Starting phenix.real_space_refine on Sun Jul 5 05:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ks9_23016/07_2026/7ks9_23016.cif" } resolution = 4.75 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= 0.016 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 109 5.16 5 C 16175 2.51 5 N 4153 2.21 5 O 4943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25380 Number of models: 1 Model: "" Number of chains: 20 Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 858 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Conformer: "B" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} bond proxies already assigned to first conformer: 875 Chain: "A" Number of atoms: 7639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 992, 7630 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Conformer: "B" Number of residues, atoms: 992, 7630 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 bond proxies already assigned to first conformer: 7791 Chain: "B" Number of atoms: 7607 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 987, 7601 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Conformer: "B" Number of residues, atoms: 987, 7601 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 bond proxies already assigned to first conformer: 7766 Chain: "C" Number of atoms: 7624 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 991, 7616 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 991, 7616 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 7780 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 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 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 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 chiralities: 12 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 residue: pdb=" N ASER B 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER B 459 " occ=0.40 residue: pdb=" N ASER C 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER C 459 " occ=0.40 Time building chain proxies: 9.50, per 1000 atoms: 0.37 Number of scatterers: 25380 At special positions: 0 Unit cell: (129.47, 140.17, 221.49, 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 109 16.00 O 4943 8.00 N 4153 7.00 C 16175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 331 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5970 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 24.9% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.936A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.957A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.873A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.755A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.468A 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 438 through 443 removed outlier: 3.562A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.665A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.865A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.532A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.624A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.945A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.792A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.521A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.812A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.598A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.936A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.532A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.517A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.548A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.508A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.784A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.823A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.836A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.582A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.460A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.570A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.505A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B1009 " --> pdb=" O GLN B1005 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B1010 " --> pdb=" O THR B1006 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B1011 " --> pdb=" O TYR B1007 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.836A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.887A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.562A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.530A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.908A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.713A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.504A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.132A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.546A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.056A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.263A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.905A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.723A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE L 21 " --> pdb=" O PHE L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.146A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.760A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR H 77 " --> pdb=" O HIS