Starting phenix.real_space_refine on Mon Aug 25 01:24:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44681 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.map" model { file = "/net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h12_34422/08_2025/8h12_34422.cif" } resolution = 3.44681 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 129 5.16 5 C 15433 2.51 5 N 3955 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24221 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7861 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 6 Chain: "B" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7861 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 6 Chain: "C" Number of atoms: 7869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7869 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 49, 'TRANS': 958} Chain breaks: 6 Chain: "D" 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: "E" 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: "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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.57, per 1000 atoms: 0.27 Number of scatterers: 24221 At special positions: 0 Unit cell: (124.2, 126.9, 172.8, 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 129 16.00 O 4704 8.00 N 3955 7.00 C 15433 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS C 969 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 969 " - pdb=" SG CYS B 400 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 969 " - pdb=" SG CYS C 400 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 65 " " NAG A1202 " - " ASN A1080 " " NAG A1203 " - " ASN A 109 " " NAG A1204 " - " ASN A 119 " " NAG A1205 " - " ASN A 158 " " NAG A1206 " - " ASN A 269 " " NAG A1207 " - " ASN A 318 " " NAG A1208 " - " ASN A 357 " " NAG A1209 " - " ASN A 602 " " NAG A1210 " - " ASN A 691 " " NAG A1211 " - " ASN A 699 " " NAG A1212 " - " ASN A 783 " " NAG A1213 " - " ASN A1056 " " NAG B1201 " - " ASN B 65 " " NAG B1202 " - " ASN B1080 " " NAG B1203 " - " ASN B 109 " " NAG B1204 " - " ASN B 119 " " NAG B1205 " - " ASN B 158 " " NAG B1206 " - " ASN B 269 " " NAG B1207 " - " ASN B 318 " " NAG B1208 " - " ASN B 357 " " NAG B1209 " - " ASN B 602 " " NAG B1210 " - " ASN B 691 " " NAG B1211 " - " ASN B 699 " " NAG B1212 " - " ASN B 783 " " NAG B1213 " - " ASN B1056 " " NAG C1201 " - " ASN C 65 " " NAG C1202 " - " ASN C1080 " " NAG C1203 " - " ASN C 109 " " NAG C1204 " - " ASN C 119 " " NAG C1205 " - " ASN C 158 " " NAG C1206 " - " ASN C 269 " " NAG C1207 " - " ASN C 318 " " NAG C1208 " - " ASN C 357 " " NAG C1209 " - " ASN C 602 " " NAG C1210 " - " ASN C 691 " " NAG C1211 " - " ASN C 699 " " NAG C1212 " - " ASN C 783 " " NAG C1213 " - " ASN C1056 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 45 sheets defined 24.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.600A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.688A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.809A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.513A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.516A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.771A pdb=" N LEU A 615 " --> pdb=" O ALA A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.869A pdb=" N SER A 623 " --> pdb=" O ARG A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.659A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.802A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.577A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 855 through 864 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.770A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.542A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.885A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 940 " --> pdb=" O GLN A 936 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 965 removed outlier: 3.603A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1015 removed outlier: 3.700A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 986 " --> pdb=" O ARG A 982 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.699A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.571A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.545A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.589A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.793A pdb=" N LEU B 615 " --> pdb=" O ALA B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.625A pdb=" N SER B 623 " --> pdb=" O ARG B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.529A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 765 removed outlier: 3.962A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 764 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 832 through 837 Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.749A