Starting phenix.real_space_refine on Sun Jul 5 14:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wt7_32770/07_2026/7wt7_32770.cif" } resolution = 3.4 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= -0.002 sd= 0.078 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 125 5.16 5 C 18053 2.51 5 N 4654 2.21 5 O 5490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28322 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8630 Classifications: {'peptide': 1098} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 12 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" 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 chiralities: 14 Time building chain proxies: 6.03, per 1000 atoms: 0.21 Number of scatterers: 28322 At special positions: 0 Unit cell: (142.31, 144.45, 242.89, 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 125 16.00 O 5490 8.00 N 4654 7.00 C 18053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.05 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.05 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.02 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 340 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 233 " " NAG A1306 " - " ASN A 600 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 714 " " NAG A1310 " - " ASN A1071 " " NAG A1311 " - " ASN A 798 " " NAG A1312 " - " ASN A 706 " " NAG B1301 " - " ASN B1071 " " NAG B1302 " - " ASN B 714 " " NAG B1303 " - " ASN B 798 " " NAG B1304 " - " ASN B 706 " " NAG B1305 " - " ASN B1095 " " NAG B1306 " - " ASN B1131 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 145 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 340 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 233 " " NAG B1313 " - " ASN B 600 " " NAG B1314 " - " ASN B 328 " " NAG B1315 " - " ASN B 613 " " NAG C1301 " - " ASN C 326 " " NAG C1302 " - " ASN C 338 " " NAG C1303 " - " ASN C 598 " " NAG C1304 " - " ASN C 611 " " NAG C1305 " - " ASN C 704 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 145 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 233 " " NAG C1311 " - " ASN C 652 " " NAG C1312 " - " ASN C1069 " " NAG C1313 " - " ASN C1093 " " NAG C1314 " - " ASN C1129 " " NAG E 1 " - " ASN A1095 " " NAG F 1 " - " ASN A1131 " " NAG G 1 " - " ASN C 712 " " NAG I 1 " - " ASN C 796 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 56 sheets defined 24.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.546A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.799A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 4.087A pdb=" N ALA A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.962A pdb=" N THR A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 863 through 878 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.519A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 904 removed outlier: 3.578A pdb=" N ALA A 900 " --> pdb=" O PRO A 896 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.766A pdb=" N ILE A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.405A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1158 removed outlier: 4.960A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.608A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.519A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.798A pdb=" N LEU B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.393A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.833A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.585A pdb=" N THR B 635 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 743 through 754 removed outlier: 4.087A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 780 removed outlier: 3.984A pdb=" N THR B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 878 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 898 Processing helix chain 'B' and resid 902 through 907 removed outlier: 3.636A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 938 removed outlier: 4.007A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 960 removed outlier: 3.546A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 965 removed outlier: 3.806A pdb=" N SER B 964 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 965 " --> pdb=" O GLN B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.102A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B1022 " --> pdb=" O SER B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1158 removed outlier: 4.434A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.675A pdb=" N VAL C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.710A pdb=" N TYR C 364 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.582A pdb=" N ASN C 746 " --> pdb=" O THR C 742 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 749 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 removed outlier: 3.776A pdb=" N ALA C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN C 774 " --> pdb=" O ASP C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 844 through 849 Processing helix chain 'C' and resid 861 through 877 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 897 Processing helix chain 'C' and resid 898 through 900 No H-bonds generated for 'chain 'C' and resid 898 through 900' Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 910 through 936 removed outlier: 4.616A pdb=" N LYS C 916 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU C 917 " --> pdb=" O GLU C 913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 939 No H-bonds generated for 'chain 'C' and resid 937 through 939' Processing helix chain 'C' and resid 940 through 960 removed outlier: 3.581A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1027 removed outlier: 3.670A pdb=" N ARG C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1156 removed outlier: 4.013A pdb=" N PHE C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU C1146 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C1148 " --> pdb=" O LYS C1144 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS C1149 " --> pdb=" O GLU C1145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C1153 " --> pdb=" O LYS C1149 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.919A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.744A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 261 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 226 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.549A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.661A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 11.777A pdb=" N VAL A 126 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU A 166 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N ILE A 128 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR A 164 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 130 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN A 162 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 132 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA A 160 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 134 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.606A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 592 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.299A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.299A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.755A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 508 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 389 removed outlier: 4.082A pdb=" N VAL A 521 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 607 through 609 removed outlier: 3.564A pdb=" N TYR A 609 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.115A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.756A pdb=" N ASN A 700 " --> pdb=" O LYS C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 717 removed outlier: 6.132A pdb=" N PHE A 715 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE A 717 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A1064 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A1044 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 720 through 725 Processing sheet with id=AB8, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.514A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.578A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 261 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 126 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 168 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 128 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 166 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 130 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.578A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.522A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.756A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.963A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 535 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.219A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 719 removed outlier: 6.846A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 722 through 725 removed outlier: 3.736A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD7, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.591A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.601A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN C 61 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 264 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 259 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 185 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N HIS C 204 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU C 222 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 36 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.778A pdb=" N ASP C 282 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.022A pdb=" N ILE C 105 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 126 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 168 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 128 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU C 166 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 130 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 132 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN C 162 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLN C 134 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA C 160 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 306 through 307 removed outlier: 3.526A pdb=" N THR C 594 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 638 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.756A pdb=" N TRP C 431 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 349 through 352 removed outlier: 5.133A pdb=" N ASN C 389 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 511 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE7, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AE8, first strand: chain 'C' and resid 533 through 534 Processing sheet with id=AE9, first strand: chain 'C' and resid 537 through 538 removed outlier: 3.531A pdb=" N PHE C 538 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 649 through 650 removed outlier: 5.801A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 717 removed outlier: 3.701A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 717 removed outlier: 7.358A pdb=" N GLY C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER C1050 " --> pdb=" O GLY C1054 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1056 " --> pdb=" O PRO C1048 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1115 through 1117 removed outlier: 4.236A pdb=" N CYS C1077 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1092 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.744A pdb=" N THR D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 45 through 46 966 hydrogen bonds defined for protein. 