Starting phenix.real_space_refine on Mon Jul 6 21:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yc5_33734/07_2026/7yc5_33734.cif" } resolution = 3.1 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= 0.002 sd= 0.202 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 159 5.16 5 C 24808 2.51 5 N 6494 2.21 5 O 7696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "B" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "C" Number of atoms: 8094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8094 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 8 Chain: "D" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "E" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "F" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3313 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 2 Chain: "G" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1496 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Chain: "A" 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: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.06, per 1000 atoms: 0.21 Number of scatterers: 39157 At special positions: 0 Unit cell: (137.899, 144.208, 248.759, 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 159 16.00 O 7696 8.00 N 6494 7.00 C 24808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 458 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 283 " - pdb=" SG CYS E 350 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 165 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 801 " " NAG C1407 " - " ASN C1074 " " NAG C1408 " - " ASN C1098 " " NAG C1409 " - " ASN C1134 " Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.9 seconds 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9294 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 110 sheets defined 17.7% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.042A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.658A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.680A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.065A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.200A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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: 3.862A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.261A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1148 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.041A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.661A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.775A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.504A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.151A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.204A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.875A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.040A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.660A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.538A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.226A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.265A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 984 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1141 through 1148 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.553A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 91' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP D 219 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 220 " --> pdb=" O SER D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.617A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 removed outlier: 4.223A pdb=" N GLU D 451 " --> pdb=" O LYS D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.555A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP E 219 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 220 " --> pdb=" O SER E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'E' and resid 385 through 392 removed outlier: 3.615A pdb=" N LEU E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU E 451 " --> pdb=" O LYS E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.554A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'F' and resid 216 through 220 removed outlier: 3.526A pdb=" N ASP F 219 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 220 " --> pdb=" O SER F 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 216 through 220' Processing helix chain 'F' and resid 385 through 392 removed outlier: 3.616A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 452 removed outlier: 4.222A pdb=" N GLU F 451 " --> pdb=" O LYS F 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 170 through 172 No H-bonds generated for 'chain 'G' and resid 170 through 172' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.681A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 170 through 172 No H-bonds generated for 'chain 'I' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.167A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.243A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.535A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.048A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.298A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.252A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.090A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.618A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.999A pdb=" N TYR A 660 