pdb=" N ALA B 857 " --> pdb=" O ALA B 853 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 858 " --> pdb=" O ALA B 854 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 861 " --> pdb=" O ALA B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 removed outlier: 3.675A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.655A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.588A pdb=" N GLN B 908 " --> pdb=" O GLN B 904 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 917 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.384A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.535A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1015 removed outlier: 4.385A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.619A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.727A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 3.504A pdb=" N ASP C 393 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.553A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.796A pdb=" N LEU C 615 " --> pdb=" O ALA C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 742 through 765 removed outlier: 3.769A pdb=" N ALA C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 832 through 837 Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.557A pdb=" N ALA C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 857 " --> pdb=" O ALA C 853 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 860 " --> pdb=" O THR C 856 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 861 " --> pdb=" O ALA C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 3.521A pdb=" N ALA C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.381A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 921 removed outlier: 3.710A pdb=" N ILE C 916 " --> pdb=" O ALA C 912 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 917 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.018A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.993A pdb=" N SER C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1015 removed outlier: 4.071A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.713A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.876A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.084A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.546A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.855A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.845A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.670A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 710 removed outlier: 6.638A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA A1037 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A1043 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.642A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.696A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.502A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.885A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.178A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 315 Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.698A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 540 removed outlier: 3.604A pdb=" N SER B 574 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.546A pdb=" N ILE B 656 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.578A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 694 through 710 removed outlier: 6.635A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B1034 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.675A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.507A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS B1064 " --> pdb=" O ILE B1115 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD5, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.650A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.829A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.132A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 127 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AD9, first strand: chain 'C' and resid 312 through 315 Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.789A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE3, first strand: chain 'C' and resid 537 through 540 removed outlier: 3.874A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 640 through 641 Processing sheet with id=AE5, first strand: chain 'C' and resid 694 through 710 removed outlier: 6.678A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.615A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AE8, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.830A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1076 through 1079 863 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7675 