2580 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: 6.93 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4576 1.30 - 1.44: 8124 1.44 - 1.57: 16125 1.57 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 28984 Sorted by residual: bond pdb=" C PRO B 894 " pdb=" O PRO B 894 " ideal model delta sigma weight residual 1.233 1.167 0.065 1.16e-02 7.43e+03 3.17e+01 bond pdb=" C PRO C 892 " pdb=" O PRO C 892 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.24e-02 6.50e+03 2.89e+01 bond pdb=" C MET B1047 " pdb=" O MET B1047 " ideal model delta sigma weight residual 1.237 1.188 0.049 9.40e-03 1.13e+04 2.76e+01 bond pdb=" CA SER A 813 " pdb=" CB SER A 813 " ideal model delta sigma weight residual 1.530 1.453 0.076 1.57e-02 4.06e+03 2.36e+01 bond pdb=" C PRO A 894 " pdb=" O PRO A 894 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.39e-02 5.18e+03 2.15e+01 ... (remaining 28979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 38308 2.56 - 5.12: 979 5.12 - 7.68: 109 7.68 - 10.23: 38 10.23 - 12.79: 4 Bond angle restraints: 39438 Sorted by residual: angle pdb=" N PRO A 894 " pdb=" CA PRO A 894 " pdb=" CB PRO A 894 " ideal model delta sigma weight residual 103.19 93.79 9.40 9.00e-01 1.23e+00 1.09e+02 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.25 94.82 8.43 8.80e-01 1.29e+00 9.18e+01 angle pdb=" C PRO A 894 " pdb=" CA PRO A 894 " pdb=" CB PRO A 894 " ideal model delta sigma weight residual 111.64 100.46 11.18 1.27e+00 6.20e-01 7.75e+01 angle pdb=" N PRO A 983 " pdb=" CA PRO A 983 " pdb=" C PRO A 983 " ideal model delta sigma weight residual 110.70 120.80 -10.10 1.22e+00 6.72e-01 6.85e+01 angle pdb=" N PRO A 896 " pdb=" CA PRO A 896 " pdb=" C PRO A 896 " ideal model delta sigma weight residual 113.47 102.39 11.08 1.43e+00 4.89e-01 6.00e+01 ... (remaining 39433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15290 17.88 - 35.75: 1307 35.75 - 53.63: 246 53.63 - 71.50: 51 71.50 - 89.38: 24 Dihedral angle restraints: 16918 sinusoidal: 6645 harmonic: 10273 Sorted by residual: dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual -180.00 -132.10 -47.90 0 5.00e+00 4.00e-02 9.18e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -2.18 -83.82 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA ASN A 145 " pdb=" C ASN A 145 " pdb=" N ASN A 146 " pdb=" CA ASN A 146 " ideal model delta harmonic sigma weight residual -180.00 -136.79 -43.21 0 5.00e+00 4.00e-02 7.47e+01 ... (remaining 16915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 4521 0.184 - 0.367: 59 0.367 - 0.551: 6 0.551 - 0.734: 0 0.734 - 0.918: 1 Chirality restraints: 4587 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA TYR C 912 " pdb=" N TYR C 912 " pdb=" C TYR C 912 " pdb=" CB TYR C 912 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 4584 not shown) Planarity restraints: 5081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 937 " -0.030 2.00e-02 2.50e+03 6.12e-02 3.75e+01 pdb=" C SER A 937 " 0.106 2.00e-02 2.50e+03 pdb=" O SER A 937 " -0.040 2.00e-02 2.50e+03 pdb=" N THR A 938 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 911 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C ASN A 911 " -0.099 2.00e-02 2.50e+03 pdb=" O ASN A 911 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL A 912 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 617 " 0.097 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 618 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " 0.076 5.00e-02 4.00e+02 ... (remaining 5078 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 783 2.69 - 3.24: 27681 3.24 - 3.79: 41018 3.79 - 4.35: 54071 4.35 - 4.90: 90489 Nonbonded interactions: 214042 Sorted by model distance: nonbonded pdb=" OH TYR C 669 " pdb=" OE1 GLN C 685 " model vdw 2.132 3.040 nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.145 3.040 nonbonded pdb=" OG SER A 98 " pdb=" O GLU A 177 " model vdw 2.162 3.040 nonbonded pdb=" OD1 ASN B 706 " pdb=" ND2 ASN B 707 " model vdw 2.166 3.120 nonbonded pdb=" O GLY C 875 " pdb=" OG SER C 879 " model vdw 2.197 3.040 ... (remaining 214037 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 14 through 442 or (resid 443 through 444 and (name N or na \ me CA or name C or name O )) or resid 445 through 1312)) selection = (chain 'B' and (resid 14 through 442 or (resid 443 through 444 and (name N or na \ me CA or name C or name O )) or resid 445 through 1312)) selection = (chain 'C' and resid 14 through 1312) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 27.390 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29076 Z= 0.340 Angle : 0.953 21.671 39670 Z= 0.591 Chirality : 0.059 0.918 4587 Planarity : 0.006 0.141 5036 Dihedral : 13.842 89.380 10185 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.11 % Favored : 92.61 % Rotamer: Outliers : 0.91 % Allowed : 1.16 % Favored : 97.93 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -1.79 (0.13), residues: 3489 helix: -0.31 (0.19), residues: 709 sheet: -0.57 (0.19), residues: 709 loop : -1.80 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 405 TYR 0.024 0.001 TYR B 633 PHE 0.034 0.002 PHE B 133 TRP 0.028 0.001 TRP H 36 HIS 0.005 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.34 (28984) covalent geometry : angle 0.92423 / 0.59 (39438) SS BOND : bond 0.00523 / 0.34 ( 41) SS BOND : angle 1.52905 / 1.00 ( 82) hydrogen bonds : bond 0.21630 / 14.05 ( 947) hydrogen bonds : angle 8.24580 / 5.63 ( 2580) Misc. bond : bond 0.00111 / 0.06 ( 1) link_BETA1-4 : bond 0.00709 / 0.37 ( 5) link_BETA1-4 : angle 2.03204 / 1.11 ( 15) link_NAG-ASN : bond 0.00694 / 0.48 ( 45) link_NAG-ASN : angle 3.90214 / 2.95 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 1.669 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: A 167 TYR cc_start: 0.6939 (t80) cc_final: 0.6699 (t80) REVERT: B 147 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6806 (mmtt) REVERT: B 618 PRO cc_start: 0.6448 (Cg_exo) cc_final: 0.6177 (Cg_endo) REVERT: C 447 LEU cc_start: 0.8452 (mp) cc_final: 0.8232 (tt) REVERT: C 820 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8741 (mtpp) REVERT: C 989 ASP cc_start: 0.6797 (m-30) cc_final: 0.5961 (m-30) REVERT: D 42 LYS cc_start: 0.6923 (pptt) cc_final: 0.6056 (pptt) REVERT: D 50 ASP cc_start: 0.8146 (t0) cc_final: 0.7914 (t0) REVERT: D 71 PHE cc_start: 0.7716 (t80) cc_final: 0.7436 (t80) REVERT: D 86 TYR cc_start: 0.6437 (m-10) cc_final: 