Starting phenix.real_space_refine on Sun Jul 5 07:56:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kl9_22916/07_2026/7kl9_22916.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kl9_22916/07_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_22916/07_2026/7kl9_22916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kl9_22916/07_2026/7kl9_22916.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kl9_22916/07_2026/7kl9_22916.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kl9_22916/07_2026/7kl9_22916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kl9_22916/07_2026/7kl9_22916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kl9_22916/07_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 chiralities: 8 Time building chain proxies: 6.23, per 1000 atoms: 0.24 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 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: 1.17 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: 6.57 Time building geometry restraints manager: 3.45 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: 14451 17.95 - 35.90: 1160 35.90 - 53.86: 153 53.86 - 71.81: 36 71.81 - 89.76: 28 Dihedral angle restraints: 15828 sinusoidal: 5724 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 15825 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: 7.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.180 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 13.658 89.762 9198 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/Z covalent geometry : bond 0.00855 / 0.41 (26898) covalent geometry : angle 0.90322 / 0.49 (36620) SS BOND : bond 0.00553 / 0.38 ( 34) SS BOND : angle 2.70805 / 1.89 ( 68) hydrogen bonds : bond 0.33082 / 21.96 ( 1069) hydrogen bonds : angle 10.85558 / 7.61 ( 2988) link_BETA1-4 : bond 0.01587 / 0.79 ( 2) link_BETA1-4 : angle 7.03699 / 4.15 ( 6) link_NAG-ASN : bond 0.00935 / 0.53 ( 29) link_NAG-ASN : angle 4.36073 / 2.90 ( 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 : 1.069 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: 0.1754 time to fit residues: 51.2381 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 : 1.089 ------------------------------------------------------------------------------- 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... A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 913 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 644 GLN 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** F 106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.074921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053350 restraints weight = 149529.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054804 restraints weight = 74650.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055759 restraints weight = 45780.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056334 restraints weight = 32456.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056746 restraints weight = 25678.429| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26963 Z= 0.189 Angle : 0.751 18.513 36781 Z= 0.388 Chirality : 0.050 0.448 4282 Planarity : 0.005 0.077 4758 Dihedral : 5.952 31.476 3704 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % 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: -2.18 (0.14), residues: 3410 helix: -0.44 (0.16), residues: 963 sheet: -1.12 (0.22), residues: 515 loop : -2.14 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 403 TYR 0.030 0.002 TYR F 113 PHE 0.055 0.002 PHE F 144 TRP 0.017 0.002 TRP C 104 HIS 0.011 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (26898) covalent geometry : angle 0.71674 / 0.38 (36620) SS BOND : bond 0.00491 / 0.33 ( 34) SS BOND : angle 2.02047 / 1.28 ( 68) hydrogen bonds : bond 0.07378 / 4.91 ( 1069) hydrogen bonds : angle 7.34309 / 5.14 ( 2988) link_BETA1-4 : bond 0.03521 / 1.68 ( 2) link_BETA1-4 : angle 8.31399 / 4.93 ( 6) link_NAG-ASN : bond 0.00637 / 0.41 ( 29) link_NAG-ASN : angle 3.73456 / 2.50 ( 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 173 