Starting phenix.real_space_refine on Fri Mar 6 00:25:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kl9_22916/03_2026/7kl9_22916.map" } resolution = 4.1 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= 0.019 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 110 5.16 5 C 16803 2.51 5 N 4454 2.21 5 O 4991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26358 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7433 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 53, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 12, 'ASN:plan1': 13, 'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 192 Chain: "B" Number of atoms: 7435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7435 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 12, 'ASN:plan1': 14, 'GLN:plan1': 3, 'PHE:plan': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 7435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7435 Classifications: {'peptide': 995} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 53, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 11, 'ASN:plan1': 13, 'GLN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "F" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1207 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.65, per 1000 atoms: 0.25 Number of scatterers: 26358 At special positions: 0 Unit cell: (134.695, 158.158, 203.346, 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 110 16.00 O 4991 8.00 N 4454 7.00 C 16803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 122 " " NAG C1308 " - " ASN C 709 " " NAG G 1 " - " ASN C 165 " " NAG H 1 " - " ASN C 331 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6528 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 46 sheets defined 33.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.551A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.288A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.252A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.909A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.568A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.876A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.552A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.306A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.272A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.629A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.145A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 343' Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.552A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.512A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.104A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.623A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.602A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.020A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.564A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.580A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.887A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.726A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.580A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.209A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.105A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.581A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.233A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.709A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.319A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.505A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.360A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'E' and resid 17 through 48 removed outlier: 3.968A pdb=" N ARG E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 82 removed outlier: 3.729A pdb=" N GLU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 117 removed outlier: 4.444A pdb=" N ALA E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU E 116 " --> pdb=" O MET E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 156 removed outlier: 3.648A pdb=" N PHE E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 removed outlier: 3.868A pdb=" N ALA D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.577A pdb=" N ILE D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 79 removed outlier: 3.766A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'D' and resid 85 through 95 removed outlier: 3.763A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 114 removed outlier: 4.176A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 151 removed outlier: 4.090A pdb=" N LYS D 130 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 17 through 26 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.505A pdb=" N LYS F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 83 removed outlier: 4.268A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 89 through 120 removed outlier: 3.589A pdb=" N GLU F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 116 " --> pdb=" O MET F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 158 removed outlier: 3.836A pdb=" N ASP F 134 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE F 152 " --> pdb=" O ALA F 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.533A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.206A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.673A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 