Starting phenix.real_space_refine on Tue Jun 24 12:21:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wt7_32770/06_2025/7wt7_32770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt7_32770/06_2025/7wt7_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_32770/06_2025/7wt7_32770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt7_32770/06_2025/7wt7_32770.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt7_32770/06_2025/7wt7_32770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt7_32770/06_2025/7wt7_32770.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 1.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 36 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 dihedrals: 45 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 dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 16.02, per 1000 atoms: 0.57 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: 6.92 Conformation dependent library (CDL) restraints added in 3.7 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: 4.51 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: 18.86 Time building geometry restraints manager: 8.06 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 - 21.81: 16685 21.81 - 43.62: 1059 43.62 - 65.42: 171 65.42 - 87.23: 34 87.23 - 109.04: 17 Dihedral angle restraints: 17966 sinusoidal: 7693 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 17963 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 1159 or resid 1301 through 131 \ 2)) 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 1159 or resid 1301 through 131 \ 2)) selection = (chain 'C' and (resid 14 through 1157 or resid 1301 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: 0.010 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 68.090 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 14.356 109.040 11233 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (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 TRP 0.028 0.001 TRP H 36 HIS 0.005 0.001 HIS B 143 PHE 0.034 0.002 PHE B 133 TYR 0.024 0.001 TYR B 633 ARG 0.007 0.000 ARG A 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 45) link_NAG-ASN : angle 3.90214 ( 135) link_BETA1-4 : bond 0.00709 ( 5) link_BETA1-4 : angle 2.03204 ( 15) hydrogen bonds : bond 0.21630 ( 947) hydrogen bonds : angle 8.24580 ( 2580) SS BOND : bond 0.00523 ( 41) SS BOND : angle 1.52905 ( 82) covalent geometry : bond 0.00539 (28984) covalent geometry : angle 0.92423 (39438) Misc. bond : bond 0.00111 ( 1) *********************** 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 : 4.669 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: 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: 0.5959 (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: 0.7715 (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: 0.4648 time to fit residues: 222.2241 Evaluate side-chains 207 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 4.654 ------------------------------------------------------------------------------- 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 294 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 90 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4192 r_free = 0.4192 target = 0.143637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106324 restraints weight = 64478.397| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 4.12 r_work: 0.3334 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29076 Z= 0.194 Angle : 0.705 19.638 39670 Z= 0.353 Chirality : 0.049 0.665 4587 Planarity : 0.005 0.094 5036 Dihedral : 8.308 77.201 4859 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 0.94 % Allowed : 7.99 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3489 helix: 0.08 (0.19), residues: 734 sheet: -0.54 (0.19), residues: 726 loop : -1.81 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 149 HIS 0.005 0.001 HIS B1156 PHE 0.023 0.002 PHE B 133 TYR 0.026 0.002 TYR A 492 ARG 0.004 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 45) link_NAG-ASN : angle 3.41609 ( 135) link_BETA1-4 : bond 0.00736 ( 5) link_BETA1-4 : angle 2.24022 ( 15) hydrogen bonds : bond 0.05458 ( 947) hydrogen bonds : angle 6.02964 ( 2580) SS BOND : bond 0.00388 ( 41) SS BOND : angle 1.58111 ( 82) covalent geometry : bond 0.00457 (28984) covalent geometry : angle 0.67336 (39438) Misc. bond : bond 0.00142 ( 1) *********************** 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 245 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7519 (t80) cc_final: 0.7097 (t80) REVERT: C 150 MET cc_start: 0.5788 (tpt) cc_final: 0.5559 (tpp) REVERT: C 300 SER cc_start: 0.8890 (t) cc_final: 0.8660 (p) REVERT: C 487 LEU cc_start: 0.7488 (mm) cc_final: 0.6763 (tp) REVERT: C 541 LEU cc_start: 0.8329 (mt) cc_final: 0.7938 (mt) REVERT: H 17 SER cc_start: 0.6384 (OUTLIER) cc_final: 0.5883 (t) REVERT: H 34 MET cc_start: 0.4897 (mmm) cc_final: 0.4670 (mmm) REVERT: H 36 TRP cc_start: 0.5136 (OUTLIER) cc_final: 0.4475 (t-100) REVERT: H 43 LYS cc_start: 0.6531 (pttm) cc_final: 0.6331 (pttm) REVERT: H 58 TYR cc_start: 0.7891 (m-10) cc_final: 0.7543 (m-10) REVERT: H 59 TYR cc_start: 0.6506 (p90) cc_final: 0.5845 (p90) REVERT: H 88 GLU cc_start: 0.5547 (pm20) cc_final: 0.5318 (pm20) REVERT: D 39 LYS cc_start: 0.8350 (tppt) cc_final: 0.8047 (mptt) REVERT: D 71 PHE cc_start: 0.7709 (t80) cc_final: 0.7390 (t80) REVERT: D 98 PHE cc_start: 0.6848 (m-80) cc_final: 0.6532 (m-80) outliers start: 29 outliers final: 17 residues processed: 238 average time/residue: 0.3868 time to fit residues: 154.0317 Evaluate side-chains 207 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 3.299 ------------------------------------------------------------------------------- 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 908 VAL 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 436 LEU Chi-restraints excluded: chain C residue 603 VAL 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 197 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 175 optimal weight: 0.3980 chunk 338 optimal weight: 20.0000 chunk 234 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 HIS B 707 ASN B 954 GLN C 329 ASN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.143403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097751 restraints weight = 64122.972| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.32 r_work: 0.3307 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29076 Z= 0.140 Angle : 0.637 16.734 39670 Z= 0.317 Chirality : 0.047 0.736 4587 Planarity : 0.004 0.060 5036 Dihedral : 7.104 59.861 4840 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 1.58 % Allowed : 10.41 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3489 helix: 0.41 (0.19), residues: 743 sheet: -0.47 (0.19), residues: 741 loop : -1.72 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 109 HIS 0.006 0.001 HIS B1156 PHE 0.024 0.001 PHE B 133 TYR 0.019 0.001 TYR A 492 ARG 0.007 0.000 ARG B 980 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 45) link_NAG-ASN : angle 3.13594 ( 135) link_BETA1-4 : bond 0.00738 ( 5) link_BETA1-4 : angle 2.19277 ( 15) hydrogen bonds : bond 0.04754 ( 947) hydrogen bonds : angle 5.61700 ( 2580) SS BOND : bond 0.00450 ( 41) SS BOND : angle 1.34022 ( 82) covalent geometry : bond 0.00320 (28984) covalent geometry : angle 0.60715 (39438) Misc. bond : bond 0.00094 ( 1) *********************** 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 257 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8493 (t80) cc_final: 0.7989 (m-80) REVERT: A 1106 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: B 133 PHE cc_start: 0.6879 (m-10) cc_final: 0.6650 (m-10) REVERT: B 793 TYR cc_start: 0.6119 (t80) cc_final: 0.5904 (t80) REVERT: C 300 SER cc_start: 0.8777 (t) cc_final: 0.8385 (p) REVERT: C 487 LEU cc_start: 0.7432 (mm) cc_final: 0.6881 (tp) REVERT: C 1133 TYR cc_start: 0.8055 (t80) cc_final: 0.7301 (t80) REVERT: H 17 SER cc_start: 0.6726 (OUTLIER) cc_final: 0.6423 (t) REVERT: H 36 TRP cc_start: 0.5334 (OUTLIER) cc_final: 0.4876 (t-100) REVERT: H 46 GLU cc_start: 0.7480 (tp30) cc_final: 0.6240 (pm20) REVERT: H 58 TYR cc_start: 0.7914 (m-10) cc_final: 0.7641 (m-80) REVERT: H 109 TRP cc_start: 0.6186 (m100) cc_final: 0.5635 (m100) REVERT: D 36 TYR cc_start: 0.7535 (m-80) cc_final: 0.7225 (m-80) REVERT: D 71 PHE cc_start: 0.7563 (t80) cc_final: 0.7232 (t80) REVERT: D 87 TYR cc_start: 0.7012 (m-80) cc_final: 0.6206 (m-10) outliers start: 49 outliers final: 28 residues processed: 243 average time/residue: 0.3436 time to fit residues: 142.2981 Evaluate side-chains 220 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 2.895 ------------------------------------------------------------------------------- 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 365 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 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 B residue 978 PHE Chi-restraints excluded: chain C residue 162 ASN 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 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 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 302 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN C 921 GLN ** C1154 HIS ** 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 = 0.4216 r_free = 0.4216 target = 0.143135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.097357 restraints weight = 64523.164| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.39 r_work: 0.3322 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29076 Z= 0.144 Angle : 0.624 16.569 39670 Z= 0.310 Chirality : 0.047 0.677 4587 Planarity : 0.004 0.053 5036 Dihedral : 6.426 56.891 4839 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Rotamer: Outliers : 1.94 % Allowed : 12.29 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3489 helix: 0.53 (0.19), residues: 741 sheet: -0.44 (0.19), residues: 759 loop : -1.69 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 PHE 0.022 0.001 PHE B 65 TYR 0.025 0.001 TYR C 702 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 45) link_NAG-ASN : angle 3.02734 ( 135) link_BETA1-4 : bond 0.00722 ( 5) link_BETA1-4 : angle 2.01039 ( 15) hydrogen bonds : bond 0.04437 ( 947) hydrogen bonds : angle 5.46492 ( 2580) SS BOND : bond 0.00317 ( 41) SS BOND : angle 1.30022 ( 82) covalent geometry : bond 0.00337 (28984) covalent geometry : angle 0.59588 (39438) Misc. bond : bond 0.00103 ( 1) *********************** 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 262 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.8437 (t80) cc_final: 0.7963 (m-80) REVERT: A 174 MET cc_start: 0.1061 (mtt) cc_final: 0.0811 (mtt) REVERT: A 1141 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8516 (mt-10) REVERT: B 174 MET cc_start: 0.4835 (mmt) cc_final: 0.2930 (mtt) REVERT: B 793 TYR cc_start: 0.6438 (t80) cc_final: 0.6196 (t80) REVERT: B 901 TYR cc_start: 0.8198 (m-10) cc_final: 0.7959 (m-80) REVERT: B 985 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: B 1139 GLN cc_start: 0.8527 (tp40) cc_final: 0.8103 (tp-100) REVERT: C 174 MET cc_start: 0.2384 (mtt) cc_final: 0.2084 (mtt) REVERT: C 300 SER cc_start: 0.8806 (t) cc_final: 0.8375 (p) REVERT: C 404 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7877 (tm-30) REVERT: C 487 LEU cc_start: 0.7439 (mm) cc_final: 0.6869 (tp) REVERT: C 541 LEU cc_start: 0.7872 (mt) cc_final: 0.7648 (mt) REVERT: C 848 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8596 (tp-100) REVERT: C 971 VAL cc_start: 0.8237 (t) cc_final: 0.7974 (m) REVERT: C 1133 TYR cc_start: 0.8039 (t80) cc_final: 0.7303 (t80) REVERT: H 17 SER cc_start: 0.6587 (OUTLIER) cc_final: 0.6238 (t) REVERT: H 36 TRP cc_start: 0.5099 (OUTLIER) cc_final: 0.4727 (t-100) REVERT: H 38 ARG cc_start: 0.5894 (tmm160) cc_final: 0.5635 (tpt90) REVERT: H 58 TYR cc_start: 0.7937 (m-10) cc_final: 0.7660 (m-80) REVERT: H 83 ASN cc_start: 0.8560 (p0) cc_final: 0.8177 (t0) REVERT: H 109 TRP cc_start: 0.6291 (m100) cc_final: 0.5558 (m100) REVERT: D 36 TYR cc_start: 0.7657 (m-80) cc_final: 0.7085 (m-80) REVERT: D 71 PHE cc_start: 0.7525 (t80) cc_final: 0.7131 (t80) REVERT: D 87 TYR cc_start: 0.6862 (m-80) cc_final: 0.6101 (m-10) outliers start: 60 outliers final: 37 residues processed: 247 average time/residue: 0.3921 time to fit residues: 165.4355 Evaluate side-chains 234 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 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 1119 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 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP 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 329 ASN 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 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 156 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 288 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 342 optimal weight: 0.0270 chunk 113 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN B1002 GLN ** C1154 HIS ** 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 = 0.4223 r_free = 0.4223 target = 0.143591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097957 restraints weight = 64009.204| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.39 r_work: 0.3333 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29076 Z= 0.124 Angle : 0.605 14.314 39670 Z= 0.299 Chirality : 0.045 0.353 4587 Planarity : 0.004 0.053 5036 Dihedral : 5.949 55.415 4839 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.18 % Rotamer: Outliers : 1.84 % Allowed : 13.00 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3489 helix: 0.66 (0.19), residues: 738 sheet: -0.39 (0.19), residues: 748 loop : -1.66 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 PHE 0.022 0.001 PHE A 589 TYR 0.023 0.001 TYR C 702 ARG 0.003 0.000 ARG B 980 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 45) link_NAG-ASN : angle 3.06700 ( 135) link_BETA1-4 : bond 0.00818 ( 5) link_BETA1-4 : angle 1.67549 ( 