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 ASN cc_start: 0.9458 (m-40) cc_final: 0.8931 (m110) REVERT: A 1005 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 160 TYR cc_start: 0.7620 (p90) cc_final: 0.7116 (p90) REVERT: B 882 ILE cc_start: 0.9334 (mt) cc_final: 0.9075 (tt) REVERT: C 346 ARG cc_start: 0.6910 (tmt170) cc_final: 0.6474 (tmt170) REVERT: C 390 LEU cc_start: 0.8295 (tp) cc_final: 0.8092 (tp) REVERT: C 740 MET cc_start: 0.7761 (tpt) cc_final: 0.7448 (tpp) REVERT: C 777 ASN cc_start: 0.8743 (m110) cc_final: 0.8339 (m110) REVERT: E 34 MET cc_start: 0.6894 (tmm) cc_final: 0.6551 (mtp) REVERT: E 72 ILE cc_start: 0.8559 (pt) cc_final: 0.8315 (pt) REVERT: D 140 MET cc_start: 0.5656 (ptt) cc_final: 0.4447 (mtt) REVERT: F 132 PHE cc_start: 0.8055 (p90) cc_final: 0.7710 (t80) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.1653 time to fit residues: 47.8670 Evaluate side-chains 101 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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: 10.0000 chunk 191 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 138 optimal weight: 0.0040 chunk 198 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 498 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 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1054 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.074733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053163 restraints weight = 150291.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054603 restraints weight = 75188.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055538 restraints weight = 46195.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056148 restraints weight = 32668.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056574 restraints weight = 25687.741| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26963 Z= 0.204 Angle : 0.690 16.678 36781 Z= 0.353 Chirality : 0.048 0.443 4282 Planarity : 0.005 0.053 4758 Dihedral : 5.592 36.767 3704 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.68 % Favored : 92.26 % Rotamer: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % 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: -2.04 (0.14), residues: 3410 helix: -0.35 (0.16), residues: 987 sheet: -1.05 (0.21), residues: 550 loop : -2.06 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 143 TYR 0.022 0.002 TYR C 380 PHE 0.025 0.002 PHE F 144 TRP 0.022 0.002 TRP A 436 HIS 0.012 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (26898) covalent geometry : angle 0.65909 / 0.35 (36620) SS BOND : bond 0.00361 / 0.26 ( 34) SS BOND : angle 1.84204 / 1.09 ( 68) hydrogen bonds : bond 0.05709 / 3.79 ( 1069) hydrogen bonds : angle 6.69743 / 4.67 ( 2988) link_BETA1-4 : bond 0.02973 / 1.46 ( 2) link_BETA1-4 : angle 7.12705 / 4.22 ( 6) link_NAG-ASN : bond 0.00587 / 0.37 ( 29) link_NAG-ASN : angle 3.54039 / 2.36 ( 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 173 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 777 ASN cc_start: 0.9490 (m-40) cc_final: 0.9033 (m110) REVERT: A 1005 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 160 TYR cc_start: 0.7419 (p90) cc_final: 0.7043 (p90) REVERT: B 223 LEU cc_start: 0.9190 (mp) cc_final: 0.8958 (mp) REVERT: B 432 CYS cc_start: 0.7778 (m) cc_final: 0.7570 (m) REVERT: B 882 ILE cc_start: 0.9367 (mt) cc_final: 0.9108 (tt) REVERT: C 464 PHE cc_start: 0.6070 (m-10) cc_final: 0.5374 (p90) REVERT: C 697 MET cc_start: 0.8667 (ppp) cc_final: 0.8293 (ppp) REVERT: C 740 MET cc_start: 0.7804 (tpt) cc_final: 0.7546 (tpt) REVERT: C 777 ASN cc_start: 0.9001 (m110) cc_final: 0.8508 (m110) REVERT: E 34 MET cc_start: 0.7106 (tmm) cc_final: 0.6799 (mtp) REVERT: E 72 ILE cc_start: 0.8694 (pt) cc_final: 0.8426 (pt) REVERT: E 91 ASN cc_start: 0.9331 (m110) cc_final: 0.9058 (m110) REVERT: E 140 MET cc_start: 0.8967 (tpp) cc_final: 0.8297 (tpp) REVERT: E 144 PHE cc_start: 0.8082 (m-10) cc_final: 0.7811 (m-10) REVERT: D 49 ARG cc_start: 0.5783 (tpm170) cc_final: 0.5370 (tpm170) REVERT: D 140 MET cc_start: 0.4925 (ptt) cc_final: 