0.6106 (m-10) outliers start: 28 outliers final: 8 residues processed: 287 average time/residue: 0.1759 time to fit residues: 83.6601 Evaluate side-chains 206 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 820 LYS Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 1067 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 759 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN B 898 GLN B 923 GLN B 954 GLN B1002 GLN C 185 ASN C 217 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.143935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106540 restraints weight = 64712.792| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.08 r_work: 0.3342 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29076 Z= 0.185 Angle : 0.693 19.577 39670 Z= 0.348 Chirality : 0.048 0.617 4587 Planarity : 0.005 0.094 5036 Dihedral : 5.556 59.740 3811 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.59 % Favored : 93.32 % Rotamer: Outliers : 0.81 % Allowed : 7.89 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.62 (0.14), residues: 3489 helix: 0.09 (0.19), residues: 736 sheet: -0.52 (0.19), residues: 726 loop : -1.79 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1014 TYR 0.025 0.002 TYR A 492 PHE 0.022 0.002 PHE B 133 TRP 0.009 0.001 TRP A 433 HIS 0.005 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (28984) covalent geometry : angle 0.66227 / 0.34 (39438) SS BOND : bond 0.00380 / 0.23 ( 41) SS BOND : angle 1.56522 / 1.02 ( 82) hydrogen bonds : bond 0.05636 / 3.69 ( 947) hydrogen bonds : angle 6.05012 / 4.13 ( 2580) Misc. bond : bond 0.00107 / 0.06 ( 1) link_BETA1-4 : bond 0.00633 / 0.32 ( 5) link_BETA1-4 : angle 1.86276 / 1.02 ( 15) link_NAG-ASN : bond 0.00490 / 0.32 ( 45) link_NAG-ASN : angle 3.35013 / 2.55 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8352 (t80) cc_final: 0.7757 (m-80) REVERT: A 167 TYR cc_start: 0.7515 (t80) cc_final: 0.7051 (t80) REVERT: C 150 MET cc_start: 0.5841 (tpt) cc_final: 0.5563 (ttt) REVERT: C 447 LEU cc_start: 0.8823 (mp) cc_final: 0.8422 (tt) REVERT: C 541 LEU cc_start: 0.8305 (mt) cc_final: 0.8077 (mt) REVERT: C 1102 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7837 (mtm-85) REVERT: H 17 SER cc_start: 0.6630 (OUTLIER) cc_final: 0.6145 (t) REVERT: H 36 TRP cc_start: 0.5110 (OUTLIER) cc_final: 0.4291 (t60) REVERT: H 46 GLU cc_start: 0.7715 (tp30) cc_final: 0.7513 (tp30) REVERT: H 58 TYR cc_start: 0.7846 (m-10) cc_final: 0.7499 (m-10) REVERT: H 88 GLU cc_start: 0.5542 (pm20) cc_final: 0.5305 (pm20) REVERT: D 39 LYS cc_start: 0.8363 (tppt) cc_final: 0.8056 (mptt) REVERT: D 71 PHE cc_start: 0.7709 (t80) cc_final: 0.7389 (t80) outliers start: 25 outliers final: 14 residues processed: 236 average time/residue: 0.1672 time to fit residues: 65.5896 Evaluate side-chains 199 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 169 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 214 optimal weight: 0.5980 chunk 149 optimal weight: 30.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 HIS B 954 GLN C 329 ASN C 921 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.142779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101966 restraints weight = 64716.846| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.26 r_work: 0.3322 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29076 Z= 0.155 Angle : 0.643 16.553 39670 Z= 0.321 Chirality : 0.047 0.604 4587 Planarity : 0.004 0.061 5036 Dihedral : 5.115 56.336 3792 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 1.62 % Allowed : 10.28 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.47 (0.14), residues: 3489 helix: 0.34 (0.19), residues: 743 sheet: -0.49 (0.19), residues: 739 loop : -1.75 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.022 0.001 TYR A 492 PHE 0.019 0.001 PHE C 387 TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (28984) covalent geometry : angle 0.61670 / 0.32 (39438) SS BOND : bond 0.00330 / 0.20 ( 41) SS BOND : angle 1.35574 / 0.88 ( 82) hydrogen bonds : bond 0.04896 / 3.20 ( 947) hydrogen bonds : angle 5.66602 / 3.89 ( 2580) Misc. bond : bond 0.00105 / 0.06 ( 1) link_BETA1-4 : bond 0.00744 / 0.38 ( 5) link_BETA1-4 : angle 1.82944 / 1.03 ( 15) link_NAG-ASN : bond 0.00617 / 0.44 ( 45) link_NAG-ASN : angle 2.98981 / 2.22 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8395 (t80) cc_final: 0.7857 (m-80) REVERT: A 167 TYR cc_start: 0.7750 (t80) cc_final: 0.7224 (t80) REVERT: A 1106 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: B 133 PHE cc_start: 0.6787 (m-10) cc_final: 0.6473 (m-10) REVERT: C 150 MET cc_start: 0.5340 (tpt) cc_final: 0.5067 (tpp) REVERT: C 300 SER cc_start: 0.8866 (t) cc_final: 0.8495 (p) REVERT: C 487 LEU cc_start: 0.7423 (mm) cc_final: 0.6784 (tp) REVERT: C 1133 TYR cc_start: 0.7947 (t80) cc_final: 0.7255 (t80) REVERT: H 17 SER cc_start: 0.6046 (OUTLIER) cc_final: 0.5512 (t) REVERT: H 36 TRP cc_start: 0.5020 (OUTLIER) cc_final: 0.4584 (t-100) REVERT: H 59 TYR cc_start: 0.6100 (p90) cc_final: 0.5524 (p90) REVERT: H 109 TRP cc_start: 0.6188 (m100) cc_final: 0.5547 (m100) REVERT: D 36 TYR cc_start: 0.7366 (m-80) cc_final: 0.7009 (m-80) REVERT: D 71 PHE cc_start: 0.7631 (t80) cc_final: 0.7308 (t80) REVERT: D 86 TYR cc_start: 0.6881 (m-10) cc_final: 0.6626 (m-10) outliers start: 50 outliers final: 29 residues processed: 238 average time/residue: 0.1611 time to fit residues: 66.2034 Evaluate side-chains 216 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 261 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 257 optimal weight: 0.0470 chunk 327 optimal weight: 40.0000 chunk 306 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN B 954 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.140003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098154 restraints weight = 64507.946| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.17 r_work: 0.3260 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 29076 Z= 0.243 Angle : 0.716 17.043 39670 Z= 0.359 Chirality : 0.049 0.594 4587 Planarity : 0.005 0.055 5036 Dihedral : 5.365 49.518 3791 