15) hydrogen bonds : bond 0.04157 ( 947) hydrogen bonds : angle 5.31883 ( 2580) SS BOND : bond 0.00319 ( 41) SS BOND : angle 1.34003 ( 82) covalent geometry : bond 0.00286 (28984) covalent geometry : angle 0.57583 (39438) Misc. bond : bond 0.00092 ( 1) *********************** 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 264 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7486 (t80) cc_final: 0.7261 (t80) REVERT: A 174 MET cc_start: 0.0900 (mtt) cc_final: 0.0656 (mtt) REVERT: A 368 LEU cc_start: 0.6472 (mt) cc_final: 0.6055 (tt) REVERT: B 793 TYR cc_start: 0.6392 (t80) cc_final: 0.6157 (t80) REVERT: B 884 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8473 (t) REVERT: B 985 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5984 (pm20) REVERT: B 1135 TYR cc_start: 0.6957 (t80) cc_final: 0.6729 (t80) REVERT: B 1139 GLN cc_start: 0.8562 (tp40) cc_final: 0.8058 (tp-100) REVERT: C 174 MET cc_start: 0.2531 (mtt) cc_final: 0.2261 (mtt) REVERT: C 300 SER cc_start: 0.8803 (t) cc_final: 0.8370 (p) REVERT: C 404 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 487 LEU cc_start: 0.7388 (mm) cc_final: 0.6869 (tp) REVERT: C 848 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8518 (tp-100) REVERT: C 971 VAL cc_start: 0.8115 (t) cc_final: 0.7851 (m) REVERT: C 1133 TYR cc_start: 0.8058 (t80) cc_final: 0.7403 (t80) REVERT: H 36 TRP cc_start: 0.5157 (OUTLIER) cc_final: 0.4804 (t-100) REVERT: H 58 TYR cc_start: 0.8016 (m-10) cc_final: 0.7658 (m-10) REVERT: H 59 TYR cc_start: 0.6125 (p90) cc_final: 0.5242 (p90) REVERT: H 82 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5253 (ptp) REVERT: H 83 ASN cc_start: 0.8516 (p0) cc_final: 0.8171 (t0) REVERT: H 106 MET cc_start: 0.5599 (ppp) cc_final: 0.4957 (ppp) REVERT: H 109 TRP cc_start: 0.6280 (m100) cc_final: 0.5561 (m100) REVERT: D 36 TYR cc_start: 0.7687 (m-80) cc_final: 0.7151 (m-10) REVERT: D 71 PHE cc_start: 0.7567 (t80) cc_final: 0.7174 (t80) REVERT: D 87 TYR cc_start: 0.6791 (m-80) cc_final: 0.6048 (m-10) outliers start: 57 outliers final: 36 residues processed: 248 average time/residue: 0.3826 time to fit residues: 162.7520 Evaluate side-chains 236 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 365 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR 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 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 195 ASP 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 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP 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 329 ASN Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU 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 1035 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 146 optimal weight: 10.0000 chunk 263 optimal weight: 0.0010 chunk 280 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 323 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 124 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN B 954 GLN C 950 ASN ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.142113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097270 restraints weight = 64619.667| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.26 r_work: 0.3351 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29076 Z= 0.108 Angle : 0.586 11.641 39670 Z= 0.291 Chirality : 0.044 0.348 4587 Planarity : 0.004 0.052 5036 Dihedral : 5.599 54.020 4837 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 2.13 % Allowed : 13.97 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3489 helix: 0.74 (0.19), residues: 744 sheet: -0.31 (0.19), residues: 750 loop : -1.65 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.006 0.000 HIS B1156 PHE 0.032 0.001 PHE A 589 TYR 0.029 0.001 TYR C 468 ARG 0.016 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 45) link_NAG-ASN : angle 2.71301 ( 135) link_BETA1-4 : bond 0.00841 ( 5) link_BETA1-4 : angle 1.45149 ( 15) hydrogen bonds : bond 0.03905 ( 947) hydrogen bonds : angle 5.18973 ( 2580) SS BOND : bond 0.00281 ( 41) SS BOND : angle 1.26030 ( 82) covalent geometry : bond 0.00245 (28984) covalent geometry : angle 0.56237 (39438) Misc. bond : bond 0.00081 ( 1) *********************** 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 282 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 216 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7491 (t80) cc_final: 0.7190 (t80) REVERT: A 174 MET cc_start: 0.0871 (mtt) cc_final: 0.0637 (mtt) REVERT: A 897 MET cc_start: 0.8065 (mtp) cc_final: 0.7848 (mtm) REVERT: B 884 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8536 (t) REVERT: B 985 