0.4202 (ptt) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.1552 time to fit residues: 45.7894 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 : 1.065 ------------------------------------------------------------------------------- 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: 1.9990 chunk 255 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 chunk 161 optimal weight: 1.9990 chunk 220 optimal weight: 0.0000 chunk 209 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 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 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1142 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 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 = 0.3627 r_free = 0.3627 target = 0.074964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053687 restraints weight = 148092.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055096 restraints weight = 75729.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055947 restraints weight = 47047.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056592 restraints weight = 33580.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056934 restraints weight = 26264.208| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26963 Z= 0.188 Angle : 0.669 16.812 36781 Z= 0.338 Chirality : 0.048 0.472 4282 Planarity : 0.004 0.053 4758 Dihedral : 5.427 30.909 3704 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: -1.85 (0.14), residues: 3410 helix: -0.14 (0.16), residues: 991 sheet: -0.90 (0.22), residues: 537 loop : -1.99 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 81 TYR 0.020 0.002 TYR D 113 PHE 0.034 0.002 PHE A 201 TRP 0.017 0.001 TRP A 436 HIS 0.013 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (26898) covalent geometry : angle 0.63579 / 0.33 (36620) SS BOND : bond 0.00293 / 0.21 ( 34) SS BOND : angle 1.74572 / 1.04 ( 68) hydrogen bonds : bond 0.05022 / 3.36 ( 1069) hydrogen bonds : angle 6.43162 / 4.48 ( 2988) link_BETA1-4 : bond 0.03048 / 1.46 ( 2) link_BETA1-4 : angle 7.21559 / 4.29 ( 6) link_NAG-ASN : bond 0.00640 / 0.45 ( 29) link_NAG-ASN : angle 3.63510 / 2.44 ( 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 169 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7257 (m-80) cc_final: 0.6991 (m-10) REVERT: A 777 ASN cc_start: 0.9498 (m-40) cc_final: 0.9050 (m110) REVERT: A 1005 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8677 (tm-30) REVERT: B 160 TYR cc_start: 0.7510 (p90) cc_final: 0.7122 (p90) REVERT: B 223 LEU cc_start: 0.9194 (mp) cc_final: 0.8948 (mp) REVERT: B 313 TYR cc_start: 0.8926 (m-80) cc_final: 0.8243 (m-80) REVERT: B 432 CYS cc_start: 0.7895 (m) cc_final: 0.7669 (m) REVERT: B 882 ILE cc_start: 0.9412 (mt) cc_final: 0.9156 (tt) REVERT: C 464 PHE cc_start: 0.6250 (m-10) cc_final: 0.5519 (p90) REVERT: C 740 MET cc_start: 0.7849 (tpt) cc_final: 0.7626 (tpt) REVERT: C 902 MET cc_start: 0.9536 (mmm) cc_final: 0.9156 (mmt) REVERT: E 34 MET cc_start: 0.7127 (tmm) cc_final: 0.6837 (mtp) REVERT: E 72 ILE cc_start: 0.8727 (pt) cc_final: 0.8459 (pt) REVERT: E 91 ASN cc_start: 0.9338 (m110) cc_final: 0.9116 (m-40) REVERT: E 140 MET cc_start: 0.8964 (tpp) cc_final: 0.8224 (tpp) REVERT: D 49 ARG cc_start: 0.5731 (tpm170) cc_final: 0.5082 (tpt90) REVERT: D 140 MET cc_start: 0.5333 (ptt) cc_final: 0.4883 (ptt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1585 time to fit residues: 45.2091 Evaluate side-chains 105 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 0.3980 chunk 33 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 228 optimal weight: 8.9990 chunk 157 optimal weight: 0.0870 chunk 7 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 overall best weight: 1.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 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 317 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.076045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054612 restraints weight = 147153.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056100 restraints weight = 73809.