Starting phenix.real_space_refine on Tue Apr 7 08:30:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.map" model { file = "/net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cn4_30416/04_2026/7cn4_30416.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 114 5.16 5 C 16665 2.51 5 N 4341 2.21 5 O 5133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26253 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'TRP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'TRP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "C" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8499 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 54, 'TRANS': 1065} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 3, 'ASN:plan1': 5, 'PHE:plan': 3, 'ASP:plan': 4, 'TYR:plan': 3, 'TRP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.76, per 1000 atoms: 0.22 Number of scatterers: 26253 At special positions: 0 Unit cell: (150.467, 135.312, 164.54, 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 114 16.00 O 5133 8.00 N 4341 7.00 C 16665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 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=2.04 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 734 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 713 " " NAG A1309 " - " ASN A1070 " " NAG A1310 " - " ASN A 30 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 797 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 713 " " NAG B1309 " - " ASN B 797 " " NAG B1310 " - " ASN B1070 " " NAG B1311 " - " ASN B 30 " " NAG B1312 " - " ASN B 61 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 713 " " NAG C1309 " - " ASN C 797 " " NAG C1310 " - " ASN C1070 " " NAG C1311 " - " ASN C 30 " " NAG C1312 " - " ASN C 61 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN B 234 " " NAG H 1 " - " ASN C 234 " " NAG I 1 " - " ASN B 165 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN C 165 " " NAG L 1 " - " ASN C 122 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.2 seconds 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6276 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 51 sheets defined 25.1% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.079A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.635A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.527A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.642A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 779 removed outlier: 3.957A pdb=" N GLN A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN A 820 " --> pdb=" O ASP A 816 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.790A pdb=" N ALA A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 905 removed outlier: 3.926A pdb=" N TYR A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.593A pdb=" N TYR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 934 Processing helix chain 'A' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE A 976 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.078A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.528A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.641A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 779 removed outlier: 3.962A pdb=" N GLN B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY B 838 " --> pdb=" O GLY B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 849 Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 882 through 887 removed outlier: 3.791A pdb=" N ALA B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 905 removed outlier: 4.013A pdb=" N TYR B 900 " --> pdb=" O MET B 896 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 905 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.592A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 934 Processing helix chain 'B' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 946 " --> pdb=" O GLY B 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 955 " --> pdb=" O ASN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B1017 " --> pdb=" O GLU B1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.078A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.642A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.527A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.642A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 753 removed outlier: 3.626A pdb=" N LEU C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 removed outlier: 3.982A pdb=" N GLN C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 822 removed outlier: 3.916A pdb=" N ASN C 820 " --> pdb=" O ASP C 816 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 838 removed outlier: 3.658A pdb=" N GLY C 838 " --> pdb=" O GLY C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 849 Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 882 through 887 removed outlier: 3.790A pdb=" N ALA C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.200A pdb=" N TYR C 900 " --> pdb=" O MET C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.592A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 934 Processing helix chain 'C' and resid 940 through 961 removed outlier: 4.022A pdb=" N LEU C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 946 " --> pdb=" O GLY C 942 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 removed outlier: 3.560A pdb=" N ILE C 976 " --> pdb=" O VAL C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.169A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C1017 " --> pdb=" O GLU C1013 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.696A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER A 221 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.226A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.175A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.572A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 380 removed outlier: 4.133A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 542 removed outlier: 3.528A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.591A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR A1072 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER A 717 " --> pdb=" O THR A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 786 removed outlier: 5.859A pdb=" N ILE A 784 " --> pdb=" O ASN B 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.697A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER B 221 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.227A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.175A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.572A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 376 through 380 removed outlier: 4.132A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 539 through 542 removed outlier: 5.475A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR B1072 " --> pdb=" O SER B1093 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER B 717 " --> pdb=" O THR B1062 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 783 through 786 removed outlier: 5.837A pdb=" N ILE B 784 " --> pdb=" O ASN C 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.696A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 33 through 36 removed outlier: 6.282A pdb=" N SER C 221 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.443A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.639A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.226A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.573A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 376 through 380 removed outlier: 4.132A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 539 through 542 removed outlier: 5.475A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.590A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 707 through 710 removed outlier: 4.195A pdb=" N THR C1072 " --> pdb=" O SER C1093 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.618A pdb=" N SER C 717 " --> pdb=" O THR C1062 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.601A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1077 through 1079 998 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.51 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8231 1.34 - 1.46: 6576 1.46 - 1.59: 11881 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 26826 Sorted by residual: bond pdb=" C GLN A1067 " pdb=" N GLU A1068 " ideal model delta sigma weight residual 1.332 1.489 -0.156 1.40e-02 5.10e+03 1.24e+02 bond pdb=" C PRO B 859 " pdb=" N LEU B 860 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.27e-02 6.20e+03 4.11e+01 bond pdb=" C PRO A 859 " pdb=" N LEU A 860 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.27e-02 6.20e+03 4.09e+01 bond pdb=" C ALA A1066 " pdb=" N GLN A1067 " ideal model delta sigma weight residual 1.332 1.276 0.056 1.40e-02 5.10e+03 1.63e+01 bond pdb=" C LEU B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.273 0.057 1.42e-02 4.96e+03 1.62e+01 ... (remaining 26821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 34717 1.75 - 3.50: 1648 3.50 - 5.25: 180 5.25 - 7.00: 30 7.00 - 8.75: 7 Bond angle restraints: 36582 Sorted by residual: angle pdb=" N PRO C 251 " pdb=" CA PRO C 251 " pdb=" CB PRO C 251 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.18e+01 angle pdb=" N PRO A 251 " pdb=" CA PRO A 251 " pdb=" CB PRO A 251 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.17e+01 angle pdb=" N PRO B 251 " pdb=" CA PRO B 251 " pdb=" CB PRO B 251 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.16e+01 angle pdb=" CA ALA A1066 " pdb=" C ALA A1066 " pdb=" N GLN A1067 " ideal model delta sigma weight residual 116.05 122.85 -6.80 1.19e+00 7.06e-01 3.26e+01 angle pdb=" N ILE A 569 " pdb=" CA ILE A 569 " pdb=" C ILE A 569 " ideal model delta sigma weight residual 110.62 104.84 5.78 1.02e+00 9.61e-01 3.22e+01 ... (remaining 36577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.02: 15455 20.02 - 40.04: 972 40.04 - 60.05: 191 60.05 - 80.07: 41 80.07 - 100.09: 30 Dihedral angle restraints: 16689 sinusoidal: 6918 harmonic: 9771 Sorted by residual: 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 -174.13 88.13 1 1.00e+01 1.00e-02 9.29e+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 -174.12 88.12 1 1.00e+01 1.00e-02 9.29e+01 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 -174.12 88.12 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 16686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4231 0.133 - 0.266: 112 0.266 - 0.399: 11 0.399 - 0.532: 3 0.532 - 0.666: 2 Chirality restraints: 4359 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.75e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.55e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.09e+01 ... (remaining 4356 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.325 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG L 2 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.078 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.324 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG E 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " -0.309 2.00e-02 2.50e+03 2.71e-01 9.20e+02 pdb=" C7 NAG C1309 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.159 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 12 1.87 - 2.63: 295 2.63 - 3.39: 33045 3.39 - 4.14: 62719 4.14 - 4.90: 115002 Nonbonded interactions: 211073 Sorted by model distance: nonbonded pdb=" NH2 ARG B1015 " pdb=" OE1 GLU C1013 " model vdw 1.117 3.120 nonbonded pdb=" NH2 ARG A1015 " pdb=" OE1 GLU B1013 " model vdw 1.123 3.120 nonbonded pdb=" OE1 GLU A1013 " pdb=" NH2 ARG C1015 " model vdw 1.125 3.120 nonbonded pdb=" NH2 ARG B1015 " pdb=" CD GLU C1013 " model vdw 1.185 3.350 nonbonded pdb=" NH2 ARG A1015 " pdb=" CD GLU B1013 " model vdw 1.190 3.350 ... (remaining 211068 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.620 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.007 0.156 26925 Z= 0.371 Angle : 0.846 23.318 36834 Z= 0.513 Chirality : 0.060 0.666 4359 Planarity : 0.012 0.283 4698 Dihedral : 14.357 100.090 10278 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.95 % Favored : 92.70 % Rotamer: Outliers : 1.32 % Allowed : 4.23 % Favored : 94.44 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.12), residues: 3354 helix: -2.44 (0.16), residues: 657 sheet: -1.39 (0.17), residues: 696 loop : -2.69 (0.12), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1103 TYR 0.013 0.001 TYR B 423 PHE 0.016 0.002 PHE C 902 TRP 0.013 0.002 TRP C 882 HIS 0.002 0.001 HIS B1079 Details of bonding type rmsd covalent geometry : bond 0.00649 (26826) covalent geometry : angle 0.80268 (36582) SS BOND : bond 0.00399 ( 45) SS BOND : angle 1.26827 ( 90) hydrogen bonds : bond 0.21814 ( 938) hydrogen bonds : angle 8.48215 ( 2673) link_BETA1-4 : bond 0.00636 ( 9) link_BETA1-4 : angle 1.06392 ( 27) link_NAG-ASN : bond 0.01174 ( 45) link_NAG-ASN : angle 4.37833 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 900 TYR cc_start: 0.6846 (t80) cc_final: 0.6566 (t80) REVERT: A 1046 MET cc_start: 0.8513 (ptm) cc_final: 0.8261 (ptm) REVERT: B 900 TYR cc_start: 0.6741 (t80) cc_final: 0.6462 (t80) outliers start: 36 outliers final: 1 residues processed: 207 average time/residue: 0.6449 time to fit residues: 154.4472 Evaluate side-chains 105 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 800 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 137 ASN A 360 ASN A 409 GLN A 540 ASN A 760 ASN A 897 GLN A 909 GLN A 921 ASN A 951 ASN A 974 ASN B 137 ASN B 409 GLN B 760 ASN B 800 GLN B 897 GLN B 909 GLN B 921 ASN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 ASN C 137 ASN C 360 ASN C 409 GLN C 760 ASN C 800 GLN C 897 GLN C 909 GLN C 915 ASN C 921 ASN C 951 ASN C 974 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054856 restraints weight = 64171.671| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.21 r_work: 0.2632 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 26925 Z= 0.247 Angle : 0.698 11.699 36834 Z= 0.357 Chirality : 0.049 0.350 4359 Planarity : 0.005 0.051 4698 Dihedral : 9.674 87.093 4734 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.58 % Allowed : 7.95 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.13), residues: 3354 helix: -0.56 (0.19), residues: 693 sheet: -0.82 (0.18), residues: 687 loop : -2.34 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 214 TYR 0.018 0.001 TYR A 900 PHE 0.014 0.002 PHE A 902 TRP 0.014 0.002 TRP A 353 HIS 0.002 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00581 (26826) covalent geometry : angle 0.67169 (36582) SS BOND : bond 0.00341 ( 45) SS BOND : angle 1.33022 ( 90) hydrogen bonds : bond 0.04658 ( 938) hydrogen bonds : angle 5.97309 ( 2673) link_BETA1-4 : bond 0.00611 ( 9) link_BETA1-4 : angle 2.22173 ( 27) link_NAG-ASN : bond 0.00405 ( 45) link_NAG-ASN : angle 2.92894 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1046 MET cc_start: 0.9059 (ptm) cc_final: 0.8686 (ptm) REVERT: B 946 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8621 (m-30) REVERT: B 984 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8766 (mt-10) REVERT: B 998 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8713 (tm-30) outliers start: 43 outliers final: 12 residues processed: 145 average time/residue: 0.5601 time to fit residues: 96.0987 Evaluate side-chains 110 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 56 optimal weight: 0.9980 chunk 288 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 121 ASN B 99 ASN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.055654 restraints weight = 63540.891| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.22 r_work: 0.2659 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26925 Z= 0.147 Angle : 0.608 9.518 36834 Z= 0.310 Chirality : 0.046 0.266 4359 Planarity : 0.004 0.048 4698 Dihedral : 8.864 78.074 4731 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 1.14 % Allowed : 10.01 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 3354 helix: 0.27 (0.20), residues: 711 sheet: -0.43 (0.19), residues: 654 loop : -2.11 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.014 0.001 TYR A 495 PHE 0.029 0.001 PHE B 157 TRP 0.013 0.001 TRP B 882 HIS 0.001 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00336 (26826) covalent geometry : angle 0.58370 (36582) SS BOND : bond 0.00229 ( 45) SS BOND : angle 0.98860 ( 90) hydrogen bonds : bond 0.04092 ( 938) hydrogen bonds : angle 5.60970 ( 2673) link_BETA1-4 : bond 0.00339 ( 9) link_BETA1-4 : angle 2.01689 ( 27) link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.63274 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 984 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8739 (mp0) REVERT: A 998 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 1046 MET cc_start: 0.8959 (ptm) cc_final: 0.8611 (ptm) REVERT: B 131 CYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6330 (m) REVERT: B 946 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: B 984 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8710 (mt-10) REVERT: B 998 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 984 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8807 (mp0) outliers start: 31 outliers final: 15 residues processed: 139 average time/residue: 0.5728 time to fit residues: 94.4760 Evaluate side-chains 119 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 214 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 326 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.055237 restraints weight = 63474.642| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.20 r_work: 0.2649 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26925 Z= 0.170 Angle : 0.613 9.316 36834 Z= 0.311 Chirality : 0.046 0.240 4359 Planarity : 0.004 0.046 4698 Dihedral : 8.337 66.247 4731 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.40 % Allowed : 10.89 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3354 helix: 0.65 (0.20), residues: 711 sheet: -0.37 (0.19), residues: 672 loop : -1.97 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.012 0.001 TYR A 495 PHE 0.012 0.001 PHE A1085 TRP 0.017 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00399 (26826) covalent geometry : angle 0.59117 (36582) SS BOND : bond 0.00252 ( 45) SS BOND : angle 0.98612 ( 90) hydrogen bonds : bond 0.03950 ( 938) hydrogen bonds : angle 5.49504 ( 2673) link_BETA1-4 : bond 0.00331 ( 9) link_BETA1-4 : angle 2.14134 ( 27) link_NAG-ASN : bond 0.00296 ( 45) link_NAG-ASN : angle 2.51352 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 984 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8734 (mp0) REVERT: A 998 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 1046 MET cc_start: 0.8938 (ptm) cc_final: 0.8516 (ptm) REVERT: B 984 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 998 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8639 (tm-30) REVERT: B 1104 ASN cc_start: 0.8682 (m-40) cc_final: 0.8447 (m110) REVERT: C 699 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8912 (t0) REVERT: C 998 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8676 (tm-30) outliers start: 38 outliers final: 18 residues processed: 137 average time/residue: 0.5274 time to fit residues: 87.5231 Evaluate side-chains 119 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 265 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 121 ASN B 540 ASN B 951 ASN C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.077177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.057794 restraints weight = 63218.896| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.20 r_work: 0.2706 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26925 Z= 0.101 Angle : 0.569 9.390 36834 Z= 0.285 Chirality : 0.045 0.254 4359 Planarity : 0.004 0.049 4698 Dihedral : 7.591 58.560 4731 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.29 % Allowed : 11.55 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3354 helix: 1.00 (0.20), residues: 711 sheet: -0.24 (0.19), residues: 684 loop : -1.81 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 214 TYR 0.012 0.001 TYR C 495 PHE 0.030 0.001 PHE A 157 TRP 0.023 0.001 TRP A 882 HIS 0.001 0.000 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00218 (26826) covalent geometry : angle 0.54925 (36582) SS BOND : bond 0.00174 ( 45) SS BOND : angle 0.81382 ( 90) hydrogen bonds : bond 0.03357 ( 938) hydrogen bonds : angle 5.23784 ( 2673) link_BETA1-4 : bond 0.00483 ( 9) link_BETA1-4 : angle 2.20290 ( 27) link_NAG-ASN : bond 0.00375 ( 45) link_NAG-ASN : angle 2.24521 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 TYR cc_start: 0.8199 (t80) cc_final: 0.7956 (t80) REVERT: A 984 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8751 (mp0) REVERT: A 998 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 1046 MET cc_start: 0.8795 (ptm) cc_final: 0.8580 (ptm) REVERT: B 946 ASP cc_start: 0.8798 (t70) cc_final: 0.8523 (m-30) REVERT: B 984 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8641 (mt-10) REVERT: B 998 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 998 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8694 (tm-30) outliers start: 35 outliers final: 18 residues processed: 151 average time/residue: 0.5189 time to fit residues: 94.9429 Evaluate side-chains 123 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 157 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 320 