1.35 - 1.47: 6569 1.47 - 1.60: 10349 1.60 - 1.73: 0 1.73 - 1.86: 171 Bond restraints: 24764 Sorted by residual: bond pdb=" C1 NAG C1209 " pdb=" O5 NAG C1209 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" CB CYS B 969 " pdb=" SG CYS B 969 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.73e+00 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 24759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 33086 2.51 - 5.03: 528 5.03 - 7.54: 54 7.54 - 10.05: 8 10.05 - 12.57: 10 Bond angle restraints: 33686 Sorted by residual: angle pdb=" CA CYS A 159 " pdb=" CB CYS A 159 " pdb=" SG CYS A 159 " ideal model delta sigma weight residual 114.40 126.97 -12.57 2.30e+00 1.89e-01 2.99e+01 angle pdb=" CA CYS A 511 " pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " ideal model delta sigma weight residual 114.40 125.53 -11.13 2.30e+00 1.89e-01 2.34e+01 angle pdb=" C ASN B 158 " pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 122.21 114.89 7.32 1.62e+00 3.81e-01 2.04e+01 angle pdb=" CA CYS B 511 " pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " ideal model delta sigma weight residual 114.40 124.72 -10.32 2.30e+00 1.89e-01 2.01e+01 angle pdb=" CA CYS C 511 " pdb=" CB CYS C 511 " pdb=" SG CYS C 511 " ideal model delta sigma weight residual 114.40 124.72 -10.32 2.30e+00 1.89e-01 2.01e+01 ... (remaining 33681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13867 17.86 - 35.72: 1171 35.72 - 53.58: 248 53.58 - 71.45: 40 71.45 - 89.31: 27 Dihedral angle restraints: 15353 sinusoidal: 6539 harmonic: 8814 Sorted by residual: dihedral pdb=" CB CYS C 603 " pdb=" SG CYS C 603 " pdb=" SG CYS C 635 " pdb=" CB CYS C 635 " ideal model delta sinusoidal sigma weight residual -86.00 -8.97 -77.03 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual -86.00 -30.73 -55.27 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 159 " pdb=" CB CYS C 159 " ideal model delta sinusoidal sigma weight residual 93.00 45.87 47.13 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 15350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3330 0.078 - 0.155: 583 0.155 - 0.233: 26 0.233 - 0.310: 4 0.310 - 0.388: 9 Chirality restraints: 3952 Sorted by residual: chirality pdb=" C1 NAG C1202 " pdb=" ND2 ASN C1080 " pdb=" C2 NAG C1202 " pdb=" O5 NAG C1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1 NAG B1202 " pdb=" ND2 ASN B1080 " pdb=" C2 NAG B1202 " pdb=" O5 NAG B1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C1 NAG A1206 " pdb=" ND2 ASN A 269 " pdb=" C2 NAG A1206 " pdb=" O5 NAG A1206 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 3949 not shown) Planarity restraints: 4331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 469 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO C 470 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 308 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO B 309 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 469 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 470 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.058 5.00e-02 4.00e+02 ... (remaining 4328 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5212 2.78 - 3.31: 19689 3.31 - 3.84: 36923 3.84 - 4.37: 43605 4.37 - 4.90: 79256 Nonbonded interactions: 184685 Sorted by model distance: nonbonded pdb=" OH TYR B 41 " pdb=" O LEU B 58 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" O LEU A 58 " model vdw 2.261 3.040 nonbonded pdb=" OD2 ASP A 44 " pdb=" NH2 ARG A 48 " model vdw 2.267 3.120 nonbonded pdb=" O ASN C 960 " pdb=" OG SER C 964 " model vdw 2.272 3.040 ... (remaining 184680 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' selection = chain 'B' selection = (chain 'C' and (resid 31 through 808 or resid 831 through 1213)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.940 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24851 Z= 0.267 Angle : 0.868 12.567 33905 Z= 0.450 Chirality : 0.057 0.388 3952 Planarity : 0.006 0.116 4289 Dihedral : 13.958 89.307 9555 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.14), residues: 2980 helix: -2.00 (0.17), residues: 660 sheet: -0.33 (0.20), residues: 645 loop : -1.49 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 48 TYR 0.030 0.002 TYR C 491 PHE 0.041 0.003 PHE C 334 TRP 0.010 0.002 TRP C 423 HIS 0.007 0.002 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00625 (24764) covalent geometry : angle 0.81288 (33686) SS BOND : bond 0.00739 ( 42) SS BOND : angle 2.25956 ( 84) hydrogen bonds : bond 0.19497 ( 863) hydrogen bonds : angle 7.59491 ( 2340) link_BETA1-4 : bond 0.00795 ( 3) link_BETA1-4 : angle 2.88128 ( 9) link_NAG-ASN : bond 0.00911 ( 42) link_NAG-ASN : angle 4.69538 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.950 Fit side-chains