H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.906A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.860A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.504A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.725A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.587A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.824A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB7, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.396A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.608A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.289A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.533A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.646A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.616A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.486A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.664A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.845A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.803A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.630A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 728 removed outlier: 3.525A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.183A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.828A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.783A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.413A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.557A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.049A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.602A 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 660 removed outlier: 4.610A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.310A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.310A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.550A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C1088 " --> pdb=" O ILE C1081 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2637 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: 6.30 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8005 1.34 - 1.47: 6493 1.47 - 1.59: 11304 1.59 - 1.72: 0 1.72 - 1.85: 136 Bond restraints: 25938 Sorted by residual: bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N ILE H 95 " pdb=" CA ILE H 95 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.00e+01 bond pdb=" C VAL C 382 " pdb=" N SER C 383 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.37e-02 5.33e+03 9.28e+00 ... (remaining 25933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 34186 2.09 - 4.17: 1003 4.17 - 6.26: 105 6.26 - 8.35: 31 8.35 - 10.43: 8 Bond angle restraints: 35333 Sorted by residual: angle pdb=" N ASN A 764 " pdb=" CA ASN A 764 " pdb=" C ASN A 764 " ideal model delta sigma weight residual 111.07 105.84 5.23 1.07e+00 8.73e-01 2.39e+01 angle pdb=" CB LYS A 206 " pdb=" CG LYS A 206 " pdb=" CD LYS A 206 " ideal model delta sigma weight residual 111.30 121.27 -9.97 2.30e+00 1.89e-01 1.88e+01 angle pdb=" CA TYR L 91 " pdb=" C TYR L 91 " pdb=" O TYR L 91 " ideal model delta sigma weight residual 121.44 116.54 4.90 1.17e+00 7.31e-01 1.75e+01 angle pdb=" N GLN L 37 " pdb=" CA GLN L 37 " pdb=" CB GLN L 37 " ideal model delta sigma weight residual 110.87 104.10 6.77 1.63e+00 3.76e-01 1.73e+01 angle pdb=" N GLN C1010 " pdb=" CA GLN C1010 " pdb=" C GLN C1010 " ideal model delta sigma weight residual 111.36 106.95 4.41 1.09e+00 8.42e-01 1.64e+01 ... (remaining 35328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 13936 17.68 - 35.35: 786 35.35 - 53.03: 139 53.03 - 70.70: 30 70.70 - 88.38: 29 Dihedral angle restraints: 14920 sinusoidal: 5638 harmonic: 9282 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.99 82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 173.44 -80.44 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 166.79 -73.79 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 14917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3586 0.078 - 0.157: 603 0.157 - 0.235: 29 0.235 - 0.313: 8 0.313 - 0.391: 4 Chirality restraints: 4230 Sorted by residual: chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA GLN L 37 " pdb=" N GLN L 37 " pdb=" C GLN L 37 " pdb=" CB GLN L 37 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA CYS B 336 " pdb=" N CYS B 336 " pdb=" C CYS B 336 " pdb=" CB CYS B 336 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 4227 not shown) Planarity restraints: 4525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A1310 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1313 " -0.088 2.00e-02 2.50e+03 7.19e-02 6.46e+01 pdb=" C7 NAG B1313 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B1313 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG B1313 " 0.112 2.00e-02 2.50e+03 pdb=" O7 NAG B1313 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO A 987 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.036 5.00e-02 4.00e+02 ... (remaining 4522 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2657 2.76 - 3.29: 23484 3.29 - 3.83: 42739 3.83 - 4.36: 49146 4.36 - 4.90: 84241 Nonbonded interactions: 202267 Sorted by model distance: nonbonded pdb=" OG SER A 816 " pdb=" OE1 GLU A 819 " model vdw 2.222 3.040 nonbonded pdb=" O THR A1006 " pdb=" OG1 THR A1009 " model vdw 2.241 3.040 nonbonded pdb=" O THR B1006 " pdb=" OG1 THR B1009 " model vdw 2.253 3.040 nonbonded pdb=" O GLU A 298 " pdb=" OG1 THR A 302 " model vdw 2.269 3.040 nonbonded pdb=" O LEU A 296 " pdb=" OG1 THR A 299 " model vdw 2.294 3.040 ... (remaining 202262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 458 or resid 460 through 476 or resid 478 through 553 or (resid 554 and (na \ me N or name CA or name C or name O or name CB )) or resid 555 through 793 or (r \ esid 794 and (name N or name CA or name C or name O or name CB )) or resid 795 o \ r (resid 796 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 97 through 827 or resid 856 through 866 or (resid 867 through 868 and (name N or \ name CA or name C or name O or name CB )) or resid 869 through 939 or (resid 94 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1141 or (resid 1142 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1143 through 1144 or (resid 11 \ 45 through 1146 and (name N or name CA or name C or name O or name CB )) or resi \ d 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 458 or resid 