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: B 1135 TYR cc_start: 0.6816 (t80) cc_final: 0.6595 (t80) REVERT: C 174 MET cc_start: 0.2543 (mtt) cc_final: 0.2301 (mtt) REVERT: C 300 SER cc_start: 0.8818 (t) cc_final: 0.8421 (p) REVERT: C 320 SER cc_start: 0.8833 (m) cc_final: 0.8517 (p) REVERT: C 460 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: C 487 LEU cc_start: 0.7331 (mm) cc_final: 0.6745 (tp) REVERT: C 848 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8547 (tp-100) REVERT: C 971 VAL cc_start: 0.8093 (t) cc_final: 0.7829 (m) REVERT: C 1133 TYR cc_start: 0.8004 (t80) cc_final: 0.7336 (t80) REVERT: H 36 TRP cc_start: 0.5134 (OUTLIER) cc_final: 0.4785 (t-100) REVERT: H 58 TYR cc_start: 0.8027 (m-10) cc_final: 0.7697 (m-10) REVERT: H 106 MET cc_start: 0.5574 (ppp) cc_final: 0.4797 (ppp) REVERT: H 109 TRP cc_start: 0.6267 (m100) cc_final: 0.5630 (m100) REVERT: D 36 TYR cc_start: 0.7775 (m-80) cc_final: 0.7140 (m-10) REVERT: D 71 PHE cc_start: 0.7528 (t80) cc_final: 0.7109 (t80) REVERT: D 87 TYR cc_start: 0.6956 (m-80) cc_final: 0.6238 (m-10) outliers start: 66 outliers final: 40 residues processed: 267 average time/residue: 0.3354 time to fit residues: 153.8644 Evaluate side-chains 238 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 3.002 ------------------------------------------------------------------------------- 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 365 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 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 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 146 ASN Chi-restraints excluded: chain B residue 195 ASP 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 978 PHE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1101 VAL 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 460 GLU 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 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 Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 311 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 309 optimal weight: 0.0870 chunk 127 optimal weight: 0.0270 chunk 308 optimal weight: 3.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096273 restraints weight = 64141.348| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 4.26 r_work: 0.3334 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29076 Z= 0.131 Angle : 0.604 11.874 39670 Z= 0.299 Chirality : 0.045 0.335 4587 Planarity : 0.004 0.055 5036 Dihedral : 5.581 54.568 4837 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.64 % Rotamer: Outliers : 2.20 % Allowed : 14.04 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3489 helix: 0.72 (0.19), residues: 744 sheet: -0.30 (0.19), residues: 741 loop : -1.67 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 PHE 0.027 0.001 PHE A 589 TYR 0.025 0.001 TYR C 702 ARG 0.009 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 2.77509 ( 135) link_BETA1-4 : bond 0.00719 ( 5) link_BETA1-4 : angle 1.44226 ( 15) hydrogen bonds : bond 0.04046 ( 947) hydrogen bonds : angle 5.21996 ( 2580) SS BOND : bond 0.00335 ( 41) SS BOND : angle 1.35813 ( 82) covalent geometry : bond 0.00309 (28984) covalent geometry : angle 0.57935 (39438) Misc. bond : bond 0.00094 ( 1) *********************** 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 261 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.0954 (mtt) cc_final: 0.0718 (mtt) REVERT: B 174 MET cc_start: 0.5816 (mmt) cc_final: 0.3517 (mtt) REVERT: B 884 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8632 (t) REVERT: B 985 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5974 (pm20) REVERT: C 174 MET cc_start: 0.2398 (mtt) cc_final: 0.2152 (mtt) REVERT: C 300 SER cc_start: 0.8864 (t) cc_final: 0.8460 (p) REVERT: C 460 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: C 487 LEU cc_start: 0.7334 (mm) cc_final: 0.6719 (tp) REVERT: C 848 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8542 (tp-100) REVERT: C 971 VAL cc_start: 0.8211 (t) cc_final: 0.7958 (m) REVERT: C 1133 TYR cc_start: 0.7990 (t80) cc_final: 0.7368 (t80) REVERT: H 36 TRP cc_start: 0.5142 (OUTLIER) cc_final: 0.4818 (t-100) REVERT: H 58 TYR cc_start: 0.8028 (m-10) cc_final: 0.7713 (m-10) REVERT: H 82 MET cc_start: 0.5429 (OUTLIER) cc_final: 0.4993 (ptp) REVERT: H 106 MET cc_start: 0.5417 (ppp) cc_final: 0.4587 (ppp) REVERT: H 109 TRP cc_start: 0.6266 (m100) cc_final: 0.5701 (m100) REVERT: D 36 TYR cc_start: 0.7722 (m-80) cc_final: 0.7048 (m-80) REVERT: D 71 PHE cc_start: 0.7523 (t80) cc_final: 0.7089 (t80) REVERT: D 87 TYR cc_start: 0.6964 (m-80) cc_final: 0.6246 (m-10) outliers start: 68 outliers final: 53 residues