REVERT: A 849 ASP cc_start: 0.7876 (m-30) cc_final: 0.7644 (m-30) REVERT: A 882 MET cc_start: 0.8305 (mtp) cc_final: 0.8098 (mtm) REVERT: A 968 LYS cc_start: 0.7788 (tmtt) cc_final: 0.6949 (mttt) REVERT: B 713 MET cc_start: 0.8899 (ptt) cc_final: 0.8675 (ptt) REVERT: B 768 LYS cc_start: 0.8213 (mttt) cc_final: 0.6930 (mmpt) REVERT: B 968 LYS cc_start: 0.7375 (mtmt) cc_final: 0.6962 (tmtt) REVERT: B 1052 SER cc_start: 0.9009 (p) cc_final: 0.8261 (m) REVERT: B 1105 SER cc_start: 0.8840 (t) cc_final: 0.8514 (t) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1585 time to fit residues: 70.5543 Evaluate side-chains 218 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN B 301 GLN B1088 GLN C 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.099630 restraints weight = 27939.433| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.76 r_work: 0.2775 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24851 Z= 0.117 Angle : 0.585 9.390 33905 Z= 0.296 Chirality : 0.047 0.377 3952 Planarity : 0.005 0.100 4289 Dihedral : 7.213 52.644 4192 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.72 % Allowed : 5.71 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.14), residues: 2980 helix: -0.73 (0.19), residues: 675 sheet: -0.03 (0.21), residues: 628 loop : -1.25 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 48 TYR 0.024 0.001 TYR A 200 PHE 0.018 0.001 PHE C1079 TRP 0.008 0.001 TRP B 619 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00263 (24764) covalent geometry : angle 0.54284 (33686) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.41396 ( 84) hydrogen bonds : bond 0.05070 ( 863) hydrogen bonds : angle 5.41796 ( 2340) link_BETA1-4 : bond 0.00519 ( 3) link_BETA1-4 : angle 2.08843 ( 9) link_NAG-ASN : bond 0.00611 ( 42) link_NAG-ASN : angle 3.40110 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.959 Fit side-chains REVERT: A 741 PHE cc_start: 0.7645 (t80) cc_final: 0.7312 (t80) REVERT: A 937 ASN cc_start: 0.7734 (m110) cc_final: 0.7378 (m-40) REVERT: A 1020 LYS cc_start: 0.8685 (mttp) cc_final: 0.8394 (mttp) REVERT: B 562 VAL cc_start: 0.9170 (p) cc_final: 0.8823 (t) REVERT: B 796 LYS cc_start: 0.7988 (mttm) cc_final: 0.7773 (mptp) REVERT: B 968 LYS cc_start: 0.7539 (mtmt) cc_final: 0.6946 (tmtt) REVERT: C 1011 MET cc_start: 0.8577 (tpp) cc_final: 0.8194 (ttm) outliers start: 19 outliers final: 15 residues processed: 265 average time/residue: 0.1576 time to fit residues: 68.7468 Evaluate side-chains 240 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 999 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 209 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 273 optimal weight: 0.0670 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN B 201 GLN B 301 GLN B 614 GLN B 692 ASN B 937 ASN B1088 GLN C 301 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.114799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.088960 restraints weight = 28859.568| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.87 r_work: 0.2589 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 24851 Z= 0.360 Angle : 0.789 12.688 33905 Z= 0.400 Chirality : 0.055 0.356 3952 Planarity : 0.006 0.095 4289 Dihedral : 7.299 59.844 4192 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.45 % Allowed : 10.51 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 2980 helix: -0.85 (0.19), residues: 679 sheet: -0.30 (0.20), residues: 616 loop : -1.46 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 395 TYR 0.029 0.002 TYR A1049 PHE 0.036 0.003 PHE A 334 TRP 0.013 0.002 TRP C 423 HIS 0.011 0.003 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00916 (24764) covalent geometry : angle 0.74816 (33686) SS BOND : bond 0.00729 ( 42) SS BOND : angle 2.13122 ( 84) hydrogen bonds : bond 0.07337 ( 863) hydrogen bonds : angle 5.53813 ( 2340) link_BETA1-4 : bond 0.00590 ( 3) link_BETA1-4 : angle 3.05051 ( 9) link_NAG-ASN : bond 0.00569 ( 42) link_NAG-ASN : angle 3.76394 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8507 (t80) cc_final: 0.8085 (t80) REVERT: A 737 GLN cc_start: 0.6542 (mm-40) cc_final: 0.5100 (mt0) REVERT: A 770 MET cc_start: 0.8501 (mmm) cc_final: 0.8023 (mmm) REVERT: A 937 ASN cc_start: 0.7921 (m110) cc_final: 0.7586 (m-40) REVERT: A 968 LYS cc_start: 0.8429 (tmtt) cc_final: 0.7694 (mttt) REVERT: B 99 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7508 (mmt90) REVERT: B 224 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7562 (pp) REVERT: B 560 ASP cc_start: 0.8440 (m-30) cc_final: 0.8168 (m-30) REVERT: B 744 GLN cc_start: 0.8767 (tt0) cc_final: 0.8527 (tt0) REVERT: B 796 LYS cc_start: 0.8088 (mttm) cc_final: 0.7863 (mptp) REVERT: B 968 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7668 (tmtt) REVERT: C 851 