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.677A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.155A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.265A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.471A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.035A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.851A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.903A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.802A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.355A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.280A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.909A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.529A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.339A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.430A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.245A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.250A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.549A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.351A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.795A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 116 through 121 Processing sheet with id=AF1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AF2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.314A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.811A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.373A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.196A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.267A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.466A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG4, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 145 through 148 removed outlier: 3.849A pdb=" N ALA D 146 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 153 through 157 Processing sheet with id=AG9, first strand: chain 'D' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP D 172 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AH2, first strand: chain 'D' and resid 278 through 284 Processing sheet with id=AH3, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.308A pdb=" N TRP D 297 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL D 397 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR D 437 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 440 " --> pdb=" O SER D 426 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 409 through 411 Processing sheet with id=AH7, first strand: chain 'D' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR D 456 " --> pdb=" O PHE D 473 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 473 " --> pdb=" O TYR D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA E 146 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AI4, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP E 172 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AI6, first strand: chain 'E' and resid 278 through 284 Processing sheet with id=AI7, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.306A pdb=" N TRP E 297 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.530A pdb=" N VAL E 397 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR E 437 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 440 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 409 through 411 Processing sheet with id=AJ2, first strand: chain 'E' and resid 455 through 456 removed outlier: 3.526A pdb=" N TYR E 456 " --> pdb=" O PHE E 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 473 " --> pdb=" O TYR E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AJ4, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 145 through 148 removed outlier: 3.848A pdb=" N ALA F 146 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 153 through 157 Processing sheet with id=AJ8, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.332A pdb=" N TRP F 172 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 272 through 273 Processing sheet with id=AK1, first strand: chain 'F' and resid 278 through 284 Processing sheet with id=AK2, first strand: chain 'F' and resid 307 through 310 removed outlier: 6.307A pdb=" N TRP F 297 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.529A pdb=" N VAL F 397 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR F 437 " --> pdb=" O ASN F 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 440 " --> pdb=" O SER F 426 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 409 through 411 Processing sheet with id=AK5, first strand: chain 'F' and resid 455 through 456 removed outlier: 3.527A pdb=" N TYR F 456 " --> pdb=" O PHE F 473 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 473 " --> pdb=" O TYR F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AK7, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.848A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL G 116 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 134 through 137 removed outlier: 3.828A pdb=" N LEU G 152 " --> pdb=" O VAL G 196 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR G 190 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AL2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AL3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.843A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 134 through 138 removed outlier: 4.308A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU H 152 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AL7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AL8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.847A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'I' and resid 134 through 138 removed outlier: 4.310A pdb=" N GLY I 153 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU I 152 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR I 190 " --> pdb=" O ASP I 158 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'I' and resid 165 through 168 1559 hydrogen bonds defined for protein. 