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.35 % Rotamer: Outliers : 2.46 % Allowed : 12.48 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.70 (0.14), residues: 3489 helix: 0.03 (0.19), residues: 746 sheet: -0.59 (0.18), residues: 767 loop : -1.86 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.030 0.002 TYR A 492 PHE 0.025 0.002 PHE C 901 TRP 0.013 0.001 TRP C 149 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (28984) covalent geometry : angle 0.69013 / 0.35 (39438) SS BOND : bond 0.00401 / 0.25 ( 41) SS BOND : angle 1.63066 / 1.03 ( 82) hydrogen bonds : bond 0.05385 / 3.53 ( 947) hydrogen bonds : angle 5.81531 / 4.01 ( 2580) Misc. bond : bond 0.00132 / 0.07 ( 1) link_BETA1-4 : bond 0.00587 / 0.29 ( 5) link_BETA1-4 : angle 1.81761 / 1.01 ( 15) link_NAG-ASN : bond 0.00484 / 0.31 ( 45) link_NAG-ASN : angle 3.07058 / 2.23 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8513 (t80) cc_final: 0.7765 (m-80) REVERT: A 167 TYR cc_start: 0.7714 (t80) cc_final: 0.7240 (t80) REVERT: A 174 MET cc_start: 0.1474 (mtt) cc_final: 0.1216 (mtt) REVERT: A 495 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8253 (mmm-85) REVERT: A 797 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: A 1106 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: B 633 TYR cc_start: 0.5207 (t80) cc_final: 0.4835 (t80) REVERT: C 150 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5455 (tpp) REVERT: C 300 SER cc_start: 0.8981 (t) cc_final: 0.8602 (p) REVERT: C 404 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7883 (tm-30) REVERT: C 487 LEU cc_start: 0.7385 (mm) cc_final: 0.6694 (tp) REVERT: C 971 VAL cc_start: 0.8545 (t) cc_final: 0.8174 (m) REVERT: C 1133 TYR cc_start: 0.8027 (t80) cc_final: 0.7396 (t80) REVERT: H 17 SER cc_start: 0.6793 (OUTLIER) cc_final: 0.6491 (t) REVERT: H 36 TRP cc_start: 0.5085 (OUTLIER) cc_final: 0.4736 (t-100) REVERT: H 51 ILE cc_start: 0.8729 (tp) cc_final: 0.8441 (tp) REVERT: H 83 ASN cc_start: 0.8578 (p0) cc_final: 0.8219 (t0) REVERT: H 109 TRP cc_start: 0.6257 (m100) cc_final: 0.5546 (m100) REVERT: D 36 TYR cc_start: 0.7603 (m-80) cc_final: 0.7040 (m-10) REVERT: D 71 PHE cc_start: 0.7601 (t80) cc_final: 0.7211 (t80) REVERT: D 86 TYR cc_start: 0.7113 (m-10) cc_final: 0.6837 (m-10) REVERT: D 87 TYR cc_start: 0.6838 (m-80) cc_final: 0.6348 (m-80) outliers start: 76 outliers final: 46 residues processed: 259 average time/residue: 0.1637 time to fit residues: 72.5188 Evaluate side-chains 241 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 909 THR Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 243 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 173 optimal weight: 0.0570 chunk 179 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 312 optimal weight: 0.9980 chunk 150 optimal weight: 30.0000 chunk 166 optimal weight: 1.9990 chunk 327 optimal weight: 0.8980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.143237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097807 restraints weight = 64037.425| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.31 r_work: 0.3318 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29076 Z= 0.118 Angle : 0.619 13.671 39670 Z= 0.306 Chirality : 0.045 0.363 4587 Planarity : 0.004 0.054 5036 Dihedral : 4.903 46.863 3791 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.18 % Rotamer: Outliers : 1.91 % Allowed : 13.94 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.41 (0.14), residues: 3489 helix: 0.50 (0.19), residues: 739 sheet: -0.45 (0.19), residues: 751 loop : -1.75 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.021 0.001 TYR C 702 PHE 0.019 0.001 PHE A 79 TRP 0.011 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (28984) covalent geometry : angle 0.59156 / 0.30 (39438) SS BOND : bond 0.00321 / 0.18 ( 41) SS BOND : angle 1.31961 / 0.86 ( 82) hydrogen bonds : bond 0.04204 / 2.74 ( 947) hydrogen bonds : angle 5.36409 / 3.70 ( 2580) Misc. bond : bond 0.00062 / 0.03 ( 1) link_BETA1-4 : bond 0.01088 / 0.54 ( 5) link_BETA1-4 : angle 1.84800 / 1.02 ( 15) link_NAG-ASN : bond 0.00448 / 0.30 ( 45) link_NAG-ASN : angle 2.96569 / 2.20 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.0866 (mtt) cc_final: 0.0565 (mtt) REVERT: A 366 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: A 495 ARG cc_start: 0.8396 (mtt180) cc_final: 0.8183 (mmm-85) REVERT: A 1106 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: B 133 PHE cc_start: 0.7155 (m-10) cc_final: 0.6746 (m-10) REVERT: B 174 MET cc_start: 0.4900 (mmt) cc_final: 0.2771 (mtt) REVERT: B 633 TYR cc_start: 0.5027 (t80) cc_final: 0.4606 (t80) REVERT: B 985 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: B 1135 TYR cc_start: 0.6779 (t80) cc_final: 0.6535 (t80) REVERT: C 150 MET cc_start: 0.5592 (tpt) cc_final: 0.5356 (tpp) REVERT: C 174 MET cc_start: 0.2427 (mtt) cc_final: 0.2154 (mtt) REVERT: C 300 SER cc_start: 0.8812 (t) cc_final: 0.8418 (p) REVERT: C 320 SER cc_start: 0.8828 (m) cc_final: 0.8515 (p) REVERT: C 487 LEU cc_start: 0.7355 (mm) cc_final: 0.6691 (tp) REVERT: C 848 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8577 (tp-100) REVERT: C 971 VAL cc_start: 0.8238 (t) cc_final: 0.7981 (m) REVERT: C 1133 TYR cc_start: 0.8024 (t80) cc_final: 0.7342 (t80) REVERT: H 17 SER cc_start: 0.6988 (OUTLIER) cc_final: 0.6754 (t) REVERT: H 36 TRP cc_start: 0.4981 (OUTLIER) cc_final: 0.4755 (t-100) REVERT: H 83 ASN cc_start: 0.8601 (p0) cc_final: 0.8342 (t0) REVERT: H 106 MET cc_start: 0.5296 (ppp) cc_final: 0.4833 (ppp) REVERT: H 109 TRP cc_start: 0.6484 (m100) cc_final: 0.5784 (m100) REVERT: D 36 TYR cc_start: 0.7681 (m-80) cc_final: 0.7159 (m-80) REVERT: D 71 PHE cc_start: 0.7515 (t80) cc_final: 0.7118 (t80) REVERT: D 86 TYR cc_start: 0.7236 (m-10) cc_final: 0.6989 (m-10) REVERT: D 87 TYR cc_start: 0.6974 (m-80) cc_final: 0.6430 (m-80) outliers start: 59 outliers final: 33 residues processed: 254 average time/residue: 0.1628 time to fit residues: 70.9227 Evaluate side-chains 230 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1092 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 271 optimal weight: 0.0470 chunk 43 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 292 optimal weight: 0.0020 chunk 348 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 267 optimal weight: 0.0050 chunk 19 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 954 GLN ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.142050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097285 restraints weight = 64347.585| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.29 r_work: 0.3353 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29076 Z= 0.107 Angle : 0.596 12.160 39670 Z= 0.296 Chirality : 0.045 0.354 4587 Planarity : 0.004 0.054 5036 Dihedral : 4.645 48.152 3791 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 1.94 % Allowed : 14.