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057058 restraints weight = 45190.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.057691 restraints weight = 31783.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.058061 restraints weight = 24783.837| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26963 Z= 0.139 Angle : 0.626 16.202 36781 Z= 0.314 Chirality : 0.047 0.438 4282 Planarity : 0.004 0.054 4758 Dihedral : 5.139 31.334 3704 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % 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: -1.59 (0.14), residues: 3410 helix: 0.03 (0.16), residues: 1000 sheet: -0.61 (0.22), residues: 521 loop : -1.84 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 60 TYR 0.035 0.001 TYR C 873 PHE 0.033 0.001 PHE E 144 TRP 0.012 0.001 TRP A 436 HIS 0.012 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (26898) covalent geometry : angle 0.59309 / 0.31 (36620) SS BOND : bond 0.00437 / 0.31 ( 34) SS BOND : angle 1.61803 / 0.93 ( 68) hydrogen bonds : bond 0.04588 / 3.08 ( 1069) hydrogen bonds : angle 6.08669 / 4.23 ( 2988) link_BETA1-4 : bond 0.02581 / 1.23 ( 2) link_BETA1-4 : angle 6.94824 / 4.12 ( 6) link_NAG-ASN : bond 0.00643 / 0.39 ( 29) link_NAG-ASN : angle 3.49928 / 2.32 ( 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 171 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9105 (pmm) cc_final: 0.8769 (pmm) REVERT: A 869 MET cc_start: 0.9516 (mtp) cc_final: 0.9279 (mtp) REVERT: A 1005 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8627 (tm-30) REVERT: B 160 TYR cc_start: 0.7489 (p90) cc_final: 0.7168 (p90) REVERT: B 313 TYR cc_start: 0.8954 (m-80) cc_final: 0.8158 (m-80) REVERT: B 432 CYS cc_start: 0.7876 (m) cc_final: 0.7630 (m) REVERT: B 1050 MET cc_start: 0.8394 (ptp) cc_final: 0.8006 (ptp) REVERT: C 464 PHE cc_start: 0.6202 (m-10) cc_final: 0.5385 (p90) REVERT: C 740 MET cc_start: 0.7704 (tpt) cc_final: 0.7477 (tpt) REVERT: E 34 MET cc_start: 0.7159 (tmm) cc_final: 0.6765 (mtp) REVERT: E 72 ILE cc_start: 0.8659 (pt) cc_final: 0.8357 (pt) REVERT: E 140 MET cc_start: 0.9022 (tpp) cc_final: 0.8640 (tpp) REVERT: D 49 ARG cc_start: 0.5769 (tpm170) cc_final: 0.5125 (tpt90) REVERT: D 140 MET cc_start: 0.5772 (ptt) cc_final: 0.4290 (mmt) REVERT: F 34 MET cc_start: 0.1670 (mmt) cc_final: 0.1422 (mmt) REVERT: F 115 GLU cc_start: 0.8809 (pt0) cc_final: 0.8557 (tm-30) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1524 time to fit residues: 44.4224 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 : 0.985 ------------------------------------------------------------------------------- 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: 0.0870 chunk 277 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 330 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 114 optimal weight: 0.0050 chunk 181 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1010 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** E 146 GLN F 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.076330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054924 restraints weight = 146646.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056379 restraints weight = 74326.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057263 restraints weight = 45832.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.057929 restraints weight = 32692.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058293 restraints weight = 25595.842| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26963 Z= 0.130 Angle : 0.618 16.472 36781 Z= 0.308 Chirality : 0.047 0.450 4282 Planarity : 0.004 0.056 4758 Dihedral : 4.944 27.021 3704 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.08 % Rotamer: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % 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: -1.43 (0.14), residues: 3410 helix: 0.13 (0.16), residues: 1001 sheet: -0.45 (0.23), residues: 513 loop : -1.74 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 97 TYR 0.016 0.001 TYR F 145 PHE 