318 removed outlier: 6.851A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.718A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.111A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.647A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.879A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.709A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 719 removed outlier: 3.988A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.962A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.015A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.641A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.292A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 160 through 164 removed outlier: 3.787A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 319 removed outlier: 5.783A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AC4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 541 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 4.859A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.738A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.738A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.613A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.947A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 106 removed outlier: 5.978A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 205 removed outlier: 4.874A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.330A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.547A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.626A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.394A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.576A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.576A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE8, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.638A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.985A pdb=" N ILE E 4 " --> pdb=" O ARG E 12 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.473A pdb=" N ILE D 4 " --> pdb=" O ARG D 12 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 2988 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: 5.73 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6063 1.33 - 1.45: 6674 1.45 - 1.58: 14018 1.58 - 1.70: 0 1.70 - 1.83: 143 Bond restraints: 26898 Sorted by residual: bond pdb=" N ARG C 328 " pdb=" CA ARG C 328 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.53e-02 4.27e+03 2.24e+01 bond pdb=" C VAL B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.83e-02 1.25e+03 2.11e+01 bond pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 1.469 1.527 -0.059 1.28e-02 6.10e+03 2.11e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.41e-02 5.03e+03 1.92e+01 bond pdb=" CA PHE C 329 " pdb=" C PHE C 329 " ideal model delta sigma weight residual 1.524 1.574 -0.050 1.26e-02 6.30e+03 1.57e+01 ... (remaining 26893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 36211 3.13 - 6.26: 362 6.26 - 9.39: 34 9.39 - 12.52: 9 12.52 - 15.65: 4 Bond angle restraints: 36620 Sorted by residual: angle pdb=" CA PRO C 384 " pdb=" N PRO C 384 " pdb=" CD PRO C 384 " ideal model delta sigma weight residual 112.00 99.45 12.55 1.40e+00 5.10e-01 8.04e+01 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 99.69 12.31 1.40e+00 5.10e-01 7.73e+01 angle pdb=" N ARG C 328 " pdb=" CA ARG C 328 " pdb=" C ARG C 328 " ideal model delta sigma weight residual 108.34 119.52 -11.18 1.31e+00 5.83e-01 7.28e+01 angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 112.47 127.71 -15.24 2.06e+00 2.36e-01 5.47e+01 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 128.52 -8.68 1.25e+00 6.40e-01 4.82e+01 ... (remaining 36615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15023 17.95 - 35.90: 1195 35.90 - 53.86: 190 53.86 - 71.81: 43 71.81 - 89.76: 28 Dihedral angle restraints: 16479 sinusoidal: 6375 harmonic: 10104 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -161.43 75.43 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 35.81 57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA CYS A 760 " pdb=" C CYS A 760 " pdb=" N THR A 761 " pdb=" CA THR A 761 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 16476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 4207 0.132 - 0.264: 67 0.264 - 0.396: 3 0.396 - 0.528: 3 0.528 - 0.660: 2 Chirality restraints: 4282 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.09e+03 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 4279 not shown) Planarity restraints: 4787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.292 2.00e-02 2.50e+03 2.47e-01 7.63e+02 pdb=" C7 NAG H 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.425 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.277 2.00e-02 2.50e+03 2.32e-01 6.75e+02 pdb=" C7 NAG H 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.393 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " -0.160 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" C7 NAG B1311 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " 0.212 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.022 2.00e-02 2.50e+03 ... (remaining 4784 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 3 1.97 - 2.70: 1624 2.70 - 3.44: 42107 3.44 - 4.17: 63266 4.17 - 4.90: 107496 Nonbonded interactions: 214496 Sorted by model distance: nonbonded pdb=" OE2 GLU C 406 " pdb=" OH TYR C 495 " model vdw 1.240 3.040 nonbonded pdb=" CD2 PHE C 374 " pdb=" CG2 ILE C 434 " model vdw 1.871 3.760 nonbonded pdb=" CD GLU C 406 " pdb=" OH TYR C 495 " model vdw 1.921 3.270 nonbonded pdb=" NH1 ARG B 328 " pdb=" O ASN B 532 " model vdw 2.020 3.120 nonbonded pdb=" OG1 THR C 323 " pdb=" NZ LYS C 537 " model vdw 2.054 3.120 ... (remaining 214491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 333 or \ (resid 334 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 416 or (resid 417 and (name N or name CA or name C or name \ O or name CB )) or resid 418 through 443 or (resid 444 and (name N or name CA o \ r name C or name O or name CB )) or resid 445 through 920 or (resid 921 and (nam \ e N or name CA or name C or name O or name CB )) or resid 922 through 1308)) selection = (chain 'B' and (resid 27 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 405 or (resid 406 and (name N o \ r name CA or name C or name O or name CB )) or resid 407 through 416 or (resid 4 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 418 through \ 443 or (resid 444 and (name N or name CA or name C or name O or name CB )) or r \ esid 445 through 516 or resid 520 through 1308)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 166 or (resid 167 through 188 and \ (name N or name CA or name C or name O or name CB )) or resid 189 through 333 or \ (resid 334 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 402 or (resid 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 920 or (resid 921 and (nam \ e N or name CA or name C or name O or name CB )) or resid 922 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.009 0.130 26963 Z= 0.406 Angle : 0.937 16.078 36781 Z= 0.501 Chirality : 0.056 0.660 4282 Planarity : 0.008 0.247 4758 Dihedral : 13.709 89.762 9849 Min Nonbonded Distance : 1.240 Molprobity Statistics. All-atom Clashscore : 30.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.85 % Favored : 87.95 % Rotamer: Outliers : 0.27 % Allowed : 0.59 % Favored : 99.14 % Cbeta Deviations : 0.06 % 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 are not related in a simple way. whole: -2.99 (0.13), residues: 3410 helix: -1.63 (0.15), residues: 894 sheet: -1.55 (0.21), residues: 545 loop : -2.35 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 509 TYR 0.030 0.003 TYR A 904 PHE 0.041 0.003 PHE B 275 TRP 0.037 0.003 TRP A 886 HIS 0.010 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00855 (26898) covalent geometry : angle 0.90322 (36620) SS BOND : bond 0.00553 ( 34) SS BOND : angle 2.70805 ( 68) hydrogen bonds : bond 0.33082 ( 1069) hydrogen bonds : angle 10.85558 ( 2988) link_BETA1-4 : bond 0.01587 ( 2) link_BETA1-4 : angle 7.03699 ( 6) link_NAG-ASN : bond 0.00935 ( 29) link_NAG-ASN : angle 4.36073 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8144 (t) REVERT: B 160 TYR cc_start: 0.7899 (p90) cc_final: 0.7327 (p90) REVERT: B 201 PHE cc_start: 0.9098 (t80) cc_final: 0.8855 (t80) REVERT: C 104 TRP cc_start: 0.7647 (m-90) cc_final: 0.7437 (m-90) REVERT: C 390 LEU cc_start: 0.8473 (tp) cc_final: 0.8247 (tp) REVERT: C 740 MET cc_start: 0.8019 (tpt) cc_final: 0.7699 (tpp) REVERT: E 34 MET cc_start: 0.7389 (tmm) cc_final: 0.7170 (mtp) REVERT: E 140 MET cc_start: 0.8830 (mmp) cc_final: 0.8120 (mmp) REVERT: D 109 LEU cc_start: 0.3933 (mt) cc_final: 0.3634 (mt) REVERT: D 140 MET cc_start: 0.5570 (ptt) cc_final: 0.4562 (mtt) outliers start: 7 outliers final: 4 residues processed: 178 average time/residue: 0.1554 time to fit residues: 45.8780 Evaluate side-chains 105 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 804 GLN A 935 GLN B 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN C 437 ASN C 544 ASN C 895 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1113 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054727 restraints weight = 153075.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055950 restraints weight = 79751.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056675 restraints weight = 50667.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057246 restraints weight = 37519.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057514 restraints weight = 30778.769| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26963 Z= 0.179 Angle : 0.738 17.531 36781 Z= 0.379 Chirality : 0.051 0.474 4282 Planarity : 0.005 0.071 4758 Dihedral : 7.011 55.440 4355 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 0.12 % Allowed : 5.75 % Favored : 94.13 % 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 are not related in a simple way. whole: -2.20 (0.14), residues: 3410 helix: -0.48 (0.16), residues: 973 sheet: -1.25 (0.22), residues: 502 loop : -2.11 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 403 TYR 0.035 0.002 TYR F 113 PHE 0.062 0.002 PHE F 144 TRP 0.017 0.001 TRP C 104 HIS 0.011 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00367 (26898) covalent geometry : angle 0.70426 (36620) SS BOND : bond 0.00820 ( 34) SS BOND : angle 1.98371 ( 68) hydrogen bonds : bond 0.06839 ( 1069) hydrogen bonds : angle 7.13437 ( 2988) link_BETA1-4 : bond 0.02814 ( 