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.23 (0.14), residues: 3489 helix: 0.70 (0.20), residues: 740 sheet: -0.32 (0.19), residues: 742 loop : -1.67 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.026 0.001 TYR C 468 PHE 0.033 0.001 PHE A 589 TRP 0.012 0.001 TRP H 36 HIS 0.006 0.000 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (28984) covalent geometry : angle 0.57485 / 0.29 (39438) SS BOND : bond 0.00356 / 0.18 ( 41) SS BOND : angle 1.33089 / 0.88 ( 82) hydrogen bonds : bond 0.03872 / 2.53 ( 947) hydrogen bonds : angle 5.19750 / 3.59 ( 2580) Misc. bond : bond 0.00078 / 0.04 ( 1) link_BETA1-4 : bond 0.00744 / 0.38 ( 5) link_BETA1-4 : angle 1.49394 / 0.85 ( 15) link_NAG-ASN : bond 0.00395 / 0.26 ( 45) link_NAG-ASN : angle 2.52539 / 1.84 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.0917 (mtt) cc_final: 0.0616 (mtt) REVERT: A 366 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: A 1106 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: B 174 MET cc_start: 0.4663 (mmt) cc_final: 0.2640 (mtt) REVERT: B 633 TYR cc_start: 0.5106 (t80) cc_final: 0.4583 (t80) REVERT: B 901 TYR cc_start: 0.8279 (m-10) cc_final: 0.8073 (m-80) REVERT: B 954 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8303 (tp40) REVERT: B 985 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6027 (pm20) REVERT: B 1135 TYR cc_start: 0.6755 (t80) cc_final: 0.6530 (t80) REVERT: C 150 MET cc_start: 0.5721 (tpt) cc_final: 0.5475 (tpp) REVERT: C 174 MET cc_start: 0.2469 (mtt) cc_final: 0.2228 (mtt) REVERT: C 300 SER cc_start: 0.8830 (t) cc_final: 0.8464 (p) REVERT: C 320 SER cc_start: 0.8866 (m) cc_final: 0.8525 (p) REVERT: C 487 LEU cc_start: 0.7186 (mm) cc_final: 0.6465 (tp) REVERT: C 913 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: C 971 VAL cc_start: 0.8124 (t) cc_final: 0.7863 (m) REVERT: C 1133 TYR cc_start: 0.8027 (t80) cc_final: 0.7341 (t80) REVERT: H 36 TRP cc_start: 0.4920 (OUTLIER) cc_final: 0.4678 (t-100) REVERT: H 82 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4980 (ptp) REVERT: H 83 ASN cc_start: 0.8502 (p0) cc_final: 0.8245 (t0) REVERT: H 106 MET cc_start: 0.5398 (ppp) cc_final: 0.4629 (ppp) REVERT: H 109 TRP cc_start: 0.6344 (m100) cc_final: 0.5667 (m100) REVERT: D 36 TYR cc_start: 0.7648 (m-80) cc_final: 0.6978 (m-10) REVERT: D 71 PHE cc_start: 0.7539 (t80) cc_final: 0.7130 (t80) REVERT: D 86 TYR cc_start: 0.7220 (m-10) cc_final: 0.6961 (m-10) REVERT: D 87 TYR cc_start: 0.6978 (m-80) cc_final: 0.6118 (m-10) outliers start: 60 outliers final: 33 residues processed: 254 average time/residue: 0.1651 time to fit residues: 70.1979 Evaluate side-chains 225 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 22 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 313 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 155 optimal weight: 0.0670 chunk 249 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099156 restraints weight = 64278.471| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.38 r_work: 0.3332 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29076 Z= 0.106 Angle : 0.585 11.786 39670 Z= 0.289 Chirality : 0.044 0.352 4587 Planarity : 0.004 0.054 5036 Dihedral : 4.514 50.280 3789 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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 are not related in a simple way. whole: -1.15 (0.14), residues: 3489 helix: 0.78 (0.20), residues: 746 sheet: -0.27 (0.19), residues: 744 loop : -1.63 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.016 0.001 TYR C 702 PHE 0.027 0.001 PHE A 589 TRP 0.011 0.001 TRP H 36 HIS 0.006 0.000 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (28984) covalent geometry : angle 0.56605 / 0.29 (39438) SS BOND : bond 0.00355 / 0.18 ( 41) SS BOND : angle 1.25396 / 0.81 ( 82) hydrogen bonds : bond 0.03772 / 2.47 ( 947) hydrogen bonds : angle 5.12432 / 3.54 ( 2580) Misc. bond : bond 0.00084 / 0.04 ( 1) link_BETA1-4 : bond 0.00680 / 0.34 ( 5) link_BETA1-4 : angle 1.36649 / 0.79 ( 15) link_NAG-ASN : bond 0.00382 / 0.25 ( 45) link_NAG-ASN : angle 2.38813 / 1.71 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: A 1106 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: B 633 TYR cc_start: 0.5100 (t80) cc_final: 0.4582 (t80) REVERT: B 884 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8532 (t) REVERT: B 1135 TYR cc_start: 0.6890 (t80) cc_final: 0.6665 (t80) REVERT: C 150 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5508 (tpp) REVERT: C 174 MET cc_start: 0.2473 (mtt) cc_final: 0.2247 (mtt) REVERT: C 300 SER cc_start: 0.8775 (t) cc_final: 0.8372 (p) REVERT: C 320 SER cc_start: 0.8845 (m) cc_final: 0.8546 (p) REVERT: C 460 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: C 487 LEU cc_start: 0.7204 (mm) cc_final: 0.6545 (tp) REVERT: C 913 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: C 971 VAL cc_start: 0.8038 (t) cc_final: 0.7781 (m) REVERT: C 1133 TYR cc_start: 0.8045 (t80) cc_final: 0.7392 (t80) REVERT: H 36 TRP cc_start: 0.4911 (OUTLIER) cc_final: 0.4710 (t-100) REVERT: H 59 TYR cc_start: 0.6131 (p90) cc_final: 0.5483 (p90) REVERT: H 82 MET cc_start: 0.5541 (OUTLIER) cc_final: 0.5154 (ptp) REVERT: H 106 MET cc_start: 0.5179 (ppp) cc_final: 0.4473 (ppp) REVERT: H 109 TRP cc_start: 0.6369 (m100) cc_final: 0.5709 (m100) REVERT: D 36 TYR cc_start: 0.7755 (m-80) cc_final: 