0.023 0.001 PHE A 201 TRP 0.010 0.001 TRP A 436 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (26898) covalent geometry : angle 0.58524 / 0.30 (36620) SS BOND : bond 0.00243 / 0.17 ( 34) SS BOND : angle 1.64297 / 0.94 ( 68) hydrogen bonds : bond 0.04367 / 2.93 ( 1069) hydrogen bonds : angle 5.90602 / 4.10 ( 2988) link_BETA1-4 : bond 0.02958 / 1.41 ( 2) link_BETA1-4 : angle 6.96192 / 4.12 ( 6) link_NAG-ASN : bond 0.00572 / 0.35 ( 29) link_NAG-ASN : angle 3.43961 / 2.29 ( 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 172 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.046 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: A 731 MET cc_start: 0.9150 (pmm) cc_final: 0.8894 (pmm) REVERT: A 777 ASN cc_start: 0.9261 (m-40) cc_final: 0.8867 (m110) REVERT: A 869 MET cc_start: 0.9566 (mtp) cc_final: 0.9201 (mtp) REVERT: A 1005 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 1058 HIS cc_start: 0.7924 (m-70) cc_final: 0.7716 (m-70) REVERT: B 160 TYR cc_start: 0.7488 (p90) cc_final: 0.7158 (p90) REVERT: B 223 LEU cc_start: 0.9106 (mp) cc_final: 0.8847 (mp) REVERT: B 313 TYR cc_start: 0.8883 (m-80) cc_final: 0.7983 (m-80) REVERT: B 329 PHE cc_start: 0.7820 (m-80) cc_final: 0.7614 (m-10) REVERT: B 432 CYS cc_start: 0.8162 (m) cc_final: 0.7857 (m) REVERT: B 1050 MET cc_start: 0.8527 (ptp) cc_final: 0.7584 (ptp) REVERT: C 40 ASP cc_start: 0.8988 (p0) cc_final: 0.8681 (p0) REVERT: C 464 PHE cc_start: 0.6276 (m-10) cc_final: 0.5387 (p90) REVERT: C 697 MET cc_start: 0.8549 (ppp) cc_final: 0.8195 (ppp) REVERT: E 34 MET cc_start: 0.7263 (tmm) cc_final: 0.6992 (mtp) REVERT: E 72 ILE cc_start: 0.8732 (pt) cc_final: 0.8419 (pt) REVERT: E 140 MET cc_start: 0.9074 (tpp) cc_final: 0.8312 (tpp) REVERT: D 49 ARG cc_start: 0.5824 (tpm170) cc_final: 0.5148 (tpt90) REVERT: D 140 MET cc_start: 0.5542 (ptt) cc_final: 0.4032 (mmt) REVERT: F 115 GLU cc_start: 0.8777 (pt0) cc_final: 0.8501 (tm-30) outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.1684 time to fit residues: 48.6748 Evaluate side-chains 112 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 4.9990 chunk 219 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 0.0030 chunk 327 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.076501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054142 restraints weight = 151930.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055375 restraints weight = 79953.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056173 restraints weight = 50976.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056646 restraints weight = 37458.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056920 restraints weight = 30629.710| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26963 Z= 0.221 Angle : 0.670 16.851 36781 Z= 0.338 Chirality : 0.047 0.440 4282 Planarity : 0.004 0.053 4758 Dihedral : 5.123 32.327 3704 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -1.49 (0.14), residues: 3410 helix: 0.14 (0.16), residues: 1000 sheet: -0.57 (0.22), residues: 535 loop : -1.79 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 81 TYR 0.036 0.002 TYR C 873 PHE 0.034 0.002 PHE B 306 TRP 0.031 0.002 TRP C 436 HIS 0.014 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (26898) covalent geometry : angle 0.63881 / 0.33 (36620) SS BOND : bond 0.00470 / 0.27 ( 34) SS BOND : angle 1.93662 / 1.22 ( 68) hydrogen bonds : bond 0.04555 / 3.06 ( 1069) hydrogen bonds : angle 5.96124 / 4.15 ( 2988) link_BETA1-4 : bond 0.02963 / 1.42 ( 2) link_BETA1-4 : angle 7.12589 / 4.23 ( 6) link_NAG-ASN : bond 0.00567 / 0.37 ( 29) link_NAG-ASN : angle 3.43324 / 2.30 ( 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 153 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9167 (pmm) cc_final: 0.8955 (pmm) REVERT: A 869 MET cc_start: 0.9487 (mtp) cc_final: 0.9107 (mtp) REVERT: A 1005 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 313 TYR cc_start: 0.9018 (m-80) cc_final: 0.8320 (m-80) REVERT: B 432 CYS cc_start: 0.8236 (m) cc_final: 0.7927 (m) REVERT: B 467 ASP cc_start: 