4095 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: 11.81 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11584 1.33 - 1.46: 8105 1.46 - 1.58: 20152 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 40039 Sorted by residual: bond pdb=" N ILE G 101 " pdb=" CA ILE G 101 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.61e+01 bond pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.58e+01 bond pdb=" N ILE H 101 " pdb=" CA ILE H 101 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.55e+01 bond pdb=" N ILE I 101 " pdb=" CA ILE I 101 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.30e-03 1.16e+04 1.49e+01 bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.30e+01 ... (remaining 40034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 52180 2.02 - 4.03: 2067 4.03 - 6.05: 193 6.05 - 8.06: 38 8.06 - 10.08: 10 Bond angle restraints: 54488 Sorted by residual: angle pdb=" C ASN B 544 " pdb=" CA ASN B 544 " pdb=" CB ASN B 544 " ideal model delta sigma weight residual 116.54 109.82 6.72 1.15e+00 7.56e-01 3.41e+01 angle pdb=" C ASN A 331 " pdb=" CA ASN A 331 " pdb=" CB ASN A 331 " ideal model delta sigma weight residual 109.84 118.28 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N MET G 114 " pdb=" CA MET G 114 " pdb=" C MET G 114 " ideal model delta sigma weight residual 109.15 101.69 7.46 1.44e+00 4.82e-01 2.68e+01 angle pdb=" N PHE B 456 " pdb=" CA PHE B 456 " pdb=" C PHE B 456 " ideal model delta sigma weight residual 108.02 117.05 -9.03 1.75e+00 3.27e-01 2.66e+01 angle pdb=" N MET H 114 " pdb=" CA MET H 114 " pdb=" C MET H 114 " ideal model delta sigma weight residual 109.15 101.82 7.33 1.44e+00 4.82e-01 2.59e+01 ... (remaining 54483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21233 17.92 - 35.83: 1844 35.83 - 53.75: 345 53.75 - 71.66: 76 71.66 - 89.58: 43 Dihedral angle restraints: 23541 sinusoidal: 9033 harmonic: 14508 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.25 71.25 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.23 71.23 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.51e+01 ... (remaining 23538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 6222 0.237 - 0.473: 12 0.473 - 0.710: 4 0.710 - 0.947: 2 0.947 - 1.184: 1 Chirality restraints: 6241 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 6238 not shown) Planarity restraints: 7033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG B1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1402 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1408 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C1408 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1408 " 0.064 2.00e-02 2.50e+03 pdb=" N2 NAG C1408 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG C1408 " 0.196 2.00e-02 2.50e+03 ... (remaining 7030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6083 2.76 - 3.29: 39350 3.29 - 3.83: 66571 3.83 - 4.36: 82445 4.36 - 4.90: 139124 Nonbonded interactions: 333573 Sorted by model distance: nonbonded pdb=" OH TYR E 173 " pdb=" OH TYR E 235 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR F 173 " pdb=" OH TYR F 235 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR D 173 " pdb=" OH TYR D 235 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR E 298 " pdb=" OH TYR E 360 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR D 298 " pdb=" OH TYR D 360 " model vdw 2.224 3.040 ... (remaining 333568 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 16 through 1310) selection = (chain 'B' and resid 16 through 1310) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.550 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 40125 Z= 0.386 Angle : 0.891 30.104 54689 Z= 0.526 Chirality : 0.061 1.184 6241 Planarity : 0.015 0.305 7004 Dihedral : 14.131 89.576 14076 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.78 % Allowed : 10.66 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.47 (0.12), residues: 4938 helix: 0.16 (0.19), residues: 733 sheet: -1.03 (0.14), residues: 1272 loop : -1.25 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1107 TYR 0.044 0.002 TYR B 904 PHE 0.029 0.002 PHE C 168 TRP 0.017 0.002 TRP A 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.38 (40039) covalent geometry : angle 0.83367 / 0.52 (54488) SS BOND : bond 0.00480 / 0.25 ( 57) SS BOND : angle 1.45811 / 1.05 ( 114) hydrogen bonds : bond 0.17234 / 11.21 ( 1481) hydrogen bonds : angle 8.19337 / 5.66 ( 4095) link_NAG-ASN : bond 0.03656 / 2.20 ( 29) link_NAG-ASN : angle 7.83364 / 4.97 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 586 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6694 (m-40) cc_final: 0.5803 (p0) REVERT: A 314 GLN cc_start: 0.8147 (tt0) cc_final: 0.7793 (tp40) REVERT: A 319 ARG cc_start: 0.7573 (ptp90) cc_final: 0.6232 (ptm-80) REVERT: A 554 GLU cc_start: 0.8154 (pt0) cc_final: 0.7779 (mt-10) REVERT: A 663 ASP cc_start: 0.7549 (t0) cc_final: 0.7322 (t0) REVERT: A 775 ASP cc_start: 0.7420 (m-30) cc_final: 0.6923 (m-30) REVERT: A 787 GLN cc_start: 0.7928 (mt0) cc_final: 0.7174 (mt0) REVERT: A 796 ASP cc_start: 0.7267 (p0) cc_final: 0.6708 (t70) REVERT: A 875 SER cc_start: 0.7780 (t) cc_final: 0.7366 (p) REVERT: A 886 TRP cc_start: 0.6844 (p90) cc_final: 0.6033 (p90) REVERT: A 919 ASN cc_start: 0.7083 (m-40) cc_final: 0.6870 (m110) REVERT: A 921 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6484 (tttt) REVERT: A 985 ASP cc_start: 0.5820 (m-30) cc_final: 0.5442 (t0) REVERT: A 1017 GLU cc_start: 0.6657 (tt0) cc_final: 0.6437 (tt0) REVERT: A 1045 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7192 (tptp) REVERT: A 1136 THR cc_start: 0.8446 (m) cc_final: 0.8230 (t) REVERT: B 48 LEU cc_start: 0.8414 (mt) cc_final: 0.8109 (mt) REVERT: B 191 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 271 GLN cc_start: 0.7096 (mt0) cc_final: 0.6709 (mt0) REVERT: B 314 GLN cc_start: 0.8065 (tt0) cc_final: 0.7532 (tm-30) REVERT: B 675 GLN cc_start: 0.7211 (mt0) cc_final: 0.6604 (mt0) REVERT: B 790 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8073 (mtpp) REVERT: B 804 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 875 SER cc_start: 0.8039 (t) cc_final: 0.7376 (m) REVERT: B 964 LYS cc_start: 0.7543 (mmtp) cc_final: 0.6952 (mptt) REVERT: B 1138 TYR cc_start: 0.6970 (t80) cc_final: 0.6586 (t80) REVERT: C 202 LYS cc_start: 0.6633 (mttm) cc_final: 0.6319 (mttp) REVERT: C 314 GLN