460 through 476 or resid 478 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 613 or \ (resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 827 or resid 8 \ 56 through 866 or (resid 867 through 868 and (name N or name CA or name C or nam \ e O or name CB )) or resid 869 through 920 or (resid 921 and (name N or name CA \ or name C or name O or name CB )) or resid 922 through 939 or (resid 940 and (na \ me N or name CA or name C or name O or name CB )) or resid 941 through 984 or (r \ esid 985 and (name N or name CA or name C or name O or name CB )) or resid 986 t \ hrough 987 or (resid 988 through 989 and (name N or name CA or name C or name O \ or name CB )) or resid 990 through 1072 or (resid 1073 and (name N or name CA or \ name C or name O or name CB )) or resid 1074 through 1117 or (resid 1118 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1119 through 1143 or \ (resid 1144 through 1146 and (name N or name CA or name C or name O or name CB \ )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 458 or resid 460 throu \ gh 476 or resid 478 through 553 or (resid 554 and (name N or name CA or name C o \ r name O or name CB )) or resid 555 through 567 or (resid 568 and (name N or nam \ e CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 an \ d (name N or name CA or name C or name O or name CB )) or resid 572 through 581 \ or (resid 582 through 583 and (name N or name CA or name C or name O or name CB \ )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C or na \ me O or name CB )) or resid 587 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 645 or (resid 646 throug \ h 647 and (name N or name CA or name C or name O or name CB )) or resid 648 thro \ ugh 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) o \ r resid 795 or (resid 796 and (name N or name CA or name C or name O or name CB \ )) or resid 797 through 920 or (resid 921 and (name N or name CA or name C or na \ me O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N or name \ CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid 1118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1119 through 11 \ 41 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or re \ sid 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O \ or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.790 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.005 0.044 26038 Z= 0.283 Angle : 0.820 10.570 35592 Z= 0.474 Chirality : 0.054 0.391 4230 Planarity : 0.007 0.297 4478 Dihedral : 11.854 88.376 8827 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.07 % Allowed : 0.82 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3141 helix: -1.65 (0.17), residues: 647 sheet: 0.64 (0.18), residues: 708 loop : -0.30 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.024 0.001 TYR A 449 PHE 0.040 0.001 PHE A 782 TRP 0.027 0.001 TRP C 436 HIS 0.015 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.28 (25938) covalent geometry : angle 0.80307 / 0.47 (35333) SS BOND : bond 0.00389 / 0.30 ( 41) SS BOND : angle 2.49761 / 1.57 ( 82) hydrogen bonds : bond 0.26609 / 17.45 ( 937) hydrogen bonds : angle 9.48691 / 6.60 ( 2637) link_BETA1-4 : bond 0.00531 / 0.35 ( 12) link_BETA1-4 : angle 1.17439 / 0.80 ( 36) link_NAG-ASN : bond 0.00527 / 0.31 ( 47) link_NAG-ASN : angle 2.03152 / 1.36 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 251 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7450 (tpt90) cc_final: 0.7017 (tpt170) REVERT: H 71 ARG cc_start: 0.5132 (ptt180) cc_final: 0.3473 (mtp85) REVERT: H 72 HIS cc_start: 0.8201 (t-90) cc_final: 0.7965 (t70) REVERT: H 82 MET cc_start: 0.2889 (ptp) cc_final: 0.2599 (mpp) REVERT: H 82 ASN cc_start: 0.7041 (m-40) cc_final: 0.6407 (m-40) REVERT: A 714 ILE cc_start: 0.9708 (mp) cc_final: 0.9496 (tp) REVERT: A 718 PHE cc_start: 0.9693 (p90) cc_final: 0.9338 (p90) REVERT: A 740 MET cc_start: 0.9634 (mmm) cc_final: 0.9187 (tpp) REVERT: A 826 VAL cc_start: 0.8683 (t) cc_final: 0.8377 (t) REVERT: A 869 MET cc_start: 0.9834 (mpp) cc_final: 0.9596 (mpp) REVERT: A 902 MET cc_start: 0.9829 (mmp) cc_final: 0.9409 (mmm) REVERT: A 970 PHE cc_start: 0.9138 (m-10) cc_final: 0.8587 (m-10) REVERT: A 979 ASP cc_start: 0.9458 (t0) cc_final: 0.9167 (t0) REVERT: A 996 LEU cc_start: 0.9624 (tt) cc_final: 0.9408 (pp) REVERT: A 1067 TYR cc_start: 0.9225 (t80) cc_final: 0.8832 (t80) REVERT: B 55 PHE cc_start: 0.9439 (m-10) cc_final: 0.8626 (m-80) REVERT: B 727 LEU cc_start: 0.9763 (mm) cc_final: 0.9547 (tp) REVERT: B 759 PHE cc_start: 0.9201 (m-10) cc_final: 0.8704 (m-10) REVERT: B 856 ASN cc_start: 0.8660 (m110) cc_final: 0.8453 (m-40) REVERT: B 1004 LEU cc_start: 0.9488 (mt) cc_final: 0.9252 (mt) REVERT: B 1029 MET cc_start: 0.8935 (ppp) cc_final: 0.8621 (tmm) REVERT: B 1034 LEU cc_start: 0.9507 (mt) cc_final: 0.8959 (mt) REVERT: B 1067 TYR cc_start: 0.9381 (t80) cc_final: 0.9091 (t80) REVERT: B 1108 ASN cc_start: 0.9212 (m110) cc_final: 0.8917 (m-40) REVERT: C 55 PHE cc_start: 0.9278 (m-80) cc_final: 0.8458 (m-10) REVERT: C 238 PHE cc_start: 0.9299 (p90) cc_final: 0.8684 (p90) REVERT: C 365 TYR cc_start: 0.9334 (m-80) cc_final: 0.8992 (m-80) REVERT: C 773 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8773 (tp30) REVERT: C 777 ASN cc_start: 0.9725 (m-40) cc_final: 0.8521 (m-40) REVERT: C 902 MET cc_start: 0.9524 (mmp) cc_final: 0.9176 (mmp) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.1543 time to fit residues: 65.3480 Evaluate side-chains 182 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN L 37 GLN ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS A 360 ASN A 388 ASN A 450 ASN A 493 GLN A 580 GLN A 755 GLN A 762 GLN A 957 GLN ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 450 ASN B 501 ASN B 532 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1002 GLN B1119 ASN C 370 ASN C 762 GLN C 777 ASN C 978 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.042450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.026168 restraints weight = 476096.