0.7610 (t0) cc_final: 0.7297 (t0) REVERT: C 464 PHE cc_start: 0.6606 (m-10) cc_final: 0.6147 (p90) REVERT: C 697 MET cc_start: 0.8713 (ppp) cc_final: 0.8077 (ppp) REVERT: E 34 MET cc_start: 0.7355 (tmm) cc_final: 0.7092 (mtp) REVERT: E 72 ILE cc_start: 0.8691 (pt) cc_final: 0.8413 (pt) REVERT: E 140 MET cc_start: 0.8896 (mmt) cc_final: 0.7853 (mmp) REVERT: E 149 LEU cc_start: 0.8609 (mt) cc_final: 0.8391 (mm) REVERT: D 49 ARG cc_start: 0.5553 (tpm170) cc_final: 0.5038 (tpt90) REVERT: D 140 MET cc_start: 0.5675 (ptt) cc_final: 0.5324 (ptt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1693 time to fit residues: 43.5095 Evaluate side-chains 105 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 2.9990 chunk 105 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 136 optimal weight: 0.0870 chunk 48 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 895 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN E 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.075843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054570 restraints weight = 152796.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055440 restraints weight = 89938.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055918 restraints weight = 62146.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056577 restraints weight = 37892.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056602 restraints weight = 31605.305| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 26963 Z= 0.246 Angle : 0.708 16.748 36781 Z= 0.358 Chirality : 0.048 0.445 4282 Planarity : 0.004 0.054 4758 Dihedral : 5.350 26.963 3704 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.48 % Favored : 91.47 % Rotamer: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.12 % 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: 0.07 (0.16), residues: 1000 sheet: -0.74 (0.22), residues: 551 loop : -1.85 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 328 TYR 0.031 0.002 TYR A 495 PHE 0.034 0.002 PHE D 144 TRP 0.025 0.002 TRP B 436 HIS 0.013 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (26898) covalent geometry : angle 0.67601 / 0.35 (36620) SS BOND : bond 0.00361 / 0.25 ( 34) SS BOND : angle 2.07133 / 1.16 ( 68) hydrogen bonds : bond 0.04613 / 3.11 ( 1069) hydrogen bonds : angle 6.06316 / 4.21 ( 2988) link_BETA1-4 : bond 0.02894 / 1.40 ( 2) link_BETA1-4 : angle 7.08104 / 4.20 ( 6) link_NAG-ASN : bond 0.00662 / 0.46 ( 29) link_NAG-ASN : angle 3.59660 / 2.42 ( 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 146 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9478 (mtp) cc_final: 0.9038 (mtp) REVERT: A 1005 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 160 TYR cc_start: 0.8033 (p90) cc_final: 0.7808 (p90) REVERT: B 223 LEU cc_start: 0.9103 (mp) cc_final: 0.8857 (mp) REVERT: B 313 TYR cc_start: 0.8989 (m-80) cc_final: 0.8302 (m-80) REVERT: B 432 CYS cc_start: 0.8539 (m) cc_final: 0.8213 (m) REVERT: B 467 ASP cc_start: 0.7469 (t0) cc_final: 0.7248 (t0) REVERT: B 1050 MET cc_start: 0.8349 (ptp) cc_final: 0.7838 (ptp) REVERT: C 104 TRP cc_start: 0.7338 (m-90) cc_final: 0.7028 (m-90) REVERT: C 464 PHE cc_start: 0.6634 (m-10) cc_final: 0.5926 (p90) REVERT: C 697 MET cc_start: 0.8805 (ppp) cc_final: 0.8242 (ppp) REVERT: C 1050 MET cc_start: 0.8435 (ptp) cc_final: 0.7893 (ptp) REVERT: E 34 MET cc_start: 0.7499 (tmm) cc_final: 0.6965 (mtp) REVERT: E 72 ILE cc_start: 0.8875 (pt) cc_final: 0.8564 (pt) REVERT: E 140 MET cc_start: 0.8903 (mmt) cc_final: 0.7935 (mmp) REVERT: E 149 LEU cc_start: 0.8696 (mt) cc_final: 0.8467 (mm) REVERT: D 49 ARG cc_start: 0.5646 (tpm170) cc_final: 0.4968 (tpt90) REVERT: D 126 LEU cc_start: 0.6887 (pp) cc_final: 0.6645 (pp) REVERT: D 140 MET cc_start: 0.5606 (ptt) cc_final: 0.5231 (ptt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.1745 time to fit residues: 42.4294 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 : 1.696 ------------------------------------------------------------------------------- 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: 3.