0.7099 (m-10) REVERT: D 71 PHE cc_start: 0.7542 (t80) cc_final: 0.7093 (t80) REVERT: D 86 TYR cc_start: 0.7317 (m-80) cc_final: 0.7022 (m-10) REVERT: D 87 TYR cc_start: 0.6968 (m-80) cc_final: 0.6149 (m-10) outliers start: 64 outliers final: 37 residues processed: 248 average time/residue: 0.1547 time to fit residues: 66.3758 Evaluate side-chains 230 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 235 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 337 optimal weight: 30.0000 chunk 262 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 12 optimal weight: 40.0000 chunk 156 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN C 848 GLN C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.139862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097672 restraints weight = 64857.445| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.24 r_work: 0.3261 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 29076 Z= 0.256 Angle : 0.711 11.393 39670 Z= 0.358 Chirality : 0.049 0.338 4587 Planarity : 0.005 0.053 5036 Dihedral : 5.112 49.915 3789 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.61 % Rotamer: Outliers : 2.13 % Allowed : 14.75 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -1.50 (0.14), residues: 3489 helix: 0.25 (0.19), residues: 739 sheet: -0.38 (0.19), residues: 758 loop : -1.80 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1102 TYR 0.033 0.002 TYR A 492 PHE 0.028 0.002 PHE C 560 TRP 0.017 0.002 TRP C 64 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (28984) covalent geometry : angle 0.69125 / 0.35 (39438) SS BOND : bond 0.00432 / 0.25 ( 41) SS BOND : angle 1.69353 / 1.05 ( 82) hydrogen bonds : bond 0.05173 / 3.41 ( 947) hydrogen bonds : angle 5.62918 / 3.90 ( 2580) Misc. bond : bond 0.00122 / 0.06 ( 1) link_BETA1-4 : bond 0.00608 / 0.30 ( 5) link_BETA1-4 : angle 1.61639 / 0.89 ( 15) link_NAG-ASN : bond 0.00433 / 0.27 ( 45) link_NAG-ASN : angle 2.60664 / 1.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7508 (t80) cc_final: 0.7282 (t80) REVERT: A 306 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8279 (mp0) REVERT: A 366 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.7262 (m-10) REVERT: B 174 MET cc_start: 0.4809 (mmt) cc_final: 0.4555 (mmp) REVERT: B 633 TYR cc_start: 0.5618 (t80) cc_final: 0.4932 (t80) REVERT: B 866 MET cc_start: 0.8959 (mtp) cc_final: 0.8731 (mtp) REVERT: B 884 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8780 (t) REVERT: B 1135 TYR cc_start: 0.6617 (t80) cc_final: 0.6394 (t80) REVERT: B 1139 GLN cc_start: 0.8540 (tp40) cc_final: 0.8020 (tp-100) REVERT: C 174 MET cc_start: 0.2453 (mtt) cc_final: 0.2240 (mtt) REVERT: C 300 SER cc_start: 0.8942 (t) cc_final: 0.8595 (p) REVERT: C 487 LEU cc_start: 0.7325 (mm) cc_final: 0.6534 (tp) REVERT: C 848 GLN cc_start: 0.8783 (tp40) cc_final: 0.8505 (tp-100) REVERT: C 913 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: C 971 VAL cc_start: 0.8461 (t) cc_final: 0.8197 (m) REVERT: C 1133 TYR cc_start: 0.7975 (t80) cc_final: 0.7341 (t80) REVERT: H 36 TRP cc_start: 0.4917 (OUTLIER) cc_final: 0.4681 (t-100) REVERT: H 59 TYR cc_start: 0.6191 (p90) cc_final: 0.5514 (p90) REVERT: H 82 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5144 (ptp) REVERT: H 109 TRP cc_start: 0.6305 (m100) cc_final: 0.5731 (m100) REVERT: D 36 TYR cc_start: 0.7699 (m-80) cc_final: 0.7132 (m-80) REVERT: D 49 TYR cc_start: 0.7439 (m-80) cc_final: 0.7237 (m-80) REVERT: D 86 TYR cc_start: 0.7360 (m-80) cc_final: 0.7037 (m-10) REVERT: D 87 TYR cc_start: 0.6815 (m-80) cc_final: 0.6040 (m-10) outliers start: 66 outliers final: 49 residues processed: 237 average time/residue: 0.1581 time to fit residues: 64.6841 Evaluate side-chains 227 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 182 optimal weight: 1.9990 chunk 347 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 193 optimal weight: 0.0670 chunk 332 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 954 GLN C 185 ASN C 365 ASN C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.142126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.101385 restraints weight = 64168.869| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.44 r_work: 0.3305 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29076 Z= 0.135 Angle : 0.622 12.494 39670 Z= 0.310 Chirality : 0.045 0.323 4587 Planarity : 0.004 0.051 5036 Dihedral : 4.812 52.671 3789 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 1.88 % Allowed : 15.17 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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 are not related in a simple way. whole: -1.32 (0.14), residues: 3489 helix: 0.47 (0.19), residues: 748 sheet: -0.35 (0.19), residues: 761 loop : -1.68 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.018 0.001 TYR A 167 PHE 0.028 0.001 PHE D 71 TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (28984) covalent geometry : angle 0.60448 / 0.31 (39438) SS BOND : bond 0.00332 / 0.18 ( 41) SS BOND : angle 1.37753 / 0.86 ( 82) hydrogen bonds : bond 0.04208 / 2.76 ( 947) hydrogen bonds : angle 5.32390 / 3.68 ( 2580) Misc. bond : bond 0.00089 / 0.05 ( 1) link_BETA1-4 : bond 0.00600 / 0.30 ( 5) link_BETA1-4 : angle 1.43652 / 0.82 ( 15) link_NAG-ASN : bond 0.00378 / 0.24 ( 45) link_NAG-ASN : angle 2.37340 / 1.65 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7475 (t80) cc_final: 0.7229 (t80) REVERT: A 366 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7163 (m-10) REVERT: A 411 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8400 (mm-40) REVERT: A 897 MET cc_start: 0.8190 (mtp) cc_final: 0.7960 (mtm) REVERT: A 915 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: B 633 TYR cc_start: 0.5536 (t80) cc_final: 0.4906 (t80) REVERT: B 978 PHE cc_start: 0.7696 (m-80) cc_final: 0.7424 (m-10) REVERT: B 1135 TYR cc_start: 0.7041 (t80) cc_final: 0.6837 (t80) REVERT: B 1139 GLN cc_start: 0.8572 (tp40) cc_final: 0.8153 (tp-100) REVERT: C 111 ASP cc_start: 0.7904 (t70) cc_final: 0.7617 (t70) REVERT: C 174 MET cc_start: 0.2664 (mtt) cc_final: 0.2442 (mtt) REVERT: C 300 SER