cc_start: 0.8430 (tt0) cc_final: 0.8226 (tt0) REVERT: C 554 GLU cc_start: 0.8099 (pt0) cc_final: 0.7853 (pt0) REVERT: C 583 GLU cc_start: 0.7182 (tt0) cc_final: 0.6954 (tt0) REVERT: C 661 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6680 (mm-30) REVERT: C 675 GLN cc_start: 0.7091 (mt0) cc_final: 0.6822 (mt0) REVERT: C 790 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7915 (mtpp) REVERT: C 796 ASP cc_start: 0.8118 (t70) cc_final: 0.7042 (p0) REVERT: C 825 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6966 (mptt) REVERT: C 867 ASP cc_start: 0.7478 (m-30) cc_final: 0.7212 (m-30) REVERT: C 875 SER cc_start: 0.7803 (t) cc_final: 0.7494 (p) REVERT: C 921 LYS cc_start: 0.6935 (mtpp) cc_final: 0.6410 (mmpt) REVERT: C 1045 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7596 (tmtt) REVERT: C 1107 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6669 (mmt90) REVERT: C 1119 ASN cc_start: 0.6807 (m-40) cc_final: 0.6293 (m-40) REVERT: D 156 LEU cc_start: -0.1523 (OUTLIER) cc_final: -0.1758 (pt) REVERT: D 387 GLU cc_start: 0.2790 (OUTLIER) cc_final: 0.2377 (mt-10) REVERT: E 344 ASP cc_start: 0.1483 (m-30) cc_final: 0.1213 (t70) outliers start: 34 outliers final: 7 residues processed: 613 average time/residue: 0.2286 time to fit residues: 229.4496 Evaluate side-chains 347 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 338 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 239 GLN A 354 ASN A 580 GLN A 616 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A1108 ASN B 125 ASN B 196 ASN B 354 ASN B 506 GLN B 613 GLN B 616 ASN B 901 GLN B 955 ASN B 965 GLN B1054 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 196 ASN C 354 ASN C 544 ASN C 764 ASN C 856 ASN C 901 GLN C1101 HIS D 113 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 388 GLN D 416 ASN E 164 ASN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 388 GLN F 174 GLN F 277 GLN F 289 ASN F 388 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.274666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.237960 restraints weight = 44746.139| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 2.14 r_work: 0.4302 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 40125 Z= 0.235 Angle : 0.725 19.364 54689 Z= 0.358 Chirality : 0.049 0.419 6241 Planarity : 0.005 0.081 7004 Dihedral : 4.989 35.177 5404 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.56 % Allowed : 12.93 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.41 (0.12), residues: 4938 helix: -0.01 (0.18), residues: 734 sheet: -1.01 (0.13), residues: 1363 loop : -1.12 (0.12), residues: 2841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 72 TYR 0.040 0.002 TYR B 904 PHE 0.023 0.002 PHE B 374 TRP 0.023 0.002 TRP F 297 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (40039) covalent geometry : angle 0.69811 / 0.35 (54488) SS BOND : bond 0.00477 / 0.28 ( 57) SS BOND : angle 1.64781 / 1.21 ( 114) hydrogen bonds : bond 0.04269 / 2.78 ( 1481) hydrogen bonds : angle 6.46287 / 4.45 ( 4095) link_NAG-ASN : bond 0.00620 / 0.39 ( 29) link_NAG-ASN : angle 4.66120 / 2.64 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 378 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 GLN cc_start: 0.8060 (mt0) cc_final: 0.7837 (mt0) REVERT: A 886 TRP cc_start: 0.7366 (p90) cc_final: 0.6918 (p90) REVERT: B 875 SER cc_start: 0.8907 (t) cc_final: 0.8405 (m) REVERT: B 886 TRP cc_start: 0.7328 (p90) cc_final: 0.6821 (p90) REVERT: C 875 SER cc_start: 0.8622 (t) cc_final: 0.8422 (p) REVERT: D 387 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.3281 (mt-10) REVERT: E 11 LEU cc_start: 0.6234 (pt) cc_final: 0.6010 (pt) REVERT: E 230 TYR cc_start: 0.2947 (p90) cc_final: 0.2286 (p90) REVERT: E 344 ASP cc_start: 0.2005 (m-30) cc_final: 0.1551 (t70) REVERT: F 153 ARG cc_start: 0.4154 (ttp80) cc_final: 0.3271 (mtt180) REVERT: F 314 ASN cc_start: 0.5243 (t0) cc_final: 0.4910 (m110) REVERT: F 440 SER cc_start: 0.1987 (OUTLIER) cc_final: 0.1737 (t) REVERT: H 114 MET cc_start: 0.1582 (tpt) cc_final: 0.1244 (tpp) outliers start: 111 outliers final: 58 residues processed: 458 average time/residue: 0.2119 time to fit residues: 163.5922 Evaluate side-chains 338 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 440 SER Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain I residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 298 optimal weight: 0.9980 chunk 326 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 435 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 417 optimal weight: 40.0000 chunk 233 optimal weight: 0.0050 chunk 68 optimal weight: 0.7980 chunk 378 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 207 HIS A 314 GLN A 506 GLN A 580 GLN A 762 GLN B 52 GLN B1101 HIS B1135 ASN C 99 ASN C 121 ASN C 580 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 ASN ** F 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.275534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.238672 restraints weight = 44776.621| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 2.17 r_work: 0.4309 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4209 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40125 Z= 0.140 Angle : 0.614 13.113 54689 Z= 0.306 Chirality : 0.045 0.324 6241 Planarity : 0.004 0.050 7004 Dihedral : 4.676 36.857 5393 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.31 % Allowed : 14.31 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.15 (0.12), residues: 4938 helix: 0.25 (0.19), residues: 740 sheet: -0.75 (0.13), residues: 1355 loop : -1.02 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.031 0.001 TYR B 904 PHE 0.019 0.002 PHE B 898 TRP 0.021 0.002 TRP E 36 HIS 0.003 0.001 HIS F 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (40039) covalent geometry : angle 0.59489 / 0.30 (54488) SS BOND : bond 0.00407 / 0.23 ( 57) SS BOND : angle 1.35721 / 0.97 ( 114) hydrogen bonds : bond 