2) link_BETA1-4 : angle 7.97723 ( 6) link_NAG-ASN : bond 0.00695 ( 29) link_NAG-ASN : angle 3.78337 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 ASN cc_start: 0.9442 (m-40) cc_final: 0.8933 (m110) REVERT: A 1005 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8445 (tm-30) REVERT: B 160 TYR cc_start: 0.7472 (p90) cc_final: 0.7032 (p90) REVERT: B 313 TYR cc_start: 0.8948 (m-80) cc_final: 0.8698 (m-80) REVERT: B 996 LEU cc_start: 0.9690 (tp) cc_final: 0.9453 (tt) REVERT: C 451 TYR cc_start: 0.4866 (m-10) cc_final: 0.4605 (m-80) REVERT: C 777 ASN cc_start: 0.8751 (m110) cc_final: 0.8349 (m110) REVERT: E 34 MET cc_start: 0.6954 (tmm) cc_final: 0.6574 (mtp) REVERT: D 49 ARG cc_start: 0.5640 (tpm170) cc_final: 0.5371 (tpm170) REVERT: D 126 LEU cc_start: 0.6654 (pp) cc_final: 0.6440 (pp) REVERT: D 140 MET cc_start: 0.5685 (ptt) cc_final: 0.4685 (mmt) REVERT: F 132 PHE cc_start: 0.8318 (p90) cc_final: 0.8052 (t80) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.1555 time to fit residues: 47.5891 Evaluate side-chains 103 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 231 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 138 optimal weight: 0.0770 chunk 198 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN F 106 GLN F 138 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053360 restraints weight = 150231.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054796 restraints weight = 74995.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055738 restraints weight = 46190.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056319 restraints weight = 32595.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.056622 restraints weight = 25696.324| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26963 Z= 0.197 Angle : 0.689 16.886 36781 Z= 0.350 Chirality : 0.048 0.454 4282 Planarity : 0.005 0.052 4758 Dihedral : 6.465 52.060 4355 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % 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 are not related in a simple way. whole: -1.98 (0.14), residues: 3410 helix: -0.29 (0.16), residues: 987 sheet: -1.06 (0.21), residues: 549 loop : -2.02 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 815 TYR 0.027 0.002 TYR F 113 PHE 0.068 0.002 PHE F 144 TRP 0.021 0.002 TRP C 436 HIS 0.010 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00424 (26898) covalent geometry : angle 0.65640 (36620) SS BOND : bond 0.00544 ( 34) SS BOND : angle 1.70179 ( 68) hydrogen bonds : bond 0.05713 ( 1069) hydrogen bonds : angle 6.63560 ( 2988) link_BETA1-4 : bond 0.03308 ( 2) link_BETA1-4 : angle 7.34508 ( 6) link_NAG-ASN : bond 0.00660 ( 29) link_NAG-ASN : angle 3.62605 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 ASN cc_start: 0.9479 (m-40) cc_final: 0.9022 (m110) REVERT: A 1005 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 160 TYR cc_start: 0.7502 (p90) cc_final: 0.7099 (p90) REVERT: B 223 LEU cc_start: 0.9175 (mp) cc_final: 0.8959 (mp) REVERT: B 432 CYS cc_start: 0.7752 (m) cc_final: 0.7544 (m) REVERT: B 882 ILE cc_start: 0.9378 (mt) cc_final: 0.9126 (tt) REVERT: B 1050 MET cc_start: 0.8382 (ptp) cc_final: 0.7827 (ptp) REVERT: C 464 PHE cc_start: 0.6063 (m-10) cc_final: 0.5359 (p90) REVERT: C 697 MET cc_start: 0.8691 (ppp) cc_final: 0.8317 (ppp) REVERT: C 740 MET cc_start: 0.7793 (tpt) cc_final: 0.7579 (tpt) REVERT: C 777 ASN cc_start: 0.8997 (m110) cc_final: 0.8506 (m110) REVERT: E 34 MET cc_start: 0.7109 (tmm) cc_final: 0.6696 (mtp) REVERT: E 72 ILE cc_start: 0.8648 (pt) cc_final: 0.8182 (pt) REVERT: E 140 MET cc_start: 0.8910 (mmp) cc_final: 0.8282 (mmt) REVERT: E 144 PHE cc_start: 0.8026 (m-10) cc_final: 0.7819 (m-10) REVERT: D 49 ARG cc_start: 0.5742 (tpm170) cc_final: 0.5509 (tpm170) REVERT: D 140 MET cc_start: 0.5130 (ptt) cc_final: 0.3596 (mtt) outliers start: 2 outliers final: 1 residues processed: 174 average time/residue: 0.1497 time to fit residues: 44.7931 Evaluate side-chains 104 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 334 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 342 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 220 optimal weight: 0.0770 chunk 209 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.074820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053533 restraints weight = 148201.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054924 restraints weight = 75197.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055836 restraints weight = 46693.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.056402 restraints weight = 33081.