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.027753 restraints weight = 215153.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.028897 restraints weight = 131137.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.029756 restraints weight = 91306.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030381 restraints weight = 68965.626| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 26038 Z= 0.295 Angle : 0.783 14.181 35592 Z= 0.406 Chirality : 0.046 0.428 4230 Planarity : 0.005 0.044 4478 Dihedral : 4.646 35.376 3414 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3141 helix: 0.14 (0.19), residues: 683 sheet: 0.45 (0.19), residues: 725 loop : -0.06 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.021 0.003 TYR B 917 PHE 0.023 0.003 PHE B1042 TRP 0.018 0.003 TRP A1102 HIS 0.013 0.003 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.30 (25938) covalent geometry : angle 0.77161 / 0.40 (35333) SS BOND : bond 0.00651 / 0.46 ( 41) SS BOND : angle 1.49293 / 1.02 ( 82) hydrogen bonds : bond 0.05290 / 3.45 ( 937) hydrogen bonds : angle 6.70761 / 4.63 ( 2637) link_BETA1-4 : bond 0.00515 / 0.36 ( 12) link_BETA1-4 : angle 1.61276 / 1.06 ( 36) link_NAG-ASN : bond 0.00464 / 0.28 ( 47) link_NAG-ASN : angle 1.86270 / 1.32 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8526 (m-80) cc_final: 0.8091 (m-80) REVERT: A 365 TYR cc_start: 0.9710 (m-80) cc_final: 0.9386 (m-80) REVERT: A 718 PHE cc_start: 0.9871 (p90) cc_final: 0.9500 (p90) REVERT: A 756 TYR cc_start: 0.9599 (m-10) cc_final: 0.9237 (m-80) REVERT: A 861 LEU cc_start: 0.9712 (mt) cc_final: 0.9500 (tp) REVERT: A 869 MET cc_start: 0.9778 (mpp) cc_final: 0.9572 (mpp) REVERT: A 902 MET cc_start: 0.9773 (mmp) cc_final: 0.9445 (mmp) REVERT: A 979 ASP cc_start: 0.9606 (t0) cc_final: 0.9363 (t0) REVERT: B 650 LEU cc_start: 0.9362 (tp) cc_final: 0.9064 (pp) REVERT: B 759 PHE cc_start: 0.9387 (m-10) cc_final: 0.8992 (m-10) REVERT: B 869 MET cc_start: 0.9850 (mpp) cc_final: 0.9482 (mpp) REVERT: B 902 MET cc_start: 0.9735 (mmp) cc_final: 0.9510 (mmm) REVERT: B 1002 GLN cc_start: 0.9766 (tt0) cc_final: 0.9518 (tm-30) REVERT: B 1004 LEU cc_start: 0.9700 (mt) cc_final: 0.9491 (mt) REVERT: B 1034 LEU cc_start: 0.9640 (mt) cc_final: 0.9184 (mt) REVERT: C 55 PHE cc_start: 0.9274 (m-80) cc_final: 0.8605 (m-80) REVERT: C 365 TYR cc_start: 0.9663 (m-80) cc_final: 0.9319 (m-80) REVERT: C 650 LEU cc_start: 0.9787 (tp) cc_final: 0.9574 (pp) REVERT: C 902 MET cc_start: 0.9631 (mmp) cc_final: 0.9304 (mmp) REVERT: C 1029 MET cc_start: 0.9696 (tpt) cc_final: 0.9454 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1500 time to fit residues: 48.3752 Evaluate side-chains 122 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 256 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 279 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 24 GLN L 34 ASN H 72 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.025152 restraints weight = 508589.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.026710 restraints weight = 221737.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.027820 restraints weight = 133201.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.028655 restraints weight = 91955.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.029248 restraints weight = 69139.992| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 26038 Z= 0.225 Angle : 0.653 11.374 35592 Z= 0.341 Chirality : 0.044 0.200 4230 Planarity : 0.004 0.040 4478 Dihedral : 4.566 23.284 3414 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3141 helix: 0.36 (0.19), residues: 680 sheet: 0.16 (0.18), residues: 754 loop : -0.11 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 403 TYR 0.016 0.002 TYR H 59 PHE 0.035 0.002 PHE A 559 TRP 0.012 0.002 TRP C 436 HIS 0.013 0.002 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (25938) covalent geometry : angle 0.64028 / 0.34 (35333) SS BOND : bond 0.00339 / 0.23 ( 41) SS BOND : angle 1.16841 / 0.74 ( 82) hydrogen bonds : bond 0.04723 / 3.11 ( 937) hydrogen bonds : angle 6.20409 / 4.30 ( 2637) link_BETA1-4 : bond 0.00161 / 0.12 ( 12) link_BETA1-4 : angle 1.30120 / 0.84 ( 36) link_NAG-ASN : bond 0.00315 / 0.20 ( 47) link_NAG-ASN : angle 1.88198 / 1.36 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8659 (m-80) cc_final: 0.8257 (m-80) REVERT: H 82 MET cc_start: 0.1873 (mpp) cc_final: 0.0643 (mpp) REVERT: H 90 TYR cc_start: 0.1076 (m-10) cc_final: 0.0551 (m-10) REVERT: A 231 ILE cc_start: 0.8407 (tp) cc_final: 0.8176 (tt) REVERT: A 365 TYR cc_start: 0.9711 (m-80) cc_final: 0.9329 (m-80) REVERT: A 718 PHE cc_start: 0.9888 (p90) cc_final: 0.9432 (p90) REVERT: A 740 MET cc_start: 0.9749 (tpt) cc_final: 0.9496 (tpp) REVERT: A 861 LEU cc_start: 0.9735 (mt) cc_final: 0.9496 (tp) REVERT: A 902 MET cc_start: 0.9790 (mmp) cc_final: 0.9561 (mmm) REVERT: A 970 PHE cc_start: 0.9297 (m-10) cc_final: 0.8854 (m-10) REVERT: A 979 ASP cc_start: 0.9593 (t0) cc_final: 0.9350 (t0) REVERT: B 571 ASP cc_start: 0.8972 (m-30) cc_final: 0.8714 (m-30) REVERT: B 650 LEU cc_start: 0.9323 (tp) cc_final: 0.9100 (pp) REVERT: B 759 PHE cc_start: 0.9327 (m-10) cc_final: 0.8948 (m-10) REVERT: B 763 LEU cc_start: 0.9784 (mp) cc_final: 0.9407 (pp) REVERT: B 902 MET cc_start: 0.9702 (mmp) cc_final: 0.9499 (mmp) REVERT: B 1001 LEU cc_start: 0.9878 (tp) cc_final: 0.9640 (pp) REVERT: B 1002 GLN cc_start: 0.9764 (tt0) cc_final: 0.9532 (tm-30) REVERT: B 1004 LEU cc_start: 0.9731 (mt) cc_final: 0.9459 (mt) REVERT: B 1029 MET cc_start: 0.9609 (tmm) cc_final: 0.9402 (tmm) REVERT: B 1034 LEU cc_start: 0.9594 (mt) cc_final: 0.9233 (mt) REVERT: B 1067 TYR cc_start: 0.9422 (t80) cc_final: 0.9170 (t80) REVERT: C 55 PHE cc_start: 0.9269 (m-80) cc_final: 0.8640 (m-80) REVERT: C 365 TYR cc_start: 0.9615 (m-80) cc_final: 0.9280 (m-80) REVERT: C 571 ASP cc_start: 0.9336 (t0) cc_final: 0.9122 (t0) REVERT: C 773 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8977 (tp30) REVERT: C 902 MET cc_start: 0.9553 (mmp) cc_final: 0.9182 (mmp) REVERT: C 1050 MET cc_start: 0.9143 (pmm) cc_final: 0.8923 (pmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1443 time to fit residues: 42.9416 Evaluate side-chains 122 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 163 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 30.0000 chunk 189 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 290 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.028956 restraints weight = 446381.