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 178 optimal weight: 0.0170 chunk 194 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 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** B 777 ASN ** C 913 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 = 0.3654 r_free = 0.3654 target = 0.076062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054371 restraints weight = 145606.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055845 restraints weight = 73187.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056784 restraints weight = 44865.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.057428 restraints weight = 31662.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057771 restraints weight = 24709.751| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26963 Z= 0.130 Angle : 0.630 16.750 36781 Z= 0.314 Chirality : 0.047 0.423 4282 Planarity : 0.004 0.053 4758 Dihedral : 5.036 30.870 3704 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % 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 : 0.03 % 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: -1.39 (0.14), residues: 3410 helix: 0.18 (0.16), residues: 1004 sheet: -0.43 (0.22), residues: 521 loop : -1.74 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.032 0.001 TYR C 873 PHE 0.028 0.002 PHE F 102 TRP 0.018 0.002 TRP B 436 HIS 0.012 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26898) covalent geometry : angle 0.59824 / 0.31 (36620) SS BOND : bond 0.00256 / 0.19 ( 34) SS BOND : angle 1.61287 / 1.05 ( 68) hydrogen bonds : bond 0.04201 / 2.83 ( 1069) hydrogen bonds : angle 5.80899 / 4.02 ( 2988) link_BETA1-4 : bond 0.03007 / 1.44 ( 2) link_BETA1-4 : angle 7.00942 / 4.15 ( 6) link_NAG-ASN : bond 0.00571 / 0.36 ( 29) link_NAG-ASN : angle 3.44641 / 2.31 ( 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 157 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9458 (mtp) cc_final: 0.9014 (mtp) REVERT: A 1005 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8714 (tm-30) REVERT: A 1058 HIS cc_start: 0.7807 (m-70) cc_final: 0.7582 (m-70) REVERT: B 223 LEU cc_start: 0.9042 (mp) cc_final: 0.8798 (mp) REVERT: B 313 TYR cc_start: 0.8863 (m-80) cc_final: 0.8065 (m-80) REVERT: B 432 CYS cc_start: 0.8517 (m) cc_final: 0.8165 (m) REVERT: B 434 ILE cc_start: 0.9439 (mt) cc_final: 0.9174 (mt) REVERT: B 902 MET cc_start: 0.8849 (mmt) cc_final: 0.8543 (mmt) REVERT: C 464 PHE cc_start: 0.6365 (m-10) cc_final: 0.5282 (p90) REVERT: C 697 MET cc_start: 0.8707 (ppp) cc_final: 0.8115 (ppp) REVERT: E 34 MET cc_start: 0.7316 (tmm) cc_final: 0.6942 (mtp) REVERT: E 72 ILE cc_start: 0.8804 (pt) cc_final: 0.8484 (pt) REVERT: E 140 MET cc_start: 0.8855 (mmt) cc_final: 0.7661 (mmp) REVERT: E 144 PHE cc_start: 0.7863 (m-10) cc_final: 0.7590 (m-10) REVERT: D 49 ARG cc_start: 0.5764 (tpm170) cc_final: 0.5037 (tpt90) REVERT: D 126 LEU cc_start: 0.6900 (pp) cc_final: 0.6681 (pp) REVERT: D 140 MET cc_start: 0.5798 (ptt) cc_final: 0.4130 (mmt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1748 time to fit residues: 45.5752 Evaluate side-chains 99 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 239 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 235 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1010 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** ** 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** E 146 GLN F 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.075252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053769 restraints weight = 147123.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055231 restraints weight = 73812.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056168 restraints weight = 45293.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056793 restraints weight = 31920.