cc_start: 0.8637 (m-80) cc_final: 0.8237 (m-80) REVERT: A 725 GLU cc_start: 0.8238 (tt0) cc_final: 0.7948 (tt0) REVERT: A 735 SER cc_start: 0.8847 (m) cc_final: 0.8575 (t) REVERT: A 814 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8276 (mppt) REVERT: A 933 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8215 (mtpp) REVERT: A 950 ASP cc_start: 0.7496 (m-30) cc_final: 0.7019 (m-30) REVERT: A 998 THR cc_start: 0.8325 (t) cc_final: 0.8089 (p) REVERT: A 1031 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7209 (tt0) REVERT: A 1045 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7780 (mmtm) REVERT: A 1105 THR cc_start: 0.8621 (p) cc_final: 0.8297 (t) REVERT: A 1122 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7935 (t) REVERT: B 41 LYS cc_start: 0.7357 (mmtt) cc_final: 0.6187 (mmtp) REVERT: B 53 ASP cc_start: 0.7623 (t0) cc_final: 0.7400 (t0) REVERT: B 171 VAL cc_start: 0.8714 (t) cc_final: 0.8482 (m) REVERT: B 436 TRP cc_start: 0.6731 (p90) cc_final: 0.6378 (p90) REVERT: B 574 ASP cc_start: 0.7714 (t70) cc_final: 0.7164 (t0) REVERT: B 619 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 702 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 723 THR cc_start: 0.8459 (p) cc_final: 0.8121 (t) REVERT: B 735 SER cc_start: 0.8689 (m) cc_final: 0.8397 (t) REVERT: B 736 VAL cc_start: 0.8877 (m) cc_final: 0.8554 (t) REVERT: B 787 GLN cc_start: 0.8290 (mt0) cc_final: 0.7892 (mt0) REVERT: B 814 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7881 (mmtt) REVERT: B 868 GLU cc_start: 0.7858 (mp0) cc_final: 0.7454 (mp0) REVERT: B 1038 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8111 (mmtm) REVERT: B 1096 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8177 (m) REVERT: B 1116 THR cc_start: 0.8108 (p) cc_final: 0.7754 (t) REVERT: B 1122 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8437 (t) REVERT: C 33 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8279 (p) REVERT: C 41 LYS cc_start: 0.6888 (mmpt) cc_final: 0.5588 (mtpp) REVERT: C 100 ILE cc_start: 0.8602 (tp) cc_final: 0.8364 (pp) REVERT: C 155 SER cc_start: 0.8833 (m) cc_final: 0.8527 (t) REVERT: C 156 GLU cc_start: 0.7363 (pm20) cc_final: 0.7056 (pp20) REVERT: C 189 LEU cc_start: 0.8722 (tt) cc_final: 0.8492 (tp) REVERT: C 304 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8306 (mmtp) REVERT: C 305 SER cc_start: 0.8671 (t) cc_final: 0.8322 (p) REVERT: C 308 VAL cc_start: 0.8698 (t) cc_final: 0.8439 (p) REVERT: C 541 PHE cc_start: 0.7894 (p90) cc_final: 0.7670 (p90) REVERT: C 578 ASP cc_start: 0.8132 (t0) cc_final: 0.7867 (t70) REVERT: C 580 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: C 581 THR cc_start: 0.8134 (m) cc_final: 0.7557 (t) REVERT: C 583 GLU cc_start: 0.7794 (pm20) cc_final: 0.7404 (pm20) REVERT: C 606 ASN cc_start: 0.8920 (m-40) cc_final: 0.8693 (m-40) REVERT: C 651 ILE cc_start: 0.8365 (pt) cc_final: 0.8161 (mt) REVERT: C 661 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6961 (tm-30) REVERT: C 748 GLU cc_start: 0.6467 (pp20) cc_final: 0.6001 (pp20) REVERT: C 776 LYS cc_start: 0.8476 (tttm) cc_final: 0.8227 (ttmm) REVERT: C 790 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7803 (mtpp) REVERT: C 904 TYR cc_start: 0.7057 (m-10) cc_final: 0.6820 (m-10) REVERT: C 990 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6827 (mm-30) REVERT: C 1031 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7717 (tt0) REVERT: C 1073 LYS cc_start: 0.8384 (mmmm) cc_final: 0.8160 (mmmm) outliers start: 74 outliers final: 54 residues processed: 584 average time/residue: 0.6281 time to fit residues: 426.1486 Evaluate side-chains 603 residues out of total 2681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 543 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 68 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A 935 GLN B 196 ASN B 239 GLN B 710 ASN B 755 GLN C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 978 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.126911 restraints weight = 35848.702| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.44 r_work: 0.3485 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25108 Z= 0.231 Angle : 0.664 11.751 34254 Z= 0.336 Chirality : 0.049 0.365 3984 Planarity : 0.004 0.041 4356 Dihedral : 5.593 59.203 4080 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 2.69 % Allowed : 20.78 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3014 helix: 2.25 (0.20), residues: 649 sheet: 0.55 (0.19), residues: 693 loop : -0.94 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.042 0.002 TYR B 904 PHE 0.032 0.002 PHE C 592 TRP 0.012 0.002 TRP B 353 HIS 0.006 0.001 HIS B 339 Details of bonding type rmsd covalent geometry : bond 0.00544 (25034) covalent geometry : angle 0.63828 (34068) SS BOND : bond 0.00593 ( 36) SS BOND : angle 1.90216 ( 72) hydrogen bonds : bond 0.04989 ( 1020) hydrogen bonds : angle 5.45336 ( 2895) link_NAG-ASN : bond 0.00507 ( 38) link_NAG-ASN : angle 2.89952 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11932.60 seconds wall clock time: 203 minutes 19.40 seconds (12199.40 seconds total)