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056817 restraints weight = 26161.470| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26963 Z= 0.205 Angle : 0.670 17.070 36781 Z= 0.340 Chirality : 0.048 0.491 4282 Planarity : 0.004 0.053 4758 Dihedral : 6.269 59.710 4355 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % 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 are not related in a simple way. whole: -1.83 (0.14), residues: 3410 helix: -0.12 (0.16), residues: 995 sheet: -0.93 (0.21), residues: 553 loop : -1.97 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 81 TYR 0.035 0.002 TYR C 873 PHE 0.033 0.002 PHE F 144 TRP 0.017 0.002 TRP A 436 HIS 0.010 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00444 (26898) covalent geometry : angle 0.63626 (36620) SS BOND : bond 0.00349 ( 34) SS BOND : angle 1.80925 ( 68) hydrogen bonds : bond 0.05002 ( 1069) hydrogen bonds : angle 6.35476 ( 2988) link_BETA1-4 : bond 0.03013 ( 2) link_BETA1-4 : angle 7.31802 ( 6) link_NAG-ASN : bond 0.00586 ( 29) link_NAG-ASN : angle 3.58773 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7278 (m-80) cc_final: 0.7010 (m-10) REVERT: A 1005 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8712 (tm-30) REVERT: B 160 TYR cc_start: 0.7555 (p90) cc_final: 0.7188 (p90) REVERT: B 223 LEU cc_start: 0.9196 (mp) cc_final: 0.8923 (mp) REVERT: B 313 TYR cc_start: 0.8890 (m-80) cc_final: 0.8186 (m-80) REVERT: B 432 CYS cc_start: 0.7988 (m) cc_final: 0.7754 (m) REVERT: B 882 ILE cc_start: 0.9483 (mt) cc_final: 0.9177 (tt) REVERT: B 1050 MET cc_start: 0.8307 (ptp) cc_final: 0.8089 (ptp) REVERT: C 464 PHE cc_start: 0.6277 (m-10) cc_final: 0.5535 (p90) REVERT: E 34 MET cc_start: 0.7088 (tmm) cc_final: 0.6670 (mtp) REVERT: E 72 ILE cc_start: 0.8685 (pt) cc_final: 0.8193 (pt) REVERT: E 140 MET cc_start: 0.8837 (mmp) cc_final: 0.7994 (mmp) REVERT: E 144 PHE cc_start: 0.7961 (m-10) cc_final: 0.7577 (m-10) REVERT: D 49 ARG cc_start: 0.5730 (tpm170) cc_final: 0.5099 (tpt90) REVERT: D 140 MET cc_start: 0.4922 (ptt) cc_final: 0.4245 (ptt) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.1592 time to fit residues: 44.1715 Evaluate side-chains 106 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 146 GLN F 138 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.073922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052715 restraints weight = 151113.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.054057 restraints weight = 78085.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054940 restraints weight = 48716.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055469 restraints weight = 34862.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.055861 restraints weight = 27544.200| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26963 Z= 0.267 Angle : 0.730 16.754 36781 Z= 0.369 Chirality : 0.049 0.456 4282 Planarity : 0.005 0.054 4758 Dihedral : 6.421 59.280 4355 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.00 % Favored : 90.94 % Rotamer: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3410 helix: -0.17 (0.16), residues: 998 sheet: -0.97 (0.21), residues: 561 loop : -2.01 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 81 TYR 0.019 0.002 TYR C 707 PHE 0.025 0.002 PHE F 144 TRP 0.016 0.002 TRP A 436 HIS 0.010 0.002 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00576 (26898) covalent geometry : angle 0.69783 (36620) SS BOND : bond 0.00463 ( 34) SS BOND : angle 1.97776 ( 68) hydrogen bonds : bond 0.05105 ( 1069) hydrogen bonds : angle 6.38325 ( 2988) link_BETA1-4 : bond 0.02847 ( 2) link_BETA1-4 : angle 7.20679 ( 6) link_NAG-ASN : bond 0.00632 ( 29) link_NAG-ASN : angle 3.65898 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7302 (m-80) cc_final: 0.7016 (m-10) REVERT: A 759 PHE cc_start: 0.8617 (m-80) cc_final: 0.8337 (m-80) REVERT: A 869 MET cc_start: 0.9562 (mtp) cc_final: 0.9205 (mtt) REVERT: A 1005 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8804 (tm-30) REVERT: B 135 PHE cc_start: 0.7418 (m-80) cc_final: 0.7157 (m-10) REVERT: B 160 TYR cc_start: 0.7742 (p90) cc_final: 0.7438 (p90) REVERT: B 223 LEU cc_start: 0.9152 (mp) cc_final: 0.8882 (mp) REVERT: B 313 TYR cc_start: 0.9001 (m-80) cc_final: 0.8239 (m-80) REVERT: B 432 CYS cc_start: 0.8131 (m) cc_final: 0.7845 (m) REVERT: B 882 ILE cc_start: 0.9481 (mt) cc_final: 0.9251 (tt) REVERT: B 1050 MET cc_start: 0.8447 (ptp) cc_final: 0.7746 (ptp) REVERT: C 104 TRP cc_start: 0.7415 (m-90) cc_final: 0.7212 (m-90) REVERT: C 464 PHE cc_start: 0.6490 (m-10) cc_final: 0.5644 (p90) REVERT: E 34 MET cc_start: 0.7194 (tmm) cc_final: 0.6726 (mtp) REVERT: E 72 ILE cc_start: 0.8757 (pt) cc_final: 0.8266 (pt) REVERT: E 140 MET cc_start: 0.8789 (mmp) cc_final: 0.7953 (mmp) REVERT: E 144 PHE cc_start: 0.8029 (m-10) cc_final: 0.7528 (m-10) REVERT: D 49 ARG cc_start: 0.5797 (tpm170) cc_final: 0.5111 (tpt90) REVERT: D 140 MET cc_start: 0.5362 (ptt) cc_final: 0.4941 (ptt) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.1544 time to fit residues: 39.8510 Evaluate side-chains 103 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 202 optimal weight: 9.9990 chunk 277 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 79 optimal weight: 0.0170 chunk 246 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.075456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053871 restraints weight = 147293.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055312 restraints weight = 74631.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056226 restraints weight = 46254.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056832 restraints weight = 32726.