MET cc_start: 0.8637 (mtm) cc_final: 0.8370 (mtt) outliers start: 38 outliers final: 29 residues processed: 253 average time/residue: 0.1598 time to fit residues: 66.5321 Evaluate side-chains 245 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 999 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 126 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 272 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 187 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 883 GLN A 917 GLN B 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.119942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.093587 restraints weight = 28203.041| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.87 r_work: 0.2706 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24851 Z= 0.114 Angle : 0.579 9.926 33905 Z= 0.292 Chirality : 0.046 0.371 3952 Planarity : 0.004 0.092 4289 Dihedral : 6.508 53.377 4192 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.64 % Allowed : 11.96 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.14), residues: 2980 helix: 0.02 (0.21), residues: 656 sheet: -0.19 (0.20), residues: 629 loop : -1.27 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.020 0.001 TYR A1049 PHE 0.014 0.001 PHE C1079 TRP 0.007 0.001 TRP B 423 HIS 0.003 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00254 (24764) covalent geometry : angle 0.53593 (33686) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.61298 ( 84) hydrogen bonds : bond 0.04963 ( 863) hydrogen bonds : angle 5.08301 ( 2340) link_BETA1-4 : bond 0.00555 ( 3) link_BETA1-4 : angle 1.98857 ( 9) link_NAG-ASN : bond 0.00671 ( 42) link_NAG-ASN : angle 3.38754 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.6822 (p90) REVERT: A 770 MET cc_start: 0.8512 (mmm) cc_final: 0.8009 (mmm) REVERT: A 937 ASN cc_start: 0.7825 (m110) cc_final: 0.7444 (m-40) REVERT: A 968 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7234 (mttt) REVERT: A 1020 LYS cc_start: 0.8766 (mttp) cc_final: 0.8486 (mttp) REVERT: B 224 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7516 (pp) REVERT: B 562 VAL cc_start: 0.9092 (p) cc_final: 0.8756 (t) REVERT: B 572 ASP cc_start: 0.8492 (m-30) cc_final: 0.8258 (m-30) REVERT: B 709 MET cc_start: 0.9040 (mtm) cc_final: 0.8781 (mtm) REVERT: B 717 SER cc_start: 0.8686 (p) cc_final: 0.8000 (m) REVERT: B 796 LYS cc_start: 0.8087 (mttm) cc_final: 0.7834 (mptp) REVERT: B 888 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8669 (m-80) REVERT: B 968 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7345 (tmtt) REVERT: C 684 ASP cc_start: 0.8024 (t70) cc_final: 0.7681 (p0) REVERT: C 851 MET cc_start: 0.8597 (mtm) cc_final: 0.8320 (mtt) outliers start: 43 outliers final: 31 residues processed: 275 average time/residue: 0.1596 time to fit residues: 71.9146 Evaluate side-chains 259 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 904 GLN B 908 GLN C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.116783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.090408 restraints weight = 28450.987| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.93 r_work: 0.2611 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24851 Z= 0.226 Angle : 0.663 10.958 33905 Z= 0.334 Chirality : 0.050 0.357 3952 Planarity : 0.005 0.087 4289 Dihedral : 6.533 51.880 4192 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.17 % Allowed : 13.14 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.14), residues: 2980 helix: -0.20 (0.20), residues: 671 sheet: -0.20 (0.20), residues: 614 loop : -1.34 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1089 TYR 0.024 0.002 TYR A1049 PHE 0.024 0.002 PHE B 220 TRP 0.011 0.002 TRP B 423 HIS 0.006 0.002 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00569 (24764) covalent geometry : angle 0.62167 (33686) SS BOND : bond 0.00511 ( 42) SS BOND : angle 1.89353 ( 84) hydrogen bonds : bond 0.06038 ( 863) hydrogen bonds : angle 5.15472 ( 2340) link_BETA1-4 : bond 0.00445 ( 3) link_BETA1-4 : angle 2.44031 ( 9) link_NAG-ASN : bond 0.00601 ( 42) link_NAG-ASN : angle 3.48396 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 181 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.6979 (p90) REVERT: A 770 MET cc_start: 0.8469 (mmm) cc_final: 0.7914 (mmm) REVERT: A 937 ASN cc_start: 0.7765 (m110) cc_final: 0.7376 (m-40) REVERT: A 968 LYS cc_start: 0.8425 (tmtt) cc_final: 0.7619 (mttt) REVERT: A 1080 ASN cc_start: 0.7576 (t0) cc_final: 0.7344 (t0) REVERT: B 99 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7619 (mmt90) REVERT: B 163 TYR cc_start: 0.8283 (t80) cc_final: 0.7920 (t80) REVERT: B 224 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7490 (pp) REVERT: B 709 MET cc_start: 0.9065 (mtm) cc_final: 0.8725 (mtm) REVERT: B 744 GLN cc_start: 0.8688 (tt0) cc_final: 0.8480 (tt0) REVERT: B 796 LYS cc_start: 0.8057 (mttm) cc_final: 0.7778 (mptp) REVERT: B 968 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7527 (tmtt) REVERT: C 684 ASP cc_start: 0.7635 (t70) cc_final: 0.7396 (p0) outliers start: 57 outliers final: 44 residues processed: 277 average time/residue: 0.1534 time to fit residues: 71.0978 Evaluate side-chains 265 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 904 GLN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 273 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN A 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.091133 restraints weight = 28445.355| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.90 r_work: 0.2647 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24851 Z= 0.186 Angle : 0.630 10.772 33905 Z= 0.318 Chirality : 0.049 0.365 3952 Planarity : 0.005 0.085 4289 Dihedral : 6.361 51.272 4192 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.51 % Allowed : 13.56 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.14), residues: 2980 helix: 0.04 (0.21), residues: 657 sheet: -0.17 (0.21), residues: 611 loop : -1.33 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1089 TYR 0.023 0.002 TYR A1049 PHE 0.022 0.002 PHE B 220 TRP 0.009 0.001 TRP B 423 HIS 0.005 0.001 HIS A 611 Details of bonding type rmsd covalent geometry : bond 0.00461 (24764) covalent geometry : angle 0.58830 (33686) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.83778 ( 84) hydrogen bonds : bond 0.05655 ( 863) hydrogen bonds : angle 5.07671 ( 2340) link_BETA1-4 : bond 0.00560 ( 3) link_BETA1-4 : angle 2.24117 ( 9) link_NAG-ASN : bond 0.00625 ( 42) link_NAG-ASN : angle 3.43042 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7030 (p90) REVERT: A 770 MET cc_start: 0.8451 (mmm) cc_final: 0.7868 (mmm) REVERT: A 937 ASN cc_start: 0.7747 (m110) cc_final: 0.7367 (m-40) REVERT: A 968 LYS cc_start: 0.8290 (tmtt) cc_final: 0.7504 (mttt) REVERT: B 99 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7592 (mmt90) REVERT: B 224 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7436 (pp) REVERT: B 709 MET cc_start: 0.9042 (mtm) cc_final: 0.8692 (mtm) REVERT: B 744 GLN cc_start: 0.8643 (tt0) cc_final: 0.8424 (tt0) REVERT: B 786 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8567 (mm110) REVERT: B 796 LYS cc_start: 0.8048 (mttm) cc_final: 0.7768 (mptp) REVERT: B 968 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7236 (tmtt) outliers start: 66 outliers final: 53 residues processed: 284 average time/residue: 0.1349 time to fit residues: 63.5857 Evaluate side-chains 276 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 999 GLU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 254 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 34 optimal weight: 0.0000 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 292 optimal weight: 0.4980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 904 GLN A 917 GLN C 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.120986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.095724 restraints weight = 28042.397| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.80 r_work: 0.2652 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24851 Z= 0.105 Angle : 0.550 9.400 33905 Z= 0.277 Chirality : 0.046 0.368 3952 Planarity : 0.004 0.083 4289 Dihedral : 5.908 50.729 4192 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.21 % Allowed : 14.43 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 2980 helix: 0.50 (0.21), residues: 653 sheet: -0.05 (0.21), residues: 601 loop : -1.21 (0.13), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1089 TYR 0.020 0.001 TYR A 200 PHE 0.020 0.001 PHE B 220 TRP 0.008 0.001 TRP A 423 HIS 0.002 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00236 (24764) covalent geometry : angle 0.50855 (33686) SS BOND : bond 0.00323 ( 42) SS BOND : angle 1.46680 ( 84) hydrogen bonds : bond 0.04487 ( 863) hydrogen bonds : angle 4.82755 ( 2340) link_BETA1-4 : bond 0.00671 ( 3) link_BETA1-4 : angle 1.61554 ( 9) link_NAG-ASN : bond 0.00660 ( 42) link_NAG-ASN : angle 3.24963 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7113 (p90) REVERT: A 503 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 572 ASP cc_start: 0.8380 (m-30) cc_final: 0.8154 (m-30) REVERT: A 770 MET cc_start: 0.8497 (mmm) cc_final: 0.7935 (mmm) REVERT: A 937 ASN cc_start: 0.7554 (m110) cc_final: 0.7172 (m-40) REVERT: A 968 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7000 (tttt) REVERT: A 1020 LYS cc_start: 0.8709 (mttp) cc_final: 0.8399 (mttp) REVERT: B 224 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7359 (pp) REVERT: B 562 VAL cc_start: 0.9066 (p) cc_final: 0.8782 (t) REVERT: B 717 SER cc_start: 0.8680 (p) cc_final: 0.8037 (m) REVERT: B 786 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8488 (mm110) REVERT: B 796 LYS cc_start: 0.8015 (mttm) cc_final: 0.7714 (mptp) REVERT: B 888 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: B 968 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7098 (tmtt) REVERT: C 421 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8812 (pt) outliers start: 58 outliers final: 45 residues processed: 292 average time/residue: 0.1469 time to fit residues: 71.5244 Evaluate side-chains 287 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1080 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 115 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 262 optimal weight: 0.4980 chunk 271 optimal weight: 2.9990 chunk 242 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 126 optimal weight: 0.0670 chunk 131 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.121505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.095076 restraints weight = 28078.101| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.87 r_work: 0.2728 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24851 Z= 0.106 Angle : 0.544 9.227 33905 Z= 0.274 Chirality : 0.046 0.350 3952 Planarity : 0.004 0.082 4289 Dihedral : 5.729 50.695 4192 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.28 % Allowed : 14.39 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 2980 helix: 0.71 (0.21), residues: 657 sheet: 0.00 (0.21), residues: 600 loop : -1.11 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1089 TYR 0.019 0.001 TYR B1049 PHE 0.028 0.001 PHE C 220 TRP 0.008 0.001 TRP B 101 HIS 0.002 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00242 (24764) covalent geometry : angle 0.50468 (33686) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.41241 ( 84) hydrogen bonds : bond 0.04383 ( 863) hydrogen bonds : angle 4.73342 ( 2340) link_BETA1-4 : bond 0.00678 ( 3) link_BETA1-4 : angle 1.59740 ( 9) link_NAG-ASN : bond 0.00652 ( 42) link_NAG-ASN : angle 3.15678 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7109 (p90) REVERT: A 503 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7965 (mt) REVERT: A 722 MET cc_start: 0.9071 (ttt) cc_final: 0.8783 (ttm) REVERT: A 770 MET cc_start: 0.8470 (mmm) cc_final: 0.7942 (mmm) REVERT: A 796 LYS cc_start: 0.7819 (mttp) cc_final: 0.7557 (mttm) REVERT: A 937 ASN cc_start: 0.7759 (m110) cc_final: 0.7361 (m-40) REVERT: A 1020 LYS cc_start: 0.8747 (mttp) cc_final: 0.8454 (mttp) REVERT: B 224 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7414 (pp) REVERT: B 562 VAL cc_start: 0.9059 (p) cc_final: 0.8806 (t) REVERT: B 717 SER cc_start: 0.8590 (p) cc_final: 0.8035 (m) REVERT: B 796 LYS cc_start: 0.8065 (mttm) cc_final: 0.7744 (mptp) REVERT: B 968 LYS cc_start: 0.7511 (mtmt) cc_final: 0.6946 (tmtt) REVERT: C 421 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8829 (pt) REVERT: C 772 LYS cc_start: 0.7935 (ptmm) cc_final: 0.7730 (pttp) outliers start: 60 outliers final: 48 residues processed: 301 average time/residue: 0.1524 time to fit residues: 76.0620 Evaluate side-chains 297 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1080 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.120037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.093807 restraints weight = 28330.328| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.89 r_work: 0.2653 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24851 Z= 0.135 Angle : 0.569 9.263 33905 Z= 0.286 Chirality : 0.047 0.352 3952 Planarity : 0.004 0.081 4289 Dihedral : 5.752 50.880 4192 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.40 % Allowed : 14.47 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 2980 helix: 0.69 (0.21), residues: 655 sheet: -0.04 (0.21), residues: 602 loop : -1.13 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1089 TYR 0.020 0.001 TYR A1049 PHE 0.026 0.001 PHE C 220 TRP 0.008 0.001 TRP B 868 HIS 0.003 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00327 (24764) covalent geometry : angle 0.52977 (33686) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.63893 ( 84) hydrogen bonds : bond 0.04743 ( 863) hydrogen bonds : angle 4.77128 ( 2340) link_BETA1-4 : bond 0.00467 ( 3) link_BETA1-4 : angle 1.81950 ( 9) link_NAG-ASN : bond 0.00627 ( 42) link_NAG-ASN : angle 3.17190 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7025 (p90) REVERT: A 503 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 770 MET cc_start: 0.8409 (mmm) cc_final: 0.7831 (mmm) REVERT: A 796 LYS cc_start: 0.7768 (mttp) cc_final: 0.7504 (mttm) REVERT: A 937 ASN cc_start: 0.7674 (m110) cc_final: 0.7271 (m-40) REVERT: A 1006 LEU cc_start: 0.8658 (tp) cc_final: 0.8408 (tp) REVERT: A 