0.03656 / 2.39 ( 1481) hydrogen bonds : angle 6.04696 / 4.13 ( 4095) link_NAG-ASN : bond 0.00554 / 0.32 ( 29) link_NAG-ASN : angle 3.59724 / 2.02 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 327 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: symmetry clash REVERT: A 34 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7610 (mmt180) REVERT: A 546 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7031 (tp) REVERT: A 565 PHE cc_start: 0.6715 (m-10) cc_final: 0.6449 (m-10) REVERT: A 886 TRP cc_start: 0.7413 (p90) cc_final: 0.6869 (p90) REVERT: B 875 SER cc_start: 0.8841 (t) cc_final: 0.8375 (m) REVERT: B 886 TRP cc_start: 0.7469 (p90) cc_final: 0.7252 (p90) REVERT: C 51 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7592 (t) REVERT: C 643 PHE cc_start: 0.8289 (t80) cc_final: 0.8076 (t80) REVERT: D 324 PHE cc_start: 0.1437 (m-80) cc_final: 0.0301 (t80) REVERT: D 349 TYR cc_start: 0.2417 (m-80) cc_final: 0.1973 (m-10) REVERT: D 387 GLU cc_start: 0.3521 (OUTLIER) cc_final: 0.2878 (pt0) REVERT: E 230 TYR cc_start: 0.3027 (p90) cc_final: 0.2426 (p90) REVERT: E 344 ASP cc_start: 0.2082 (m-30) cc_final: 0.1561 (t70) REVERT: F 153 ARG cc_start: 0.4253 (ttp80) cc_final: 0.3215 (mtt180) REVERT: F 451 GLU cc_start: 0.2473 (mp0) cc_final: 0.2186 (mt-10) REVERT: G 124 THR cc_start: 0.1250 (p) cc_final: 0.0568 (t) outliers start: 100 outliers final: 55 residues processed: 400 average time/residue: 0.1998 time to fit residues: 136.3268 Evaluate side-chains 333 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 65 optimal weight: 0.0370 chunk 105 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 389 optimal weight: 40.0000 chunk 382 optimal weight: 0.9980 chunk 310 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 160 optimal weight: 0.3980 chunk 345 optimal weight: 5.9990 chunk 408 optimal weight: 30.0000 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 271 GLN B 675 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 935 GLN C 710 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.275350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.239242 restraints weight = 44613.497| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.06 r_work: 0.4294 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40125 Z= 0.156 Angle : 0.602 11.877 54689 Z= 0.299 Chirality : 0.045 0.433 6241 Planarity : 0.004 0.097 7004 Dihedral : 4.534 37.325 5391 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.30 % Allowed : 14.15 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -1.07 (0.12), residues: 4938 helix: 0.32 (0.19), residues: 740 sheet: -0.63 (0.13), residues: 1365 loop : -1.00 (0.12), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.027 0.001 TYR B 904 PHE 0.020 0.002 PHE B 898 TRP 0.014 0.001 TRP E 36 HIS 0.003 0.001 HIS F 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (40039) covalent geometry : angle 0.58513 / 0.29 (54488) SS BOND : bond 0.00432 / 0.27 ( 57) SS BOND : angle 1.37946 / 0.98 ( 114) hydrogen bonds : bond 0.03529 / 2.30 ( 1481) hydrogen bonds : angle 5.83879 / 3.98 ( 4095) link_NAG-ASN : bond 0.00469 / 0.27 ( 29) link_NAG-ASN : angle 3.24967 / 1.84 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 305 time to evaluate : 1.566 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 34 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7626 (mmt180) REVERT: A 886 TRP cc_start: 0.7474 (p90) cc_final: 0.6997 (p90) REVERT: B 92 PHE cc_start: 0.7567 (t80) cc_final: 0.7248 (t80) REVERT: B 774 GLN cc_start: 0.7762 (mm110) cc_final: 0.7524 (mm-40) REVERT: B 875 SER cc_start: 0.8831 (t) cc_final: 0.8371 (m) REVERT: B 886 TRP cc_start: 0.7545 (p90) cc_final: 0.7310 (p90) REVERT: C 293 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7759 (pt) REVERT: C 886 TRP cc_start: 0.7441 (p90) cc_final: 0.6963 (p90) REVERT: D 67 ARG cc_start: 0.1927 (ptp-170) cc_final: 0.1607 (mtt180) REVERT: D 324 PHE cc_start: 0.1404 (m-80) cc_final: 0.0336 (t80) REVERT: D 349 TYR cc_start: 0.2604 (m-80) cc_final: 0.2020 (m-10) REVERT: D 387 GLU cc_start: 0.3662 (OUTLIER) cc_final: 0.2899 (pt0) REVERT: E 230 TYR cc_start: 0.3209 (p90) cc_final: 0.2699 (p90) REVERT: E 344 ASP cc_start: 0.2224 (m-30) cc_final: 0.1708 (t70) REVERT: E 414 VAL cc_start: 0.2783 (OUTLIER) cc_final: 0.2409 (m) REVERT: F 34 MET cc_start: 0.4062 (mmp) cc_final: 0.3140 (mmm) REVERT: F 140 LEU cc_start: 0.1337 (mm) cc_final: 0.0712 (mt) REVERT: F 153 ARG cc_start: 0.4357 (ttp80) cc_final: 0.3271 (mmt180) REVERT: F 188 ASP cc_start: 0.1283 (m-30) cc_final: 0.0719 (t0) REVERT: F 451 GLU cc_start: 0.2498 (mp0) cc_final: 0.2052 (mt-10) REVERT: G 124 THR cc_start: 0.1159 (p) cc_final: 0.0478 (t) outliers start: 143 outliers final: 81 residues processed: 410 average time/residue: 0.1934 time to fit residues: 137.3355 Evaluate side-chains 366 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 282 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 343 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 337 optimal weight: 0.2980 chunk 288 optimal weight: 0.8980 chunk 399 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 338 optimal weight: 0.0030 chunk 221 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 81 ASN B 99 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 913 GLN C 121 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.275640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.236861 restraints weight = 44774.191| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 2.23 r_work: 0.4309 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 40125 Z= 0.119 Angle : 0.568 11.539 54689 Z= 0.283 Chirality : 0.044 0.338 6241 Planarity : 0.004 0.064 7004 Dihedral : 4.387 37.066 5391 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.07 % Allowed : 14.75 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.94 (0.12), residues: 4938 helix: 0.53 (0.19), residues: 740 