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.030493 restraints weight = 206294.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.031606 restraints weight = 127250.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032429 restraints weight = 89798.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033023 restraints weight = 68814.702| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26038 Z= 0.152 Angle : 0.565 10.148 35592 Z= 0.289 Chirality : 0.043 0.182 4230 Planarity : 0.004 0.039 4478 Dihedral : 4.342 23.284 3414 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3141 helix: 0.71 (0.20), residues: 685 sheet: 0.14 (0.18), residues: 777 loop : -0.01 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.040 0.001 TYR H 90 PHE 0.025 0.001 PHE A 559 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (25938) covalent geometry : angle 0.55445 / 0.29 (35333) SS BOND : bond 0.00260 / 0.18 ( 41) SS BOND : angle 0.96153 / 0.67 ( 82) hydrogen bonds : bond 0.03758 / 2.48 ( 937) hydrogen bonds : angle 5.86971 / 4.07 ( 2637) link_BETA1-4 : bond 0.00232 / 0.13 ( 12) link_BETA1-4 : angle 1.14751 / 0.77 ( 36) link_NAG-ASN : bond 0.00232 / 0.16 ( 47) link_NAG-ASN : angle 1.59373 / 1.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8558 (m-80) cc_final: 0.7944 (m-80) REVERT: A 231 ILE cc_start: 0.8608 (tp) cc_final: 0.8403 (tt) REVERT: A 365 TYR cc_start: 0.9672 (m-80) cc_final: 0.9317 (m-80) REVERT: A 718 PHE cc_start: 0.9892 (p90) cc_final: 0.9424 (p90) REVERT: A 740 MET cc_start: 0.9727 (tpt) cc_final: 0.9511 (tpp) REVERT: A 861 LEU cc_start: 0.9764 (mt) cc_final: 0.9542 (tp) REVERT: A 869 MET cc_start: 0.9738 (mpp) cc_final: 0.9444 (mpp) REVERT: A 902 MET cc_start: 0.9832 (mmp) cc_final: 0.9541 (mmm) REVERT: A 970 PHE cc_start: 0.9324 (m-10) cc_final: 0.8942 (m-10) REVERT: A 979 ASP cc_start: 0.9606 (t0) cc_final: 0.9358 (t0) REVERT: A 1004 LEU cc_start: 0.9677 (mm) cc_final: 0.9477 (mm) REVERT: A 1005 GLN cc_start: 0.9617 (mt0) cc_final: 0.9402 (mt0) REVERT: B 365 TYR cc_start: 0.9153 (m-10) cc_final: 0.8888 (m-10) REVERT: B 571 ASP cc_start: 0.9016 (m-30) cc_final: 0.8737 (m-30) REVERT: B 650 LEU cc_start: 0.9319 (tp) cc_final: 0.8986 (pp) REVERT: B 759 PHE cc_start: 0.9276 (m-10) cc_final: 0.8880 (m-10) REVERT: B 763 LEU cc_start: 0.9766 (mp) cc_final: 0.9458 (pp) REVERT: B 902 MET cc_start: 0.9533 (mmp) cc_final: 0.9322 (mmm) REVERT: B 1002 GLN cc_start: 0.9812 (tt0) cc_final: 0.9343 (tm-30) REVERT: B 1004 LEU cc_start: 0.9650 (mt) cc_final: 0.9372 (mt) REVERT: B 1029 MET cc_start: 0.9635 (tmm) cc_final: 0.9412 (tmm) REVERT: B 1034 LEU cc_start: 0.9681 (mt) cc_final: 0.9372 (mt) REVERT: B 1067 TYR cc_start: 0.9353 (t80) cc_final: 0.9135 (t80) REVERT: C 55 PHE cc_start: 0.9225 (m-80) cc_final: 0.8574 (m-80) REVERT: C 365 TYR cc_start: 0.9650 (m-80) cc_final: 0.9320 (m-80) REVERT: C 571 ASP cc_start: 0.9359 (t0) cc_final: 0.9156 (t0) REVERT: C 759 PHE cc_start: 0.9504 (m-80) cc_final: 0.9178 (m-80) REVERT: C 902 MET cc_start: 0.9565 (mmp) cc_final: 0.9221 (mmm) REVERT: C 1050 MET cc_start: 0.9302 (pmm) cc_final: 0.8985 (pmm) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1274 time to fit residues: 38.2552 Evaluate side-chains 126 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 76 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 overall best weight: 3.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.029768 restraints weight = 310105.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.031042 restraints weight = 168387.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.031918 restraints weight = 112339.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032591 restraints weight = 83853.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.033032 restraints weight = 67575.923| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 26038 Z= 0.223 Angle : 0.640 9.710 35592 Z= 0.331 Chirality : 0.043 0.188 4230 Planarity : 0.004 0.039 4478 Dihedral : 4.618 23.571 3414 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3141 helix: 0.44 (0.19), residues: 699 sheet: 0.12 (0.18), residues: 756 loop : -0.12 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.020 0.002 TYR C1067 PHE 0.022 0.002 PHE A1052 TRP 0.011 0.001 TRP H 47 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (25938) covalent geometry : angle 0.62857 / 0.33 (35333) SS BOND : bond 0.00335 / 0.22 ( 41) SS BOND : angle 0.99110 / 0.67 ( 82) hydrogen bonds : bond 0.04017 / 2.62 ( 937) hydrogen bonds : angle 5.99541 / 4.18 ( 2637) link_BETA1-4 : bond 0.00288 / 0.19 ( 12) link_BETA1-4 : angle 1.53409 / 1.00 ( 36) link_NAG-ASN : bond 0.00387 / 0.23 ( 47) link_NAG-ASN : angle 1.80657 / 1.28 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8542 (m-80) cc_final: 0.7939 (m-80) REVERT: A 365 TYR cc_start: 0.9679 (m-80) cc_final: 0.9255 (m-80) REVERT: A 390 LEU cc_start: 0.9648 (mp) cc_final: 0.9437 (mp) REVERT: A 740 MET cc_start: 0.9721 (tpt) cc_final: 0.9452 (tpp) REVERT: A 861 LEU cc_start: 0.9750 (mt) cc_final: 0.9489 (tp) REVERT: A 902 MET cc_start: 0.9727 (mmp) cc_final: 0.9389 (mmp) REVERT: A 970 PHE cc_start: 0.9318 (m-10) cc_final: 0.8891 (m-10) REVERT: A 979 ASP cc_start: 0.9649 (t0) cc_final: 0.9400 (t0) REVERT: A 1004 LEU cc_start: 0.9664 (mm) cc_final: 0.9393 (mt) REVERT: B 227 VAL cc_start: 0.8592 (t) cc_final: 0.8353 (t) REVERT: B 365 TYR cc_start: 0.9219 (m-10) cc_final: 0.8959 (m-10) REVERT: B 759 PHE cc_start: 0.9161 (m-10) cc_final: 0.8842 (m-10) REVERT: B 763 LEU cc_start: 0.9762 (mp) cc_final: 0.9474 (pp) REVERT: B 773 GLU cc_start: 0.9555 (pm20) cc_final: 0.9167 (tp30) REVERT: B 1004 LEU cc_start: 0.9716 (mt) cc_final: 0.9419 (mt) REVERT: B 1029 MET cc_start: 0.9676 (tmm) cc_final: 0.9445 (tmm) REVERT: B 1034 LEU cc_start: 0.9693 (mt) cc_final: 0.9422 (mt) REVERT: B 1067 TYR cc_start: 0.9307 (t80) cc_final: 0.9098 (t80) REVERT: C 55 PHE cc_start: 0.9125 (m-80) cc_final: 0.8425 (m-80) REVERT: C 118 LEU cc_start: 0.9575 (tp) cc_final: 0.9135 (mm) REVERT: C 365 TYR cc_start: 0.9666 (m-80) cc_final: 0.9338 (m-80) REVERT: C 759 PHE cc_start: 0.9524 (m-80) cc_final: 0.9166 (m-80) REVERT: C 902 MET cc_start: 0.9548 (mmp) cc_final: 0.9186 (mmp) REVERT: C 1050 MET cc_start: 0.9334 (pmm) cc_final: 0.9041 (pmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1359 time to fit residues: 35.8635 Evaluate side-chains 110 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 228 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN H 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.028990 restraints weight = 427679.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.030438 restraints weight = 203038.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.031419 restraints weight = 127676.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.032124 restraints weight = 93318.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.032646 restraints weight = 74041.224| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26038 Z= 0.204 Angle : 0.612 9.079 35592 Z= 0.317 Chirality : 0.043 0.245 4230 Planarity : 0.004 0.041 4478 Dihedral : 4.627 22.294 3414 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3141 helix: 0.56 (0.19), residues: 689 sheet: -0.02 (0.18), residues: 751 loop : -0.12 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.022 0.002 TYR A 873 PHE 0.019 0.002 PHE B 898 TRP 0.009 0.001 TRP H 47 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (25938) covalent geometry : angle 0.60181 / 0.31 (35333) SS BOND : bond 0.00360 / 0.26 ( 41) SS BOND : angle 0.92558 / 0.62 ( 82) hydrogen bonds : bond 0.03845 / 2.51 ( 937) hydrogen bonds : angle 5.96621 / 4.18 ( 2637) link_BETA1-4 : bond 0.00266 / 0.17 ( 12) link_BETA1-4 : angle 1.32419 / 0.86 ( 36) link_NAG-ASN : bond 0.00317 / 0.19 ( 47) link_NAG-ASN : angle 1.72760 / 1.22 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8548 (m-80) cc_final: 0.8003 (m-80) REVERT: A 365 TYR cc_start: 0.9632 (m-80) cc_final: 0.9092 (m-80) REVERT: A 390 LEU cc_start: 0.9612 (mp) cc_final: 0.9372 (mp) REVERT: A 740 MET cc_start: 0.9680 (tpt) cc_final: 0.9478 (tpp) REVERT: A 861 LEU cc_start: 0.9748 (mt) cc_final: 0.9532 (tp) REVERT: A 902 MET cc_start: 0.9831 (mmp) cc_final: 0.9499 (mmp) REVERT: A 970 PHE cc_start: 0.9278 (m-10) cc_final: 0.8993 (m-10) REVERT: A 979 ASP cc_start: 0.9657 (t0) cc_final: 0.9412 (t0) REVERT: B 227 VAL cc_start: 0.8757 (t) cc_final: 0.8543 (t) REVERT: B 365 TYR cc_start: 0.9240 (m-10) cc_final: 0.8956 (m-80) REVERT: B 759 PHE cc_start: 0.9117 (m-10) cc_final: 0.8831 (m-10) REVERT: B 763 LEU cc_start: 0.9762 (mp) cc_final: 0.9470 (pp) REVERT: B 764 ASN cc_start: 0.9726 (t0) cc_final: 0.9489 (m110) REVERT: B 773 GLU cc_start: 0.9533 (pm20) cc_final: 0.9187 (tp30) REVERT: B 902 MET cc_start: 0.9664 (mmp) cc_final: 0.9418 (mmp) REVERT: B 1004 LEU cc_start: 0.9748 (mt) cc_final: 0.9443 (mt) REVERT: B 1029 MET cc_start: 0.9688 (tmm) cc_final: 0.9481 (tmm) REVERT: B 1034 LEU cc_start: 0.9704 (mt) cc_final: 0.9422 (mt) REVERT: B 1050 MET cc_start: 0.9148 (pmm) cc_final: 0.8754 (pmm) REVERT: B 1067 TYR cc_start: 0.9290 (t80) cc_final: 0.9029 (t80) REVERT: C 365 TYR cc_start: 0.9634 (m-80) cc_final: 0.9324 (m-80) REVERT: C 902 MET cc_start: 0.9554 (mmp) cc_final: 0.9196 (mmm) REVERT: C 1050 MET cc_start: 0.9374 (pmm) cc_final: 0.8972 (pmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1259 time to fit residues: 32.1480 Evaluate side-chains 105 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 150 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.028765 restraints weight = 390492.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.030166 restraints weight = 191928.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.031144 restraints weight = 122493.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031840 restraints weight = 89102.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.032334 restraints weight = 70360.489| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 26038 Z= 0.189 Angle : 0.600 8.638 35592 Z= 0.309 Chirality : 0.043 0.206 4230 Planarity : 0.004 0.042 4478 Dihedral : 4.605 21.811 3414 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3141 helix: 0.71 (0.20), residues: 695 sheet: -0.03 (0.18), residues: 742 loop : -0.14 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1000 TYR 0.027 0.002 TYR H 96 PHE 0.018 0.002 PHE A 970 TRP 0.010 0.001 TRP C 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (25938) covalent geometry : angle 0.58978 / 0.31 (35333) SS BOND : bond 0.00348 / 0.25 ( 41) SS BOND : angle 0.90157 / 0.60 ( 82) hydrogen bonds : bond 0.03724 / 2.45 ( 937) hydrogen bonds : angle 5.87437 / 4.12 ( 2637) link_BETA1-4 : bond 0.00309 / 0.21 ( 12) link_BETA1-4 : angle 1.35585 / 0.88 ( 