processed: 239 average time/residue: 0.3374 time to fit residues: 140.0419 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 : 3.280 ------------------------------------------------------------------------------- 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 365 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 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 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 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 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP 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 329 ASN 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 460 GLU Chi-restraints excluded: chain C residue 564 ILE 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 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1045 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 288 optimal weight: 0.4980 chunk 308 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 266 optimal weight: 7.9990 chunk 167 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** C1154 HIS ** 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 = 0.4212 r_free = 0.4212 target = 0.141085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096281 restraints weight = 64501.370| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.24 r_work: 0.3331 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29076 Z= 0.131 Angle : 0.598 11.266 39670 Z= 0.297 Chirality : 0.045 0.351 4587 Planarity : 0.004 0.054 5036 Dihedral : 5.412 54.667 4837 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 2.52 % Allowed : 13.97 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3489 helix: 0.72 (0.19), residues: 744 sheet: -0.26 (0.19), residues: 728 loop : -1.64 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 PHE 0.026 0.001 PHE A 589 TYR 0.026 0.001 TYR C 702 ARG 0.008 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 45) link_NAG-ASN : angle 2.65743 ( 135) link_BETA1-4 : bond 0.00689 ( 5) link_BETA1-4 : angle 1.46625 ( 15) hydrogen bonds : bond 0.04025 ( 947) hydrogen bonds : angle 5.18487 ( 2580) SS BOND : bond 0.00317 ( 41) SS BOND : angle 1.31855 ( 82) covalent geometry : bond 0.00308 (28984) covalent geometry : angle 0.57538 (39438) Misc. bond : bond 0.00094 ( 1) *********************** 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 271 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7432 (t80) cc_final: 0.7218 (t80) REVERT: A 174 MET cc_start: 0.1072 (mtt) cc_final: 0.0838 (mtt) REVERT: A 1141 GLU cc_start: 0.8942 (tp30) cc_final: 0.8451 (pt0) REVERT: B 174 MET cc_start: 0.5535 (mmt) cc_final: 0.3310 (mtt) REVERT: B 884 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 174 MET cc_start: 0.2541 (mtt) cc_final: 0.2296 (mtt) REVERT: C 300 SER cc_start: 0.8884 (t) cc_final: 0.8493 (p) REVERT: C 460 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: C 487 LEU cc_start: 0.7322 (mm) cc_final: 0.6602 (tp) REVERT: C 848 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8511 (tp-100) REVERT: C 913 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: C 971 VAL cc_start: 0.8178 (t) cc_final: 0.7931 (m) REVERT: C 1133 TYR cc_start: 0.7938 (t80) cc_final: 0.7316 (t80) REVERT: H 36 TRP cc_start: 0.5140 (OUTLIER) cc_final: 0.4850 (t-100) REVERT: H 58 TYR cc_start: 0.8075 (m-10) cc_final: 0.7752 (m-10) REVERT: H 82 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.4894 (ptp) REVERT: H 109 TRP cc_start: 0.6263 (m100) cc_final: 0.5689 (m100) REVERT: D 36 TYR cc_start: 0.7737 (m-80) cc_final: 0.7065 (m-80) REVERT: D 71 PHE cc_start: 0.7572 (t80) cc_final: 0.7090 (t80) REVERT: D 87 TYR cc_start: 0.6983 (m-80) cc_final: 0.6186 (m-10) outliers start: 78 outliers final: 52 residues processed: 249 average time/residue: 0.3774 time to fit residues: 162.3805 Evaluate side-chains 239 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 2.898 ------------------------------------------------------------------------------- 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 365 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 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 154 PHE Chi-restraints excluded: chain B residue 195 ASP 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 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP 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 345 VAL 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 460 GLU Chi-restraints excluded: chain C residue 564 ILE 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 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 C residue 1045 MET 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 