sheet: -0.52 (0.13), residues: 1385 loop : -0.97 (0.12), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1107 TYR 0.039 0.001 TYR B 904 PHE 0.021 0.001 PHE C 541 TRP 0.013 0.001 TRP E 36 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (40039) covalent geometry : angle 0.55380 / 0.28 (54488) SS BOND : bond 0.00371 / 0.22 ( 57) SS BOND : angle 1.17296 / 0.83 ( 114) hydrogen bonds : bond 0.03350 / 2.18 ( 1481) hydrogen bonds : angle 5.65485 / 3.86 ( 4095) link_NAG-ASN : bond 0.00519 / 0.30 ( 29) link_NAG-ASN : angle 3.01587 / 1.71 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 291 time to evaluate : 1.604 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 886 TRP cc_start: 0.7370 (p90) cc_final: 0.6952 (p90) REVERT: B 92 PHE cc_start: 0.7624 (t80) cc_final: 0.7338 (t80) REVERT: B 239 GLN cc_start: 0.7620 (mt0) cc_final: 0.7397 (tt0) REVERT: B 875 SER cc_start: 0.8830 (t) cc_final: 0.8254 (m) REVERT: C 51 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7698 (t) REVERT: C 318 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7601 (p90) REVERT: D 324 PHE cc_start: 0.1254 (m-80) cc_final: 0.0277 (t80) REVERT: D 349 TYR cc_start: 0.2588 (m-80) cc_final: 0.1993 (m-80) REVERT: D 387 GLU cc_start: 0.3610 (OUTLIER) cc_final: 0.2910 (pt0) REVERT: E 36 TRP cc_start: 0.5370 (m100) cc_final: 0.4743 (m100) REVERT: E 190 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5107 (mp10) REVERT: E 230 TYR cc_start: 0.3045 (p90) cc_final: 0.2616 (p90) REVERT: E 344 ASP cc_start: 0.2397 (m-30) cc_final: 0.1767 (t70) REVERT: E 414 VAL cc_start: 0.2845 (OUTLIER) cc_final: 0.2458 (m) REVERT: F 34 MET cc_start: 0.4153 (mmp) cc_final: 0.3277 (ttm) REVERT: F 153 ARG cc_start: 0.4397 (ttp80) cc_final: 0.3265 (mmt180) REVERT: F 188 ASP cc_start: 0.1163 (m-30) cc_final: 0.0716 (t0) REVERT: F 451 GLU cc_start: 0.2593 (mp0) cc_final: 0.2101 (mt-10) REVERT: G 124 THR cc_start: 0.0998 (p) cc_final: 0.0342 (t) outliers start: 133 outliers final: 81 residues processed: 387 average time/residue: 0.2197 time to fit residues: 146.7525 Evaluate side-chains 356 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 270 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 45 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 287 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 228 optimal weight: 0.0050 chunk 437 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1011 GLN B 52 GLN B 81 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 935 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1071 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.273556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.238411 restraints weight = 44520.443| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 1.96 r_work: 0.4305 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 40125 Z= 0.200 Angle : 0.603 10.336 54689 Z= 0.301 Chirality : 0.046 0.504 6241 Planarity : 0.004 0.053 7004 Dihedral : 4.448 36.597 5391 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 15.12 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.95 (0.12), residues: 4938 helix: 0.35 (0.19), residues: 740 sheet: -0.43 (0.13), residues: 1390 loop : -0.98 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.038 0.001 TYR B 904 PHE 0.021 0.002 PHE C 541 TRP 0.011 0.001 TRP F 111 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (40039) covalent geometry : angle 0.58867 / 0.30 (54488) SS BOND : bond 0.00496 / 0.29 ( 57) SS BOND : angle 1.41475 / 0.97 ( 114) hydrogen bonds : bond 0.03550 / 2.31 ( 1481) hydrogen bonds : angle 5.70090 / 3.89 ( 4095) link_NAG-ASN : bond 0.00475 / 0.28 ( 29) link_NAG-ASN : angle 2.96584 / 1.72 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 283 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6238 (t80) REVERT: A 886 TRP cc_start: 0.7350 (p90) cc_final: 0.6973 (p90) REVERT: B 92 PHE cc_start: 0.7694 (t80) cc_final: 0.7420 (t80) REVERT: B 978 ASN cc_start: 0.7123 (m-40) cc_final: 0.6889 (t0) REVERT: C 318 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7421 (p90) REVERT: D 34 MET cc_start: 0.3623 (mmt) cc_final: 0.3039 (mmm) REVERT: D 324 PHE cc_start: 0.1214 (m-80) cc_final: 0.0397 (t80) REVERT: D 387 GLU cc_start: 0.3687 (OUTLIER) cc_final: 0.2814 (pt0) REVERT: E 36 TRP cc_start: 0.5547 (m100) cc_final: 0.5119 (m100) REVERT: E 190 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5151 (mp10) REVERT: E 230 TYR cc_start: 0.3143 (p90) cc_final: 0.2705 (p90) REVERT: E 414 VAL cc_start: 0.2816 (OUTLIER) cc_final: 0.2534 (m) REVERT: F 34 MET cc_start: 0.4159 (mmp) cc_final: 0.3310 (ttm) REVERT: F 153 ARG cc_start: 0.4431 (ttp80) cc_final: 0.3367 (mmt90) REVERT: F 451 GLU cc_start: 0.2573 (mp0) cc_final: 0.2049 (mt-10) outliers start: 133 outliers final: 92 residues processed: 376 average time/residue: 0.2223 time to fit residues: 142.9709 Evaluate side-chains 358 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 261 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 402 ASN Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 137 optimal weight: 0.9980 chunk 151 optimal weight: 0.0670 chunk 395 optimal weight: 40.0000 chunk 96 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 261 optimal weight: 0.0970 chunk 352 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 402 optimal weight: 20.0000 chunk 83 optimal weight: 0.5980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 52 GLN B 239 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.276152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.241066 restraints weight = 44688.218| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 2.02 r_work: 0.4303 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4147 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40125 Z= 0.116 Angle : 0.555 10.242 54689 Z= 0.278 Chirality : 0.043 0.339 6241 Planarity : 0.004 0.049 7004 Dihedral : 4.295 36.510 5391 