36) link_NAG-ASN : bond 0.00294 / 0.18 ( 47) link_NAG-ASN : angle 1.70432 / 1.21 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8533 (m-80) cc_final: 0.7990 (m-80) REVERT: A 756 TYR cc_start: 0.9512 (m-10) cc_final: 0.9125 (m-80) REVERT: A 861 LEU cc_start: 0.9733 (mt) cc_final: 0.9521 (tp) REVERT: A 902 MET cc_start: 0.9826 (mmp) cc_final: 0.9523 (mmp) REVERT: A 979 ASP cc_start: 0.9678 (t0) cc_final: 0.9435 (t0) REVERT: A 994 ASP cc_start: 0.9279 (m-30) cc_final: 0.9039 (m-30) REVERT: A 1004 LEU cc_start: 0.9766 (mm) cc_final: 0.9523 (mm) REVERT: B 365 TYR cc_start: 0.9227 (m-10) cc_final: 0.8942 (m-80) REVERT: B 731 MET cc_start: 0.8922 (tmm) cc_final: 0.8627 (tmm) REVERT: B 763 LEU cc_start: 0.9759 (mp) cc_final: 0.9511 (pp) REVERT: B 1004 LEU cc_start: 0.9746 (mt) cc_final: 0.9438 (mt) REVERT: B 1029 MET cc_start: 0.9697 (tmm) cc_final: 0.9485 (tmm) REVERT: B 1034 LEU cc_start: 0.9722 (mt) cc_final: 0.9436 (mt) REVERT: B 1050 MET cc_start: 0.9223 (pmm) cc_final: 0.8912 (pmm) REVERT: B 1067 TYR cc_start: 0.9261 (t80) cc_final: 0.8993 (t80) REVERT: C 365 TYR cc_start: 0.9631 (m-80) cc_final: 0.9326 (m-80) REVERT: C 902 MET cc_start: 0.9610 (mmp) cc_final: 0.9269 (mmm) REVERT: C 1050 MET cc_start: 0.9388 (pmm) cc_final: 0.8934 (pmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1340 time to fit residues: 31.6218 Evaluate side-chains 100 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 74 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 64 optimal weight: 0.0870 chunk 253 optimal weight: 20.0000 chunk 307 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 0.0020 chunk 55 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.028939 restraints weight = 408377.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.030362 restraints weight = 196199.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.031348 restraints weight = 124001.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.032035 restraints weight = 90058.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032521 restraints weight = 71321.437| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26038 Z= 0.170 Angle : 0.580 8.380 35592 Z= 0.298 Chirality : 0.043 0.211 4230 Planarity : 0.004 0.043 4478 Dihedral : 4.505 20.858 3414 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3141 helix: 0.77 (0.20), residues: 695 sheet: -0.08 (0.18), residues: 752 loop : -0.12 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.015 0.001 TYR B 741 PHE 0.017 0.001 PHE B 559 TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (25938) covalent geometry : angle 0.56935 / 0.30 (35333) SS BOND : bond 0.00264 / 0.18 ( 41) SS BOND : angle 0.96093 / 0.63 ( 82) hydrogen bonds : bond 0.03623 / 2.39 ( 937) hydrogen bonds : angle 5.81742 / 4.08 ( 2637) link_BETA1-4 : bond 0.00298 / 0.17 ( 12) link_BETA1-4 : angle 1.27681 / 0.83 ( 36) link_NAG-ASN : bond 0.00252 / 0.16 ( 47) link_NAG-ASN : angle 1.63184 / 1.16 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8437 (m-80) cc_final: 0.7875 (m-80) REVERT: A 861 LEU cc_start: 0.9752 (mt) cc_final: 0.9534 (tp) REVERT: A 902 MET cc_start: 0.9836 (mmp) cc_final: 0.9531 (mmp) REVERT: A 979 ASP cc_start: 0.9698 (t0) cc_final: 0.9438 (t0) REVERT: A 1004 LEU cc_start: 0.9728 (mm) cc_final: 0.9515 (mm) REVERT: A 1067 TYR cc_start: 0.9147 (t80) cc_final: 0.8778 (t80) REVERT: B 365 TYR cc_start: 0.9218 (m-10) cc_final: 0.8925 (m-80) REVERT: B 731 MET cc_start: 0.8946 (tmm) cc_final: 0.8560 (tmm) REVERT: B 1004 LEU cc_start: 0.9726 (mt) cc_final: 0.9429 (mt) REVERT: B 1029 MET cc_start: 0.9690 (tmm) cc_final: 0.9470 (tmm) REVERT: B 1034 LEU cc_start: 0.9730 (mt) cc_final: 0.9453 (mt) REVERT: B 1050 MET cc_start: 0.9268 (pmm) cc_final: 0.8892 (pmm) REVERT: B 1067 TYR cc_start: 0.9280 (t80) cc_final: 0.8982 (t80) REVERT: C 365 TYR cc_start: 0.9611 (m-80) cc_final: 0.9304 (m-80) REVERT: C 902 MET cc_start: 0.9583 (mmp) cc_final: 0.9240 (mmm) REVERT: C 1050 MET cc_start: 0.9392 (pmm) cc_final: 0.8887 (pmm) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1316 time to fit residues: 31.5496 Evaluate side-chains 95 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 118 optimal weight: 20.0000 chunk 313 optimal weight: 0.8980 chunk 288 optimal weight: 0.0980 chunk 238 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 294 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.028820 restraints weight = 472354.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.030342 restraints weight = 211606.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.031386 restraints weight = 129806.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.032086 restraints weight = 92742.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032592 restraints weight = 73759.502| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26038 Z= 0.140 Angle : 0.568 8.496 35592 Z= 0.289 Chirality : 0.043 0.211 4230 Planarity : 0.004 0.044 4478 Dihedral : 4.377 20.384 3414 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3141 helix: 0.93 (0.20), residues: 695 sheet: -0.13 (0.18), residues: 766 loop : -0.06 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1000 TYR 0.014 0.001 TYR B 741 PHE 0.017 0.001 PHE A 970 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (25938) covalent geometry : angle 0.55716 / 0.29 (35333) SS BOND : bond 0.00218 / 0.15 ( 41) SS BOND : angle 1.12090 / 0.73 ( 82) hydrogen bonds : bond 0.03461 / 2.30 ( 937) hydrogen bonds : angle 5.69617 / 4.01 ( 2637) link_BETA1-4 : bond 0.00257 / 0.15 ( 12) link_BETA1-4 : angle 1.18313 / 0.77 ( 36) link_NAG-ASN : bond 0.00224 / 0.15 ( 47) link_NAG-ASN : angle 1.55977 / 1.10 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8430 (m-80) cc_final: 0.7880 (m-80) REVERT: A 861 LEU cc_start: 0.9743 (mt) cc_final: 0.9537 (tp) REVERT: A 902 MET cc_start: 