167 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 330 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 0.0970 chunk 154 optimal weight: 0.0370 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 365 ASN C 908 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** 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 = 0.4194 r_free = 0.4194 target = 0.139925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094476 restraints weight = 64355.878| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.31 r_work: 0.3302 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29076 Z= 0.158 Angle : 0.624 12.436 39670 Z= 0.311 Chirality : 0.046 0.339 4587 Planarity : 0.004 0.052 5036 Dihedral : 5.465 55.229 4837 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 2.01 % Allowed : 14.78 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3489 helix: 0.60 (0.19), residues: 742 sheet: -0.26 (0.19), residues: 736 loop : -1.67 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.006 0.001 HIS B1156 PHE 0.030 0.002 PHE B 133 TYR 0.026 0.001 TYR C 702 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 45) link_NAG-ASN : angle 2.62001 ( 135) link_BETA1-4 : bond 0.00599 ( 5) link_BETA1-4 : angle 1.54092 ( 15) hydrogen bonds : bond 0.04311 ( 947) hydrogen bonds : angle 5.28879 ( 2580) SS BOND : bond 0.00345 ( 41) SS BOND : angle 1.40221 ( 82) covalent geometry : bond 0.00378 (28984) covalent geometry : angle 0.60265 (39438) Misc. bond : bond 0.00100 ( 1) *********************** 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 250 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7476 (t80) cc_final: 0.7229 (t80) REVERT: A 1141 GLU cc_start: 0.8895 (tp30) cc_final: 0.8566 (pp20) REVERT: B 174 MET cc_start: 0.5382 (mmt) cc_final: 0.3088 (mtt) REVERT: B 884 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8636 (t) REVERT: B 1139 GLN cc_start: 0.8620 (tp40) cc_final: 0.8123 (tp-100) REVERT: C 174 MET cc_start: 0.2410 (mtt) cc_final: 0.2202 (mtt) REVERT: C 300 SER cc_start: 0.8867 (t) cc_final: 0.8505 (p) REVERT: C 487 LEU cc_start: 0.7379 (mm) cc_final: 0.6663 (tp) REVERT: C 848 GLN cc_start: 0.8876 (tp-100) cc_final: 0.8559 (tp-100) REVERT: C 913 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: C 971 VAL cc_start: 0.8236 (t) cc_final: 0.7973 (m) REVERT: C 1133 TYR cc_start: 0.8002 (t80) cc_final: 0.7384 (t80) REVERT: H 36 TRP cc_start: 0.5304 (OUTLIER) cc_final: 0.5024 (t-100) REVERT: H 58 TYR cc_start: 0.7948 (m-10) cc_final: 0.7608 (m-10) REVERT: H 83 ASN cc_start: 0.9071 (t0) cc_final: 0.8675 (p0) REVERT: H 109 TRP cc_start: 0.6303 (m100) cc_final: 0.5789 (m100) REVERT: D 36 TYR cc_start: 0.7733 (m-80) cc_final: 0.7163 (m-80) REVERT: D 49 TYR cc_start: 0.7405 (m-80) cc_final: 0.7162 (m-80) REVERT: D 71 PHE cc_start: 0.7659 (t80) cc_final: 0.7157 (t80) REVERT: D 87 TYR cc_start: 0.6956 (m-80) cc_final: 0.6210 (m-10) outliers start: 62 outliers final: 53 residues processed: 230 average time/residue: 0.3767 time to fit residues: 149.6087 Evaluate side-chains 237 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 3.105 ------------------------------------------------------------------------------- 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 365 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 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 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 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP 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 345 VAL 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 747 LEU Chi-restraints excluded: chain C residue 767 VAL 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 C residue 1045 MET Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain D residue 29 ILE 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 20 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 317 optimal weight: 0.0370 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 954 GLN C 365 ASN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** 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 = 0.4225 r_free = 0.4225 target = 0.143750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098399 restraints weight = 64182.617| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.35 r_work: 0.3332 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29076 Z= 0.113 Angle : 0.595 11.959 39670 Z= 0.296 Chirality : 0.045 0.346 4587 Planarity : 0.004 0.052 5036 Dihedral : 5.234 53.917 4837 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 1.88 % Allowed : 14.91 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3489 