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.70 % Allowed : 15.95 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.82 (0.12), residues: 4938 helix: 0.68 (0.19), residues: 738 sheet: -0.32 (0.13), residues: 1375 loop : -0.98 (0.12), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.028 0.001 TYR B 904 PHE 0.029 0.001 PHE E 403 TRP 0.023 0.001 TRP E 36 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (40039) covalent geometry : angle 0.54246 / 0.27 (54488) SS BOND : bond 0.00346 / 0.20 ( 57) SS BOND : angle 1.20363 / 0.82 ( 114) hydrogen bonds : bond 0.03257 / 2.14 ( 1481) hydrogen bonds : angle 5.49909 / 3.74 ( 4095) link_NAG-ASN : bond 0.00496 / 0.28 ( 29) link_NAG-ASN : angle 2.76386 / 1.60 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 292 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6408 (t80) REVERT: A 886 TRP cc_start: 0.7416 (p90) cc_final: 0.7091 (p90) REVERT: B 92 PHE cc_start: 0.7695 (t80) cc_final: 0.7441 (t80) REVERT: B 541 PHE cc_start: 0.7796 (p90) cc_final: 0.7392 (p90) REVERT: B 875 SER cc_start: 0.8825 (t) cc_final: 0.8240 (m) REVERT: B 978 ASN cc_start: 0.7130 (m-40) cc_final: 0.6871 (t0) REVERT: C 318 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7483 (p90) REVERT: C 886 TRP cc_start: 0.7420 (p90) cc_final: 0.7041 (p90) REVERT: C 1145 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5418 (tt) REVERT: D 34 MET cc_start: 0.3511 (mmt) cc_final: 0.2917 (mmm) REVERT: D 324 PHE cc_start: 0.1135 (m-80) cc_final: 0.0465 (t80) REVERT: D 387 GLU cc_start: 0.3601 (OUTLIER) cc_final: 0.2712 (pt0) REVERT: E 36 TRP cc_start: 0.5771 (m100) cc_final: 0.5069 (m100) REVERT: E 83 MET cc_start: 0.4065 (mmm) cc_final: 0.3849 (mmt) REVERT: E 190 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.5300 (mp10) REVERT: E 230 TYR cc_start: 0.3290 (p90) cc_final: 0.2859 (p90) REVERT: E 414 VAL cc_start: 0.2670 (OUTLIER) cc_final: 0.2420 (m) REVERT: F 34 MET cc_start: 0.3990 (mmp) cc_final: 0.3132 (ttm) REVERT: F 144 PRO cc_start: 0.3956 (Cg_exo) cc_final: 0.3733 (Cg_endo) REVERT: F 153 ARG cc_start: 0.4538 (ttp80) cc_final: 0.3412 (mmt90) REVERT: F 188 ASP cc_start: 0.1304 (m-30) cc_final: 0.0756 (t0) REVERT: F 451 GLU cc_start: 0.2467 (mp0) cc_final: 0.2042 (mt-10) REVERT: G 124 THR cc_start: 0.1184 (p) cc_final: 0.0505 (t) REVERT: G 192 LEU cc_start: 0.2903 (OUTLIER) cc_final: 0.2488 (tp) REVERT: H 114 MET cc_start: 0.1416 (tpp) cc_final: 0.1114 (tpp) outliers start: 117 outliers final: 85 residues processed: 375 average time/residue: 0.2132 time to fit residues: 139.2848 Evaluate side-chains 361 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 269 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 50 optimal weight: 0.0570 chunk 342 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 387 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 420 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 489 optimal weight: 40.0000 chunk 295 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 376 optimal weight: 30.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 969 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 113 GLN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 164 ASN G 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.270581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.235078 restraints weight = 44168.759| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 1.99 r_work: 0.4225 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 40125 Z= 0.286 Angle : 0.671 13.299 54689 Z= 0.336 Chirality : 0.048 0.475 6241 Planarity : 0.005 0.046 7004 Dihedral : 4.611 36.283 5391 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.86 % Allowed : 16.00 % Favored : 81.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.60 % 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: -0.99 (0.12), residues: 4938 helix: 0.11 (0.18), residues: 741 sheet: -0.31 (0.14), residues: 1385 loop : -1.03 (0.12), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 198 TYR 0.035 0.002 TYR B 904 PHE 0.029 0.002 PHE C 541 TRP 0.023 0.002 TRP E 36 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.29 (40039) covalent geometry : angle 0.65778 / 0.33 (54488) SS BOND : bond 0.00587 / 0.35 ( 57) SS BOND : angle 1.65226 / 1.15 ( 114) hydrogen bonds : bond 0.03867 / 2.51 ( 1481) hydrogen bonds : angle 5.81159 / 3.97 ( 4095) link_NAG-ASN : bond 0.00416 / 0.26 ( 29) link_NAG-ASN : angle 2.85232 / 1.70 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 266 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 886 TRP cc_start: 0.7316 (p90) cc_final: 0.6977 (p90) REVERT: B 92 PHE cc_start: 0.7734 (t80) cc_final: 0.7413 (t80) REVERT: B 978 ASN cc_start: 0.7340 (m-40) cc_final: 0.7128 (t0) REVERT: C 318 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7369 (p90) REVERT: C 886 TRP cc_start: 0.7443 (p90) cc_final: 0.7016 (p90) REVERT: D 34 MET cc_start: 0.3596 (mmt) cc_final: 0.3028 (mmm) REVERT: D 113 GLN cc_start: 0.2380 (OUTLIER) cc_final: 0.2063 (pm20) REVERT: D 152 GLN cc_start: 0.3249 (tt0) cc_final: 0.3025 (tt0) REVERT: D 324 PHE cc_start: 0.1266 (m-80) cc_final: 0.0571 (t80) REVERT: E 190 GLN cc_start: 0.6266 (OUTLIER) cc_final: 0.5187 (mp10) REVERT: E 230 TYR cc_start: 0.3233 (p90) cc_final: 0.2654 (p90) REVERT: E 414 VAL cc_start: 0.2868 (OUTLIER) cc_final: 0.2547 (m) REVERT: F 153 ARG cc_start: 0.4494 (ttp80) cc_final: 0.3338 (mmt180) REVERT: F 451 GLU cc_start: 0.2463 (mp0) cc_final: 0.1946 (mt-10) REVERT: G 192 LEU cc_start: 0.3017 (OUTLIER) cc_final: 0.2590 (tp) REVERT: H 34 MET cc_start: 0.2285 (mmm) cc_final: 0.1867 (mmm) REVERT: H 114 MET cc_start: 0.1611 (tpp) cc_final: 0.1315 (tpp) outliers start: 124 outliers final: 90 residues processed: 360 average time/residue: 0.2210 time to fit residues: 138.1367 Evaluate side-chains 341 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 245 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 