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057173 restraints weight = 25837.194| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26963 Z= 0.149 Angle : 0.642 17.329 36781 Z= 0.321 Chirality : 0.047 0.452 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.979 54.123 4355 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % 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 are not related in a simple way. whole: -1.60 (0.14), residues: 3410 helix: 0.06 (0.16), residues: 989 sheet: -0.65 (0.22), residues: 536 loop : -1.86 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.017 0.001 TYR C 380 PHE 0.037 0.002 PHE B 306 TRP 0.014 0.001 TRP A 436 HIS 0.011 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00321 (26898) covalent geometry : angle 0.60562 (36620) SS BOND : bond 0.00236 ( 34) SS BOND : angle 1.77038 ( 68) hydrogen bonds : bond 0.04481 ( 1069) hydrogen bonds : angle 6.02531 ( 2988) link_BETA1-4 : bond 0.03581 ( 2) link_BETA1-4 : angle 7.31674 ( 6) link_NAG-ASN : bond 0.00612 ( 29) link_NAG-ASN : angle 3.69457 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9593 (mtp) cc_final: 0.9136 (mtt) REVERT: A 1005 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8738 (tm-30) REVERT: B 135 PHE cc_start: 0.7225 (m-80) cc_final: 0.6927 (m-10) REVERT: B 160 TYR cc_start: 0.7545 (p90) cc_final: 0.7335 (p90) REVERT: B 313 TYR cc_start: 0.8948 (m-80) cc_final: 0.8194 (m-80) REVERT: B 432 CYS cc_start: 0.8100 (m) cc_final: 0.7727 (m) REVERT: B 467 ASP cc_start: 0.7573 (t0) cc_final: 0.7332 (t0) REVERT: C 464 PHE cc_start: 0.6218 (m-10) cc_final: 0.5440 (p90) REVERT: C 650 LEU cc_start: 0.9012 (tp) cc_final: 0.8746 (tt) REVERT: C 895 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7308 (pp30) REVERT: E 34 MET cc_start: 0.7193 (tmm) cc_final: 0.6713 (mtp) REVERT: E 72 ILE cc_start: 0.8747 (pt) cc_final: 0.8262 (pt) REVERT: E 140 MET cc_start: 0.8779 (mmp) cc_final: 0.7952 (mmp) REVERT: E 144 PHE cc_start: 0.7984 (m-10) cc_final: 0.7451 (m-10) REVERT: D 49 ARG cc_start: 0.5752 (tpm170) cc_final: 0.5061 (tpt90) REVERT: D 140 MET cc_start: 0.5609 (ptt) cc_final: 0.4106 (mmt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1628 time to fit residues: 44.4226 Evaluate side-chains 107 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 169 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 110 optimal weight: 40.0000 chunk 127 optimal weight: 0.0040 chunk 8 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN C 414 GLN C 755 GLN C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN F 138 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.076092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054584 restraints weight = 147210.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055996 restraints weight = 74710.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.056942 restraints weight = 46717.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057542 restraints weight = 33022.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057961 restraints weight = 25898.623| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26963 Z= 0.134 Angle : 0.621 16.883 36781 Z= 0.310 Chirality : 0.047 0.435 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.704 54.395 4355 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3410 helix: 0.20 (0.17), residues: 990 sheet: -0.45 (0.22), residues: 538 loop : -1.78 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 21 TYR 0.015 0.001 TYR A 873 PHE 0.019 0.001 PHE C 759 TRP 0.032 0.002 TRP B 436 HIS 0.012 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (26898) covalent geometry : angle 0.58794 (36620) SS BOND : bond 0.00306 ( 34) SS BOND : angle 1.67602 ( 68) hydrogen bonds : bond 0.04318 ( 1069) hydrogen bonds : angle 5.86791 ( 2988) link_BETA1-4 : bond 0.03251 ( 2) link_BETA1-4 : angle 7.15909 ( 6) link_NAG-ASN : bond 0.00570 ( 29) link_NAG-ASN : angle 3.43842 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.8429 (m-80) cc_final: 0.8164 (m-80) REVERT: A 777 ASN cc_start: 0.9401 (m-40) cc_final: 0.8944 (m110) REVERT: A 869 MET cc_start: 0.9538 (mtp) cc_final: 0.8964 (mtp) REVERT: A 1005 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 135 PHE cc_start: 0.7209 (m-80) cc_final: 0.6924 (m-10) REVERT: B 160 TYR cc_start: 0.7649 (p90) cc_final: 0.7407 (p90) REVERT: B 313 TYR cc_start: 0.8861 (m-80) cc_final: 0.8046 (m-80) REVERT: B 432 CYS cc_start: 0.8183 (m) cc_final: 0.7807 (m) REVERT: B 1050 MET cc_start: 0.8542 (ptp) cc_final: 0.7457 (ptp) REVERT: C 464 PHE cc_start: 0.6131 (m-10) cc_final: 0.5321 (p90) REVERT: C 650 LEU cc_start: 0.9013 (tp) cc_final: 0.8713 (tt) REVERT: E 34 MET cc_start: 0.7208 (tmm) cc_final: 0.6760 (mtp) REVERT: E 72 ILE cc_start: 0.8771 (pt) cc_final: 0.8286 (pt) REVERT: E 140 MET cc_start: 0.8748 (mmp) cc_final: 0.7949 (mmp) REVERT: E 144 PHE cc_start: 0.7952 (m-10) cc_final: 0.7427 (m-10) REVERT: D 49 ARG cc_start: 0.5717 (tpm170) cc_final: 0.5026 (tpt90) REVERT: D 140 MET cc_start: 0.5789 (ptt) cc_final: 0.4185 (mmt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1609 time to fit residues: 42.6956 Evaluate side-chains 107 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 158 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 146 GLN F 138 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.074427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053069 restraints weight = 149650.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054461 restraints weight = 76074.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055386 restraints weight = 47325.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055991 restraints weight = 33670.