helix: 0.78 (0.19), residues: 744 sheet: -0.30 (0.19), residues: 742 loop : -1.60 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.007 0.000 HIS B1156 PHE 0.033 0.001 PHE B 133 TYR 0.026 0.001 TYR C 702 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 45) link_NAG-ASN : angle 2.48746 ( 135) link_BETA1-4 : bond 0.00665 ( 5) link_BETA1-4 : angle 1.41632 ( 15) hydrogen bonds : bond 0.03839 ( 947) hydrogen bonds : angle 5.10045 ( 2580) SS BOND : bond 0.00308 ( 41) SS BOND : angle 1.22186 ( 82) covalent geometry : bond 0.00260 (28984) covalent geometry : angle 0.57588 (39438) Misc. bond : bond 0.00077 ( 1) ********************** 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 252 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7466 (t80) cc_final: 0.7252 (t80) REVERT: A 915 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 174 MET cc_start: 0.4720 (mmt) cc_final: 0.2380 (mtt) REVERT: B 884 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8508 (t) REVERT: B 954 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8373 (tp40) REVERT: B 1139 GLN cc_start: 0.8556 (tp40) cc_final: 0.8099 (tp-100) REVERT: C 154 PHE cc_start: 0.6600 (m-10) cc_final: 0.6394 (m-10) REVERT: C 300 SER cc_start: 0.8737 (t) cc_final: 0.8353 (p) REVERT: C 320 SER cc_start: 0.8797 (m) cc_final: 0.8544 (p) REVERT: C 487 LEU cc_start: 0.7300 (mm) cc_final: 0.6622 (tp) REVERT: C 818 PHE cc_start: 0.7756 (m-80) cc_final: 0.7357 (m-80) REVERT: C 848 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8527 (tp-100) REVERT: C 913 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: C 971 VAL cc_start: 0.8071 (t) cc_final: 0.7809 (m) REVERT: C 1133 TYR cc_start: 0.8043 (t80) cc_final: 0.7422 (t80) REVERT: H 36 TRP cc_start: 0.5142 (OUTLIER) cc_final: 0.4930 (t-100) REVERT: H 58 TYR cc_start: 0.7917 (m-10) cc_final: 0.7525 (m-10) REVERT: H 59 TYR cc_start: 0.6252 (p90) cc_final: 0.5523 (p90) REVERT: H 83 ASN cc_start: 0.8974 (t0) cc_final: 0.8592 (p0) REVERT: H 109 TRP cc_start: 0.6299 (m100) cc_final: 0.5774 (m100) REVERT: D 49 TYR cc_start: 0.7446 (m-80) cc_final: 0.7236 (m-80) REVERT: D 71 PHE cc_start: 0.7634 (t80) cc_final: 0.7128 (t80) REVERT: D 87 TYR cc_start: 0.6900 (m-80) cc_final: 0.6163 (m-10) outliers start: 58 outliers final: 43 residues processed: 235 average time/residue: 0.3235 time to fit residues: 130.5670 Evaluate side-chains 237 residues out of total 3095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 3.058 ------------------------------------------------------------------------------- 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 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 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 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 908 VAL Chi-restraints excluded: chain B residue 978 PHE 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 197 TYR 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 564 ILE 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 36 TRP Chi-restraints excluded: chain H residue 82 MET 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 318 optimal weight: 0.4980 chunk 194 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 244 optimal weight: 0.6980 chunk 213 optimal weight: 0.9980 chunk 341 optimal weight: 3.9990 chunk 290 optimal weight: 0.5980 chunk 146 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.143956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098543 restraints weight = 63767.662| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.38 r_work: 0.3339 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29076 Z= 0.113 Angle : 0.590 11.742 39670 Z= 0.293 Chirality : 0.044 0.354 4587 Planarity : 0.004 0.051 5036 Dihedral : 5.123 54.173 4837 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 1.81 % Allowed : 14.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3489 helix: 0.81 (0.19), residues: 749 sheet: -0.24 (0.19), residues: 741 loop : -1.59 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.006 0.000 HIS B1156 PHE 0.025 0.001 PHE A 589 TYR 0.025 0.001 TYR C 702 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 45) link_NAG-ASN : angle 2.43783 ( 135) link_BETA1-4 : bond 0.00611 ( 5) link_BETA1-4 : angle 1.38903 ( 15) hydrogen bonds : bond 0.03771 ( 947) hydrogen bonds : angle 5.06223 ( 2580) SS BOND : bond 0.00302 ( 41) SS BOND : angle 1.20744 ( 82) covalent geometry : bond 0.00261 (28984) covalent geometry : angle 0.57062 (39438) Misc. bond : bond 0.00093 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16393.09 seconds wall clock time: 294 minutes 8.65 seconds (17648.65 seconds total)