22 optimal weight: 0.6980 chunk 390 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 356 optimal weight: 9.9990 chunk 427 optimal weight: 30.0000 chunk 170 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1101 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1119 ASN ** D 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 388 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.274480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.239829 restraints weight = 44523.718| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 2.03 r_work: 0.4294 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4179 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40125 Z= 0.130 Angle : 0.573 10.844 54689 Z= 0.288 Chirality : 0.044 0.290 6241 Planarity : 0.004 0.046 7004 Dihedral : 4.393 36.154 5391 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.24 % Allowed : 16.60 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % 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: -0.80 (0.12), residues: 4938 helix: 0.47 (0.19), residues: 740 sheet: -0.29 (0.14), residues: 1379 loop : -0.91 (0.12), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.035 0.001 TYR C 369 PHE 0.028 0.001 PHE C 541 TRP 0.030 0.001 TRP E 36 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (40039) covalent geometry : angle 0.56145 / 0.28 (54488) SS BOND : bond 0.00381 / 0.22 ( 57) SS BOND : angle 1.31070 / 0.91 ( 114) hydrogen bonds : bond 0.03283 / 2.15 ( 1481) hydrogen bonds : angle 5.51302 / 3.75 ( 4095) link_NAG-ASN : bond 0.00453 / 0.26 ( 29) link_NAG-ASN : angle 2.63514 / 1.55 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9876 Ramachandran restraints generated. 4938 Oldfield, 0 Emsley, 4938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 268 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.7152 (tpp) cc_final: 0.6886 (ttt) REVERT: A 756 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6661 (t80) REVERT: A 886 TRP cc_start: 0.7293 (p90) cc_final: 0.6977 (p90) REVERT: B 92 PHE cc_start: 0.7734 (t80) cc_final: 0.7503 (t80) REVERT: B 875 SER cc_start: 0.8818 (t) cc_final: 0.8246 (m) REVERT: B 978 ASN cc_start: 0.7272 (m-40) cc_final: 0.7070 (t0) REVERT: C 318 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7368 (p90) REVERT: C 886 TRP cc_start: 0.7430 (p90) cc_final: 0.6859 (p90) REVERT: C 1145 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5479 (tt) REVERT: D 34 MET cc_start: 0.3468 (mmt) cc_final: 0.2909 (mmm) REVERT: D 324 PHE cc_start: 0.1194 (m-80) cc_final: 0.0568 (t80) REVERT: E 109 ASP cc_start: 0.4403 (p0) cc_final: 0.3845 (t0) REVERT: E 190 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5323 (mp10) REVERT: E 230 TYR cc_start: 0.3242 (p90) cc_final: 0.2668 (p90) REVERT: E 414 VAL cc_start: 0.2973 (OUTLIER) cc_final: 0.2698 (m) REVERT: F 153 ARG cc_start: 0.4505 (ttp80) cc_final: 0.3281 (mmt180) REVERT: F 188 ASP cc_start: 0.1336 (m-30) cc_final: 0.0869 (t0) REVERT: F 451 GLU cc_start: 0.2336 (mp0) cc_final: 0.1764 (mt-10) REVERT: G 124 THR cc_start: 0.1365 (p) cc_final: 0.0645 (t) REVERT: G 192 LEU cc_start: 0.2952 (OUTLIER) cc_final: 0.2581 (tp) REVERT: H 34 MET cc_start: 0.2284 (mmm) cc_final: 0.1858 (mmm) REVERT: H 114 MET cc_start: 0.1496 (tpp) cc_final: 0.1255 (tpp) outliers start: 97 outliers final: 78 residues processed: 338 average time/residue: 0.2089 time to fit residues: 122.7385 Evaluate side-chains 338 residues out of total 4332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 254 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 432 SER Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7043 > 50: distance: 6 - 11: 14.894 distance: 11 - 12: 27.951 distance: 12 - 13: 50.595 distance: 12 - 15: 26.085 distance: 13 - 14: 24.290 distance: 13 - 22: 22.665 distance: 15 - 16: 24.488 distance: 16 - 17: 49.209 distance: 16 - 18: 27.492 distance: 17 - 19: 42.640 distance: 18 - 20: 33.009 distance: 19 - 21: 20.855 distance: 20 - 21: 17.403 distance: 22 - 23: 19.714 distance: 22 - 28: 23.949 distance: 23 - 24: 12.618 distance: 23 - 26: 16.916 distance: 24 - 25: 12.113 distance: 24 - 29: 8.266 distance: 26 - 27: 12.136 distance: 27 - 28: 12.604 distance: 29 - 30: 7.828 distance: 30 - 31: 5.765 distance: 30 - 33: 9.082 distance: 31 - 32: 3.139 distance: 31 - 37: 38.080 distance: 33 - 34: 8.843 distance: 34 - 35: 19.348 distance: 34 - 36: 18.661 distance: 36 - 201: 23.965 distance: 37 - 38: 22.724 distance: 38 - 39: 18.976 distance: 38 - 41: 18.889 distance: 39 - 40: 27.193 distance: 39 - 45: 27.337 distance: 41 - 42: 32.485 distance: 41 - 43: 19.312 distance: 42 - 44: 16.096 distance: 45 - 46: 17.172 distance: 46 - 47: 5.156 distance: 46 - 49: 24.490 distance: 47 - 48: 24.336 distance: 47 - 52: 15.747 distance: 49 - 50: 25.173 distance: 49 - 51: 23.154 distance: 52 - 53: 25.334 distance: 53 - 54: 37.595 distance: 53 - 56: 37.052 distance: 54 - 55: 30.603 distance: 54 - 60: 27.625 distance: 56 - 57: 22.514 distance: 57 - 58: 24.174 distance: 57 - 59: 22.832 distance: 60 - 61: 50.634 distance: 61 - 62: 42.565 distance: 61 - 64: 22.192 distance: 64 - 65: 30.980 distance: 65 - 66: 11.834 distance: 65 - 67: 33.327 distance: 68 - 69: 9.713 distance: 69 - 70: 24.671 distance: 69 - 72: 37.151 distance: 70 - 71: 9.101 distance: 70 - 74: 22.195 distance: 72 - 73: 8.328 distance: 73 - 127: 28.584 distance: 74 - 75: 43.861 distance: 74 - 80: 34.034 distance: 75 - 76: 20.035 distance: 75 - 78: 53.047 distance: 76 - 77: 12.509 distance: 76 - 81: 8.482 distance: 78 - 79: 15.047 distance: 79 - 80: 16.062 distance: 81 - 82: 14.927 distance: 82 - 83: 14.576 distance: 82 - 85: 6.348 distance: 83 - 84: 11.572 distance: 83 - 92: 23.363 distance: 84 - 111: 28.722 distance: 85 - 86: 12.306 distance: 86 - 87: 10.315 distance: 86 - 88: 25.291 distance: 87 - 89: 7.103 distance: 88 - 90: 8.386 distance: 89 - 91: 19.957 distance: 90 - 91: 17.282