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056415 restraints weight = 26369.206| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26963 Z= 0.244 Angle : 0.698 16.817 36781 Z= 0.351 Chirality : 0.048 0.455 4282 Planarity : 0.004 0.055 4758 Dihedral : 6.038 58.105 4355 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.42 % Favored : 91.52 % Rotamer: Outliers : 0.16 % Allowed : 1.80 % Favored : 98.04 % 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 are not related in a simple way. whole: -1.55 (0.14), residues: 3410 helix: 0.12 (0.16), residues: 992 sheet: -0.62 (0.22), residues: 549 loop : -1.85 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 81 TYR 0.016 0.002 TYR B 873 PHE 0.022 0.002 PHE A 906 TRP 0.023 0.002 TRP B 436 HIS 0.017 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00529 (26898) covalent geometry : angle 0.66675 (36620) SS BOND : bond 0.00360 ( 34) SS BOND : angle 1.94584 ( 68) hydrogen bonds : bond 0.04574 ( 1069) hydrogen bonds : angle 6.02709 ( 2988) link_BETA1-4 : bond 0.03004 ( 2) link_BETA1-4 : angle 7.21333 ( 6) link_NAG-ASN : bond 0.00578 ( 29) link_NAG-ASN : angle 3.50196 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7226 (m-80) cc_final: 0.6951 (m-10) REVERT: A 869 MET cc_start: 0.9542 (mtp) cc_final: 0.9050 (mtp) REVERT: A 895 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7232 (pp30) REVERT: A 1005 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8886 (tm-30) REVERT: B 313 TYR cc_start: 0.8941 (m-80) cc_final: 0.8216 (m-80) REVERT: B 432 CYS cc_start: 0.8489 (m) cc_final: 0.8124 (m) REVERT: B 1050 MET cc_start: 0.8404 (ptp) cc_final: 0.7999 (ptp) REVERT: C 464 PHE cc_start: 0.6227 (m-10) cc_final: 0.5410 (p90) REVERT: C 650 LEU cc_start: 0.9075 (tp) cc_final: 0.8821 (tt) REVERT: E 34 MET cc_start: 0.7235 (tmm) cc_final: 0.6822 (mtp) REVERT: E 72 ILE cc_start: 0.8817 (pt) cc_final: 0.8440 (pt) REVERT: E 140 MET cc_start: 0.8684 (mmp) cc_final: 0.7894 (mmp) REVERT: E 144 PHE cc_start: 0.7895 (m-10) cc_final: 0.7326 (m-10) REVERT: D 49 ARG cc_start: 0.5720 (tpm170) cc_final: 0.4927 (tpt90) REVERT: D 140 MET cc_start: 0.5663 (ptt) cc_final: 0.5290 (ptt) REVERT: F 42 ARG cc_start: 0.5340 (tpm170) cc_final: 0.5095 (tpm170) outliers start: 4 outliers final: 0 residues processed: 147 average time/residue: 0.1690 time to fit residues: 41.4462 Evaluate side-chains 101 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 136 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 300 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1036 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.076545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054935 restraints weight = 145656.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056411 restraints weight = 72948.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.057361 restraints weight = 44782.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057946 restraints weight = 31637.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.058375 restraints weight = 24820.411| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26963 Z= 0.117 Angle : 0.618 16.526 36781 Z= 0.308 Chirality : 0.047 0.430 4282 Planarity : 0.004 0.056 4758 Dihedral : 5.585 51.889 4355 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.08 % Allowed : 0.43 % Favored : 99.49 % 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 are not related in a simple way. whole: -1.32 (0.14), residues: 3410 helix: 0.25 (0.17), residues: 988 sheet: -0.38 (0.23), residues: 520 loop : -1.69 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1107 TYR 0.029 0.001 TYR A 904 PHE 0.020 0.002 PHE F 102 TRP 0.019 0.001 TRP B 436 HIS 0.013 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00249 (26898) covalent geometry : angle 0.58703 (36620) SS BOND : bond 0.00293 ( 34) SS BOND : angle 1.59669 ( 68) hydrogen bonds : bond 0.04136 ( 1069) hydrogen bonds : angle 5.76088 ( 2988) link_BETA1-4 : bond 0.02803 ( 2) link_BETA1-4 : angle 7.01555 ( 6) link_NAG-ASN : bond 0.00591 ( 29) link_NAG-ASN : angle 3.33037 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 ASN cc_start: 0.9400 (m-40) cc_final: 0.8955 (m110) REVERT: A 869 MET cc_start: 0.9529 (mtp) cc_final: 0.9236 (mtp) REVERT: A 1005 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 313 TYR cc_start: 0.8840 (m-80) cc_final: 0.8061 (m-80) REVERT: B 432 CYS cc_start: 0.8496 (m) cc_final: 0.8107 (m) REVERT: B 434 ILE cc_start: 0.9463 (mt) cc_final: 0.9201 (mt) REVERT: C 464 PHE cc_start: 0.6000 (m-10) cc_final: 0.5162 (p90) REVERT: C 650 LEU cc_start: 0.9024 (tp) cc_final: 0.8687 (tt) REVERT: E 34 MET cc_start: 0.7154 (tmm) cc_final: 0.6754 (mtp) REVERT: E 72 ILE cc_start: 0.8842 (pt) cc_final: 0.8394 (pt) REVERT: E 140 MET cc_start: 0.8698 (mmp) cc_final: 0.7945 (mmp) REVERT: E 144 PHE cc_start: 0.7955 (m-10) cc_final: 0.7343 (m-10) REVERT: D 49 ARG cc_start: 0.5679 (tpm170) cc_final: 0.4918 (tpt90) REVERT: D 112 MET cc_start: 0.4383 (ppp) cc_final: 0.4140 (ppp) REVERT: D 126 LEU cc_start: 0.7016 (pp) cc_final: 0.6767 (pp) REVERT: D 140 MET cc_start: 0.5965 (ptt) cc_final: 0.4389 (mmt) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1592 time to fit residues: 43.7381 Evaluate side-chains 107 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 242 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 239 optimal weight: 0.0000 chunk 129 optimal weight: 0.0570 chunk 317 optimal weight: 4.9990 chunk 275 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 overall best weight: 1.