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 0.4980 chunk 269 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B1094 ASN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.055510 restraints weight = 63715.312| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.20 r_work: 0.2658 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26925 Z= 0.176 Angle : 0.598 9.404 36834 Z= 0.301 Chirality : 0.046 0.239 4359 Planarity : 0.004 0.045 4698 Dihedral : 7.430 59.918 4731 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.32 % Allowed : 12.36 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3354 helix: 1.16 (0.21), residues: 693 sheet: -0.15 (0.19), residues: 678 loop : -1.72 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.010 0.001 TYR A 170 PHE 0.012 0.001 PHE A1085 TRP 0.032 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00416 (26826) covalent geometry : angle 0.57932 (36582) SS BOND : bond 0.00279 ( 45) SS BOND : angle 1.01009 ( 90) hydrogen bonds : bond 0.03730 ( 938) hydrogen bonds : angle 5.31124 ( 2673) link_BETA1-4 : bond 0.00309 ( 9) link_BETA1-4 : angle 2.18776 ( 27) link_NAG-ASN : bond 0.00287 ( 45) link_NAG-ASN : angle 2.21854 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 984 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8746 (mp0) REVERT: A 1046 MET cc_start: 0.8842 (ptm) cc_final: 0.8500 (ptm) REVERT: B 242 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7723 (mm) REVERT: B 984 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8696 (mt-10) REVERT: B 998 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8614 (tm-30) REVERT: B 1013 GLU cc_start: 0.9087 (tt0) cc_final: 0.8876 (tm-30) REVERT: B 1104 ASN cc_start: 0.8803 (m-40) cc_final: 0.8599 (m110) REVERT: C 998 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8677 (tm-30) outliers start: 36 outliers final: 21 residues processed: 134 average time/residue: 0.4738 time to fit residues: 77.6413 Evaluate side-chains 120 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 273 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 331 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.074500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.055270 restraints weight = 62690.817| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.12 r_work: 0.2667 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26925 Z= 0.213 Angle : 0.620 9.355 36834 Z= 0.314 Chirality : 0.047 0.239 4359 Planarity : 0.004 0.045 4698 Dihedral : 7.326 58.024 4731 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 1.69 % Allowed : 12.21 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3354 helix: 1.14 (0.21), residues: 693 sheet: -0.16 (0.20), residues: 672 loop : -1.71 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 214 TYR 0.012 0.001 TYR A 170 PHE 0.033 0.001 PHE A 157 TRP 0.039 0.002 TRP A 882 HIS 0.003 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00506 (26826) covalent geometry : angle 0.59981 (36582) SS BOND : bond 0.00308 ( 45) SS BOND : angle 1.10028 ( 90) hydrogen bonds : bond 0.03969 ( 938) hydrogen bonds : angle 5.38588 ( 2673) link_BETA1-4 : bond 0.00413 ( 9) link_BETA1-4 : angle 2.15890 ( 27) link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.36696 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9410 (mmm) cc_final: 0.9141 (tpt) REVERT: A 984 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8798 (mp0) REVERT: A 998 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 1046 MET cc_start: 0.8918 (ptm) cc_final: 0.8509 (ptm) REVERT: B 242 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7683 (mm) REVERT: B 998 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8670 (tm-30) outliers start: 46 outliers final: 25 residues processed: 136 average time/residue: 0.4876 time to fit residues: 81.0411 Evaluate side-chains 123 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 882 TRP Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 280 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 253 optimal weight: 0.0980 chunk 238 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 360 ASN C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.055487 restraints weight = 62839.564| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.12 r_work: 0.2673 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26925 Z= 0.187 Angle : 0.610 9.345 36834 Z= 0.309 Chirality : 0.046 0.239 4359 Planarity : 0.004 0.055 4698 Dihedral : 7.208 58.304 4731 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.43 % Allowed : 12.62 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3354 helix: 1.17 (0.21), residues: 693 sheet: -0.15 (0.20), residues: 672 loop : -1.68 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 214 TYR 0.011 0.001 TYR C 423 PHE 0.013 0.001 PHE A1085 TRP 0.040 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00443 (26826) covalent geometry : angle 0.59094 (36582) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.03288 ( 90) hydrogen bonds : bond 0.03875 ( 938) hydrogen bonds : angle 5.34313 ( 2673) link_BETA1-4 : bond 0.00356 ( 9) link_BETA1-4 : angle 2.01835 ( 27) link_NAG-ASN : bond 0.00304 ( 45) link_NAG-ASN : angle 2.28300 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9403 (mmm) cc_final: 0.9144 (tpt) REVERT: A 984 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8807 (mp0) REVERT: A 998 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 1046 MET cc_start: 0.8912 (ptm) cc_final: 0.8509 (ptm) REVERT: B 242 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7752 (mm) REVERT: B 998 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8657 (tm-30) outliers start: 39 outliers final: 27 residues processed: 134 average time/residue: 0.5253 time to fit residues: 85.2977 Evaluate side-chains 122 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 286 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.056633 restraints weight = 63359.270| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.05 r_work: 0.2674 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26925 Z= 0.200 Angle : 0.617 9.364 36834 Z= 0.313 Chirality : 0.046 0.239 4359 Planarity : 0.004 0.058 4698 Dihedral : 7.165 58.459 4731 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.29 % Allowed : 12.95 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3354 helix: 1.14 (0.20), residues: 693 sheet: -0.12 (0.20), residues: 648 loop : -1.65 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.014 0.001 TYR A 900 PHE 0.031 0.001 PHE B 157 TRP 0.047 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00474 (26826) covalent geometry : angle 0.59639 (36582) SS BOND : bond 0.00343 ( 45) SS BOND : angle 1.42236 ( 90) hydrogen bonds : bond 0.03917 ( 938) hydrogen bonds : angle 5.34658 ( 2673) link_BETA1-4 : bond 0.00441 ( 9) link_BETA1-4 : angle 1.98970 ( 27) link_NAG-ASN : bond 0.00322 ( 45) link_NAG-ASN : angle 2.32776 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 984 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8928 (mp0) REVERT: A 998 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 1046 MET cc_start: 0.8994 (ptm) cc_final: 0.8698 (ptm) REVERT: B 242 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7768 (mm) REVERT: B 998 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8824 (tm-30) outliers start: 35 outliers final: 26 residues processed: 126 average time/residue: 0.4972 time to fit residues: 76.3462 Evaluate side-chains 121 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 847 CYS Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 882 TRP Chi-restraints excluded: chain B residue 1046 MET Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.057603 restraints weight = 63021.993| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.09 r_work: 0.2700 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26925 Z= 0.130 Angle : 0.590 9.430 36834 Z= 0.299 Chirality : 0.045 0.239 4359 Planarity : 0.004 0.063 4698 Dihedral : 6.978 59.644 4731 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.18 % Allowed : 13.13 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3354 helix: 1.22 (0.20), residues: 693 sheet: -0.09 (0.20), residues: 648 loop : -1.64 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 214 TYR 0.012 0.001 TYR A 495 PHE 0.013 0.001 PHE A1085 TRP 0.046 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00298 (26826) covalent geometry : angle 0.57086 (36582) SS BOND : bond 0.00259 ( 45) SS BOND : angle 1.25003 ( 90) hydrogen bonds : bond 0.03604 ( 938) hydrogen bonds : angle 5.24576 ( 2673) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 1.93874 ( 27) link_NAG-ASN : bond 0.00322 ( 45) link_NAG-ASN : angle 2.17586 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 898 MET cc_start: 0.9401 (mmm) cc_final: 0.9098 (tpt) REVERT: A 900 TYR cc_start: 0.7749 (t80) cc_final: 0.7024 (t80) REVERT: A 984 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8813 (mp0) REVERT: A 998 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 1046 MET cc_start: 0.8857 (ptm) cc_final: 0.8444 (ptm) REVERT: B 242 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 998 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8651 (tm-30) REVERT: C 214 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6668 (ptp-110) outliers start: 32 outliers final: 22 residues processed: 120 average time/residue: 0.4992 time to fit residues: 72.9083 Evaluate side-chains 114 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 1110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.057184 restraints weight = 63328.812| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.03 r_work: 0.2686 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26925 Z= 0.182 Angle : 0.602 9.400 36834 Z= 0.305 Chirality : 0.046 0.238 4359 Planarity : 0.004 0.061 4698 Dihedral : 6.995 58.953 4731 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.10 % Allowed : 13.13 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3354 helix: 1.22 (0.20), residues: 693 sheet: -0.17 (0.20), residues: 663 loop : -1.61 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 214 TYR 0.011 0.001 TYR B 900 PHE 0.034 0.001 PHE B 157 TRP 0.049 0.002 TRP A 882 HIS 0.002 0.000 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00431 (26826) covalent geometry : angle 0.58325 (36582) SS BOND : bond 0.00300 ( 45) SS BOND : angle 1.35832 ( 90) hydrogen bonds : bond 0.03773 ( 938) hydrogen bonds : angle 5.27512 ( 2673) link_BETA1-4 : bond 0.00437 ( 9) link_BETA1-4 : angle 1.86487 ( 27) link_NAG-ASN : bond 0.00297 ( 45) link_NAG-ASN : angle 2.19691 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5848.87 seconds wall clock time: 101 minutes 0.91 seconds (6060.91 seconds total)