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057202 restraints weight = 24830.413| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26963 Z= 0.185 Angle : 0.660 16.588 36781 Z= 0.330 Chirality : 0.047 0.442 4282 Planarity : 0.004 0.055 4758 Dihedral : 5.049 26.469 3704 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3410 helix: 0.22 (0.16), residues: 1003 sheet: -0.47 (0.22), residues: 529 loop : -1.74 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 97 TYR 0.018 0.001 TYR C 873 PHE 0.080 0.002 PHE F 144 TRP 0.018 0.002 TRP B 436 HIS 0.011 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (26898) covalent geometry : angle 0.62666 / 0.32 (36620) SS BOND : bond 0.00305 / 0.22 ( 34) SS BOND : angle 1.73884 / 1.08 ( 68) hydrogen bonds : bond 0.04280 / 2.89 ( 1069) hydrogen bonds : angle 5.83905 / 4.04 ( 2988) link_BETA1-4 : bond 0.03019 / 1.44 ( 2) link_BETA1-4 : angle 7.01658 / 4.16 ( 6) link_NAG-ASN : bond 0.00549 / 0.35 ( 29) link_NAG-ASN : angle 3.63300 / 2.40 ( 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: 2 poor density : 148 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7320 (m-80) cc_final: 0.6954 (m-10) REVERT: A 869 MET cc_start: 0.9491 (mtp) cc_final: 0.9098 (mtp) REVERT: A 1005 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 1058 HIS cc_start: 0.7784 (m-70) cc_final: 0.7560 (m-70) REVERT: B 223 LEU cc_start: 0.9060 (mp) cc_final: 0.8262 (mp) REVERT: B 313 TYR cc_start: 0.8912 (m-80) cc_final: 0.8152 (m-80) REVERT: B 432 CYS cc_start: 0.8556 (m) cc_final: 0.8246 (m) REVERT: B 434 ILE cc_start: 0.9451 (mt) cc_final: 0.9194 (mt) REVERT: C 464 PHE cc_start: 0.6468 (m-10) cc_final: 0.5313 (p90) REVERT: C 697 MET cc_start: 0.8729 (ppp) cc_final: 0.8135 (ppp) REVERT: C 1050 MET cc_start: 0.8504 (ptp) cc_final: 0.7781 (ptp) REVERT: E 34 MET cc_start: 0.7394 (tmm) cc_final: 0.6850 (mtp) REVERT: E 72 ILE cc_start: 0.8627 (pt) cc_final: 0.8338 (pt) REVERT: E 140 MET cc_start: 0.8848 (mmt) cc_final: 0.8334 (mmp) REVERT: D 49 ARG cc_start: 0.5760 (tpm170) cc_final: 0.5006 (tpt90) REVERT: D 126 LEU cc_start: 0.6959 (pp) cc_final: 0.6742 (pp) REVERT: D 140 MET cc_start: 0.5945 (ptt) cc_final: 0.4207 (mmt) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.1766 time to fit residues: 43.8093 Evaluate side-chains 96 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 7.9990 chunk 155 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 208 optimal weight: 0.0040 chunk 284 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 335 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** 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 501 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.076393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054790 restraints weight = 145713.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056281 restraints weight = 74114.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057230 restraints weight = 45209.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057853 restraints weight = 31663.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058204 restraints weight = 24793.497| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26963 Z= 0.126 Angle : 0.618 16.581 36781 Z= 0.307 Chirality : 0.046 0.429 4282 Planarity : 0.004 0.056 4758 Dihedral : 4.851 26.910 3704 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.30 % 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: -1.23 (0.14), residues: 3410 helix: 0.33 (0.16), residues: 1003 sheet: -0.27 (0.22), residues: 537 loop : -1.68 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 66 TYR 0.016 0.001 TYR C 873 PHE 0.063 0.002 PHE F 144 TRP 0.016 0.001 TRP B 436 HIS 0.012 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (26898) covalent geometry : angle 0.58600 / 0.30 (36620) SS BOND : bond 0.00200 / 0.14 ( 34) SS BOND : angle 1.44783 / 0.88 ( 68) hydrogen bonds : bond 0.04061 / 2.73 ( 1069) hydrogen bonds : angle 5.67051 / 3.91 ( 2988) link_BETA1-4 : bond 0.02979 / 1.42 ( 2) link_BETA1-4 : angle 6.95412 / 4.11 ( 6) link_NAG-ASN : bond 0.00562 / 0.35 ( 29) link_NAG-ASN : angle 3.45070 / 2.28 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4436.28 seconds wall clock time: 78 minutes 5.12 seconds (4685.12 seconds total)