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 207 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 501 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.076025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054365 restraints weight = 144630.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055831 restraints weight = 73111.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056707 restraints weight = 45160.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.057380 restraints weight = 32160.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057770 restraints weight = 25012.550| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26963 Z= 0.139 Angle : 0.617 16.583 36781 Z= 0.308 Chirality : 0.046 0.445 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.486 55.199 4355 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 are not related in a simple way. whole: -1.28 (0.14), residues: 3410 helix: 0.27 (0.17), residues: 997 sheet: -0.37 (0.22), residues: 544 loop : -1.67 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 66 TYR 0.013 0.001 TYR B 873 PHE 0.018 0.001 PHE A 377 TRP 0.019 0.001 TRP B 436 HIS 0.013 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00303 (26898) covalent geometry : angle 0.58518 (36620) SS BOND : bond 0.00246 ( 34) SS BOND : angle 1.59027 ( 68) hydrogen bonds : bond 0.04103 ( 1069) hydrogen bonds : angle 5.68398 ( 2988) link_BETA1-4 : bond 0.02899 ( 2) link_BETA1-4 : angle 7.05770 ( 6) link_NAG-ASN : bond 0.00591 ( 29) link_NAG-ASN : angle 3.34669 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6820 Ramachandran restraints generated. 3410 Oldfield, 0 Emsley, 3410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7228 (m-80) cc_final: 0.6940 (m-10) REVERT: A 777 ASN cc_start: 0.9398 (m-40) cc_final: 0.8976 (m110) REVERT: A 869 MET cc_start: 0.9519 (mtp) cc_final: 0.9025 (mtp) REVERT: A 1005 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8750 (tm-30) REVERT: B 135 PHE cc_start: 0.7265 (m-80) cc_final: 0.7006 (m-10) REVERT: B 223 LEU cc_start: 0.9066 (mp) cc_final: 0.8863 (mp) REVERT: B 313 TYR cc_start: 0.8807 (m-80) cc_final: 0.8058 (m-80) REVERT: B 432 CYS cc_start: 0.8590 (m) cc_final: 0.8226 (m) REVERT: B 434 ILE cc_start: 0.9445 (mt) cc_final: 0.9188 (mt) REVERT: B 1050 MET cc_start: 0.8485 (ptp) cc_final: 0.7484 (ptp) REVERT: C 464 PHE cc_start: 0.6000 (m-10) cc_final: 0.5132 (p90) REVERT: C 650 LEU cc_start: 0.9022 (tp) cc_final: 0.8691 (tt) REVERT: C 1050 MET cc_start: 0.8461 (ptp) cc_final: 0.7741 (ptp) REVERT: E 34 MET cc_start: 0.7262 (tmm) cc_final: 0.6842 (mtp) REVERT: E 72 ILE cc_start: 0.8826 (pt) cc_final: 0.8424 (pt) REVERT: E 140 MET cc_start: 0.8674 (mmp) cc_final: 0.7931 (mmp) REVERT: E 144 PHE cc_start: 0.7911 (m-10) cc_final: 0.7296 (m-10) REVERT: E 145 TYR cc_start: 0.9012 (t80) cc_final: 0.8741 (t80) REVERT: D 49 ARG cc_start: 0.5644 (tpm170) cc_final: 0.4824 (tpt90) REVERT: D 126 LEU cc_start: 0.7067 (pp) cc_final: 0.6852 (pp) REVERT: D 140 MET cc_start: 0.5944 (ptt) cc_final: 0.4332 (mmt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1663 time to fit residues: 41.4525 Evaluate side-chains 103 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 199 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 208 optimal weight: 0.4980 chunk 284 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 335 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 895 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.076603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054983 restraints weight = 144563.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056460 restraints weight = 73506.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.057413 restraints weight = 44955.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058056 restraints weight = 31550.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058427 restraints weight = 24463.155| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26963 Z= 0.121 Angle : 0.603 16.483 36781 Z= 0.301 Chirality : 0.046 0.439 4282 Planarity : 0.004 0.056 4758 Dihedral : 5.328 53.426 4355 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % 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 are not related in a simple way. whole: -1.22 (0.14), residues: 3410 helix: 0.30 (0.16), residues: 1007 sheet: -0.28 (0.22), residues: 544 loop : -1.65 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.035 0.001 TYR F 145 PHE 0.023 0.001 PHE F 144 TRP 0.017 0.001 TRP B 436 HIS 0.013 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00263 (26898) covalent geometry : angle 0.57294 (36620) SS BOND : bond 0.00209 ( 34) SS BOND : angle 1.46357 ( 68) hydrogen bonds : bond 0.04011 ( 1069) hydrogen bonds : angle 5.56972 ( 2988) link_BETA1-4 : bond 0.02884 ( 2) link_BETA1-4 : angle 7.00234 ( 6) link_NAG-ASN : bond 0.00554 ( 29) link_NAG-ASN : angle 3.26319 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.09 seconds wall clock time: 72 minutes 33.65 seconds (4353.65 seconds total)