1020 LYS cc_start: 0.8676 (mttp) cc_final: 0.8369 (mttp) REVERT: B 224 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7338 (pp) REVERT: B 562 VAL cc_start: 0.9020 (p) cc_final: 0.8734 (t) REVERT: B 717 SER cc_start: 0.8624 (p) cc_final: 0.8012 (m) REVERT: B 968 LYS cc_start: 0.7183 (mtmt) cc_final: 0.6733 (tmtt) REVERT: C 421 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8816 (pt) REVERT: C 772 LYS cc_start: 0.7930 (ptmm) cc_final: 0.7718 (pttp) outliers start: 63 outliers final: 54 residues processed: 287 average time/residue: 0.1309 time to fit residues: 63.6809 Evaluate side-chains 296 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1080 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 117 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 297 optimal weight: 0.1980 chunk 294 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 231 optimal weight: 0.0060 chunk 270 optimal weight: 0.8980 chunk 263 optimal weight: 0.7980 chunk 262 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN C 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.122476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.096478 restraints weight = 28085.205| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.83 r_work: 0.2748 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24851 Z= 0.100 Angle : 0.534 9.043 33905 Z= 0.268 Chirality : 0.045 0.352 3952 Planarity : 0.004 0.081 4289 Dihedral : 5.552 50.301 4192 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.09 % Allowed : 14.85 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.15), residues: 2980 helix: 0.93 (0.22), residues: 655 sheet: 0.03 (0.21), residues: 602 loop : -1.08 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1089 TYR 0.019 0.001 TYR B1049 PHE 0.023 0.001 PHE C 220 TRP 0.008 0.001 TRP B 868 HIS 0.002 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00224 (24764) covalent geometry : angle 0.49565 (33686) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.38107 ( 84) hydrogen bonds : bond 0.04141 ( 863) hydrogen bonds : angle 4.64311 ( 2340) link_BETA1-4 : bond 0.00503 ( 3) link_BETA1-4 : angle 1.50761 ( 9) link_NAG-ASN : bond 0.00654 ( 42) link_NAG-ASN : angle 3.08221 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7063 (p90) REVERT: A 503 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 770 MET cc_start: 0.8526 (mmm) cc_final: 0.7996 (mmm) REVERT: A 796 LYS cc_start: 0.7845 (mttp) cc_final: 0.7571 (mttm) REVERT: A 937 ASN cc_start: 0.7695 (m110) cc_final: 0.7323 (m-40) REVERT: A 1020 LYS cc_start: 0.8725 (mttp) cc_final: 0.8432 (mttp) REVERT: B 163 TYR cc_start: 0.8226 (t80) cc_final: 0.7754 (t80) REVERT: B 224 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7416 (pp) REVERT: B 562 VAL cc_start: 0.9064 (p) cc_final: 0.8843 (t) REVERT: B 709 MET cc_start: 0.9071 (mtm) cc_final: 0.8722 (mtm) REVERT: B 717 SER cc_start: 0.8569 (p) cc_final: 0.8106 (m) REVERT: C 421 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8789 (pt) outliers start: 55 outliers final: 49 residues processed: 297 average time/residue: 0.1444 time to fit residues: 72.3672 Evaluate side-chains 299 residues out of total 2626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 969 CYS Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1052 SER Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 CYS Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1080 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 257 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.120101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.094679 restraints weight = 28238.066| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.81 r_work: 0.2648 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24851 Z= 0.147 Angle : 0.574 9.354 33905 Z= 0.289 Chirality : 0.047 0.332 3952 Planarity : 0.004 0.081 4289 Dihedral : 5.680 51.019 4192 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.09 % Allowed : 15.16 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 2980 helix: 0.81 (0.21), residues: 655 sheet: 0.01 (0.21), residues: 610 loop : -1.12 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.021 0.001 TYR A1049 PHE 0.031 0.001 PHE B1079 TRP 0.009 0.001 TRP B 868 HIS 0.003 0.001 HIS C 611 Details of bonding type rmsd covalent geometry : bond 0.00360 (24764) covalent geometry : angle 0.53610 (33686) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.64245 ( 84) hydrogen bonds : bond 0.04848 ( 863) hydrogen bonds : angle 4.74390 ( 2340) link_BETA1-4 : bond 0.00412 ( 3) link_BETA1-4 : angle 1.88023 ( 9) link_NAG-ASN : bond 0.00617 ( 42) link_NAG-ASN : angle 3.13884 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.07 seconds wall clock time: 86 minutes 45.95 seconds (5205.95 seconds total)