0.9838 (mmp) cc_final: 0.9541 (mmp) REVERT: A 979 ASP cc_start: 0.9715 (t0) cc_final: 0.9474 (t0) REVERT: A 1004 LEU cc_start: 0.9734 (mm) cc_final: 0.9516 (mm) REVERT: A 1067 TYR cc_start: 0.9156 (t80) cc_final: 0.8793 (t80) REVERT: B 365 TYR cc_start: 0.9208 (m-10) cc_final: 0.8901 (m-80) REVERT: B 731 MET cc_start: 0.8936 (tmm) cc_final: 0.8507 (tmm) REVERT: B 900 MET cc_start: 0.9823 (mmp) cc_final: 0.9578 (mmm) REVERT: B 1004 LEU cc_start: 0.9710 (mt) cc_final: 0.9411 (mt) REVERT: B 1029 MET cc_start: 0.9685 (tmm) cc_final: 0.9431 (tmm) REVERT: B 1034 LEU cc_start: 0.9746 (mt) cc_final: 0.9393 (mt) REVERT: B 1050 MET cc_start: 0.9189 (pmm) cc_final: 0.8825 (pmm) REVERT: B 1067 TYR cc_start: 0.9272 (t80) cc_final: 0.8960 (t80) REVERT: C 365 TYR cc_start: 0.9602 (m-80) cc_final: 0.9281 (m-80) REVERT: C 902 MET cc_start: 0.9582 (mmp) cc_final: 0.9261 (mmm) REVERT: C 1050 MET cc_start: 0.9385 (pmm) cc_final: 0.8872 (pmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1214 time to fit residues: 29.8778 Evaluate side-chains 97 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 212 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 141 optimal weight: 0.3980 chunk 209 optimal weight: 0.7980 chunk 192 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 234 optimal weight: 0.0570 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.045914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.029592 restraints weight = 380420.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.031065 restraints weight = 183669.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.032116 restraints weight = 115410.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.032811 restraints weight = 83266.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.033333 restraints weight = 66252.681| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26038 Z= 0.095 Angle : 0.570 10.426 35592 Z= 0.283 Chirality : 0.045 0.245 4230 Planarity : 0.003 0.045 4478 Dihedral : 4.114 19.012 3414 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3141 helix: 1.15 (0.20), residues: 685 sheet: 0.06 (0.18), residues: 759 loop : -0.01 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.015 0.001 TYR A1007 PHE 0.012 0.001 PHE A 817 TRP 0.017 0.001 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (25938) covalent geometry : angle 0.55713 / 0.28 (35333) SS BOND : bond 0.00258 / 0.18 ( 41) SS BOND : angle 1.19511 / 0.78 ( 82) hydrogen bonds : bond 0.03231 / 2.16 ( 937) hydrogen bonds : angle 5.42400 / 3.81 ( 2637) link_BETA1-4 : bond 0.00349 / 0.22 ( 12) link_BETA1-4 : angle 0.91807 / 0.58 ( 36) link_NAG-ASN : bond 0.00371 / 0.22 ( 47) link_NAG-ASN : angle 1.80500 / 1.35 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6282 Ramachandran restraints generated. 3141 Oldfield, 0 Emsley, 3141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8423 (m-80) cc_final: 0.7930 (m-80) REVERT: A 902 MET cc_start: 0.9845 (mmp) cc_final: 0.9424 (mmp) REVERT: A 979 ASP cc_start: 0.9712 (t0) cc_final: 0.9477 (t0) REVERT: A 1004 LEU cc_start: 0.9743 (mm) cc_final: 0.9533 (mm) REVERT: A 1067 TYR cc_start: 0.9154 (t80) cc_final: 0.8535 (t80) REVERT: B 365 TYR cc_start: 0.9080 (m-10) cc_final: 0.8820 (m-80) REVERT: B 731 MET cc_start: 0.8971 (tmm) cc_final: 0.8536 (tmm) REVERT: B 902 MET cc_start: 0.9713 (mmp) cc_final: 0.9500 (mmp) REVERT: B 1004 LEU cc_start: 0.9704 (mt) cc_final: 0.9421 (mt) REVERT: B 1009 THR cc_start: 0.9607 (p) cc_final: 0.9403 (p) REVERT: B 1029 MET cc_start: 0.9655 (tmm) cc_final: 0.9345 (tmm) REVERT: B 1034 LEU cc_start: 0.9748 (mt) cc_final: 0.9371 (mt) REVERT: B 1050 MET cc_start: 0.9068 (pmm) cc_final: 0.8682 (pmm) REVERT: B 1067 TYR cc_start: 0.9277 (t80) cc_final: 0.8907 (t80) REVERT: C 277 LEU cc_start: 0.9719 (mt) cc_final: 0.9351 (tt) REVERT: C 365 TYR cc_start: 0.9583 (m-80) cc_final: 0.9243 (m-80) REVERT: C 902 MET cc_start: 0.9578 (mmp) cc_final: 0.9260 (mmm) REVERT: C 960 ASN cc_start: 0.9732 (m110) cc_final: 0.9490 (m110) REVERT: C 1050 MET cc_start: 0.9312 (pmm) cc_final: 0.8909 (pmm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1224 time to fit residues: 34.3173 Evaluate side-chains 121 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 305 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN H 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.045413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.029273 restraints weight = 397080.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.030726 restraints weight = 191334.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.031758 restraints weight = 120672.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.032467 restraints weight = 87210.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032949 restraints weight = 68769.537| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26038 Z= 0.125 Angle : 0.565 10.118 35592 Z= 0.285 Chirality : 0.043 0.285 4230 Planarity : 0.004 0.044 4478 Dihedral : 4.117 21.407 3414 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3141 helix: 1.16 (0.20), residues: 685 sheet: 0.04 (0.18), residues: 765 loop : 0.01 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 61 TYR 0.018 0.001 TYR C 396 PHE 0.014 0.001 PHE B 559 TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (25938) covalent geometry : angle 0.55163 / 0.28 (35333) SS BOND : bond 0.00274 / 0.19 ( 41) SS BOND : angle 1.27311 / 0.75 ( 82) hydrogen bonds : bond 0.03297 / 2.20 ( 937) hydrogen bonds : angle 5.44049 / 3.82 ( 2637) link_BETA1-4 : bond 0.00278 / 0.17 ( 12) link_BETA1-4 : angle 1.09834 / 0.73 ( 36) link_NAG-ASN : bond 0.00198 / 0.14 ( 47) link_NAG-ASN : angle 1.73956 / 1.28 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3919.64 seconds wall clock time: 69 minutes 18.32 seconds (4158.32 seconds total)