cc_start: 0.8866 (t) cc_final: 0.8520 (p) REVERT: C 320 SER cc_start: 0.8802 (m) cc_final: 0.8570 (p) REVERT: C 487 LEU cc_start: 0.7213 (mm) cc_final: 0.6486 (tp) REVERT: C 848 GLN cc_start: 0.8805 (tp40) cc_final: 0.8545 (tp-100) REVERT: C 971 VAL cc_start: 0.8178 (t) cc_final: 0.7947 (m) REVERT: C 1133 TYR cc_start: 0.7920 (t80) cc_final: 0.7285 (t80) REVERT: H 57 THR cc_start: 0.8762 (t) cc_final: 0.8555 (m) REVERT: H 59 TYR cc_start: 0.6186 (p90) cc_final: 0.5658 (p90) REVERT: H 82 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5028 (ptp) REVERT: H 109 TRP cc_start: 0.6158 (m100) cc_final: 0.5444 (m100) REVERT: D 36 TYR cc_start: 0.7429 (m-80) cc_final: 0.6839 (m-10) REVERT: D 86 TYR cc_start: 0.7407 (m-80) cc_final: 0.7025 (m-10) REVERT: D 87 TYR cc_start: 0.6681 (m-80) cc_final: 0.6095 (m-80) outliers start: 58 outliers final: 45 residues processed: 232 average time/residue: 0.1451 time to fit residues: 58.3118 Evaluate side-chains 225 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 291 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 255 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN C 185 ASN C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.144408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107584 restraints weight = 64626.525| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.33 r_work: 0.3362 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29076 Z= 0.118 Angle : 0.607 11.806 39670 Z= 0.302 Chirality : 0.045 0.342 4587 Planarity : 0.004 0.051 5036 Dihedral : 4.634 53.970 3789 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 1.71 % Allowed : 15.49 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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 are not related in a simple way. whole: -1.22 (0.14), residues: 3489 helix: 0.62 (0.19), residues: 752 sheet: -0.34 (0.19), residues: 755 loop : -1.62 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.018 0.001 TYR A 167 PHE 0.028 0.001 PHE B 133 TRP 0.031 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28984) covalent geometry : angle 0.58947 / 0.30 (39438) SS BOND : bond 0.00323 / 0.18 ( 41) SS BOND : angle 1.28702 / 0.81 ( 82) hydrogen bonds : bond 0.03903 / 2.56 ( 947) hydrogen bonds : angle 5.16530 / 3.58 ( 2580) Misc. bond : bond 0.00098 / 0.05 ( 1) link_BETA1-4 : bond 0.00512 / 0.26 ( 5) link_BETA1-4 : angle 1.36577 / 0.78 ( 15) link_NAG-ASN : bond 0.00388 / 0.25 ( 45) link_NAG-ASN : angle 2.35879 / 1.64 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6332 (m-80) cc_final: 0.5790 (m-80) REVERT: A 167 TYR cc_start: 0.7422 (t80) cc_final: 0.7109 (t80) REVERT: A 366 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: A 915 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: B 174 MET cc_start: 0.5138 (mmt) cc_final: 0.2631 (mtt) REVERT: B 633 TYR cc_start: 0.5521 (t80) cc_final: 0.5007 (t80) REVERT: B 884 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8710 (t) REVERT: B 978 PHE cc_start: 0.7823 (m-80) cc_final: 0.7538 (m-10) REVERT: B 1139 GLN cc_start: 0.8396 (tp40) cc_final: 0.7776 (tp-100) REVERT: C 111 ASP cc_start: 0.7663 (t70) cc_final: 0.7379 (t70) REVERT: C 300 SER cc_start: 0.8954 (t) cc_final: 0.8714 (p) REVERT: C 320 SER cc_start: 0.8747 (m) cc_final: 0.8442 (p) REVERT: C 487 LEU cc_start: 0.7224 (mm) cc_final: 0.6378 (tp) REVERT: C 541 LEU cc_start: 0.7778 (mt) cc_final: 0.7520 (mp) REVERT: C 848 GLN cc_start: 0.8520 (tp40) cc_final: 0.8309 (tp-100) REVERT: C 1133 TYR cc_start: 0.7737 (t80) cc_final: 0.7262 (t80) REVERT: H 57 THR cc_start: 0.8712 (t) cc_final: 0.8504 (m) REVERT: H 59 TYR cc_start: 0.6074 (p90) cc_final: 0.5470 (p90) REVERT: H 78 LEU cc_start: 0.6918 (tp) cc_final: 0.6255 (tt) REVERT: H 82 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.4862 (ptp) REVERT: H 83 ASN cc_start: 0.8567 (p0) cc_final: 0.8274 (t0) REVERT: H 109 TRP cc_start: 0.5782 (m100) cc_final: 0.5166 (m100) REVERT: D 36 TYR cc_start: 0.7181 (m-80) cc_final: 0.6667 (m-10) REVERT: D 49 TYR cc_start: 0.7091 (m-80) cc_final: 0.6755 (m-80) REVERT: D 86 TYR cc_start: 0.7357 (m-80) cc_final: 0.6931 (m-10) REVERT: D 87 TYR cc_start: 0.6757 (m-80) cc_final: 0.5866 (m-80) REVERT: D 98 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6241 (t80) outliers start: 53 outliers final: 40 residues processed: 233 average time/residue: 0.1503 time to fit residues: 60.1173 Evaluate side-chains 226 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 852 PHE Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 249 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 141 optimal weight: 0.0470 chunk 294 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.144550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107749 restraints weight = 64957.338| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 4.44 r_work: 0.3371 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29076 Z= 0.110 Angle : 0.597 11.393 39670 Z= 0.296 Chirality : 0.045 0.322 4587 Planarity : 0.004 0.050 5036 Dihedral : 4.530 55.074 3789 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 1.55 % Allowed : 15.56 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % 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 are not related in a simple way. whole: -1.12 (0.14), residues: 3489 helix: 0.75 (0.19), residues: 752 sheet: -0.32 (0.19), residues: 755 loop : -1.57 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.018 0.001 TYR A 167 PHE 0.022 0.001 PHE A 589 TRP 0.036 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (28984) covalent geometry : angle 0.58086 / 0.29 (39438) SS BOND : bond 0.00312 / 0.18 ( 41) SS BOND : angle 1.20616 / 0.78 ( 82) hydrogen bonds : bond 0.03750 / 2.46 ( 947) hydrogen bonds : angle 5.10886 / 3.53 ( 2580) Misc. bond : bond 0.00094 / 0.05 ( 1) link_BETA1-4 : bond 0.00517 / 0.26 ( 5) link_BETA1-4 : angle 1.31261 / 0.75 ( 15) link_NAG-ASN : bond 0.00375 / 0.24 ( 45) link_NAG-ASN : angle 2.26414 / 1.57 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6942.51 seconds wall clock time: 119 minutes 55.82 seconds (7195.82 seconds total)