Starting phenix.real_space_refine on Thu Mar 5 22:13:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ks9_23016/03_2026/7ks9_23016.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ks9_23016/03_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_23016/03_2026/7ks9_23016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ks9_23016/03_2026/7ks9_23016.map" model { file = "/net/cci-nas-00/data/ceres_data/7ks9_23016/03_2026/7ks9_23016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ks9_23016/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 39 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 dihedrals: 36 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: 9.68, per 1000 atoms: 0.38 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: 1.72 Conformation dependent library (CDL) restraints added in 1.9 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: 1.01 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: 6.04 Time building geometry restraints manager: 2.33 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: 15089 17.68 - 35.35: 844 35.35 - 53.03: 163 53.03 - 70.70: 34 70.70 - 88.38: 29 Dihedral angle restraints: 16159 sinusoidal: 6877 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 16156 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: 4.090 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 28.920 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 11.623 88.376 10066 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 covalent geometry : bond 0.00458 (25938) covalent geometry : angle 0.80307 (35333) SS BOND : bond 0.00389 ( 41) SS BOND : angle 2.49761 ( 82) hydrogen bonds : bond 0.26609 ( 937) hydrogen bonds : angle 9.48691 ( 2637) link_BETA1-4 : bond 0.00531 ( 12) link_BETA1-4 : angle 1.17439 ( 36) link_NAG-ASN : bond 0.00527 ( 47) link_NAG-ASN : angle 2.03152 ( 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 : 0.974 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: 0.1431 time to fit residues: 60.2891 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 : 0.946 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 34 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3021 r_free = 0.3021 target = 0.042809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.026360 restraints weight = 489085.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.027982 restraints weight = 217141.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.029135 restraints weight = 131051.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.029952 restraints weight = 90918.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030582 restraints weight = 69115.199| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 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 = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 26038 Z= 0.292 Angle : 0.774 14.354 35592 Z= 0.403 Chirality : 0.047 0.578 4230 Planarity : 0.005 0.046 4478 Dihedral : 5.932 59.564 4653 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 0.09 (0.19), residues: 686 sheet: 0.48 (0.19), residues: 723 loop : -0.06 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.019 0.002 TYR C 313 PHE 0.021 0.002 PHE B1042 TRP 0.018 0.003 TRP A1102 HIS 0.013 0.002 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00566 (25938) covalent geometry : angle 0.76406 (35333) SS BOND : bond 0.00420 ( 41) SS BOND : angle 1.37068 ( 82) hydrogen bonds : bond 0.05274 ( 937) hydrogen bonds : angle 6.71806 ( 2637) link_BETA1-4 : bond 0.00462 ( 12) link_BETA1-4 : angle 1.61205 ( 36) link_NAG-ASN : bond 0.00435 ( 47) link_NAG-ASN : angle 1.77959 ( 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 184 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8571 (m-80) cc_final: 0.8159 (m-80) REVERT: A 365 TYR cc_start: 0.9700 (m-80) cc_final: 0.9378 (m-80) REVERT: A 718 PHE cc_start: 0.9861 (p90) cc_final: 0.9490 (p90) REVERT: A 861 LEU cc_start: 0.9716 (mt) cc_final: 0.9499 (tp) REVERT: A 869 MET cc_start: 0.9765 (mpp) cc_final: 0.9562 (mpp) REVERT: A 902 MET cc_start: 0.9767 (mmp) cc_final: 0.9445 (mmp) REVERT: A 979 ASP cc_start: 0.9602 (t0) cc_final: 0.9356 (t0) REVERT: B 650 LEU cc_start: 0.9365 (tp) cc_final: 0.9122 (pp) REVERT: B 759 PHE cc_start: 0.9414 (m-10) cc_final: 0.9018 (m-10) REVERT: B 869 MET cc_start: 0.9851 (mpp) cc_final: 0.9487 (mpp) REVERT: B 902 MET cc_start: 0.9732 (mmp) cc_final: 0.9509 (mmm) REVERT: B 1002 GLN cc_start: 0.9748 (tt0) cc_final: 0.9511 (tm-30) REVERT: B 1004 LEU cc_start: 0.9693 (mt) cc_final: 0.9482 (mt) REVERT: B 1034 LEU cc_start: 0.9637 (mt) cc_final: 0.9162 (mt) REVERT: C 55 PHE cc_start: 0.9262 (m-80) cc_final: 0.8601 (m-80) REVERT: C 365 TYR cc_start: 0.9661 (m-80) cc_final: 0.9307 (m-80) REVERT: C 650 LEU cc_start: 0.9785 (tp) cc_final: 0.9569 (pp) REVERT: C 902 MET cc_start: 0.9621 (mmp) cc_final: 0.9282 (mmp) REVERT: C 1029 MET cc_start: 0.9676 (tpt) cc_final: 0.9430 (tpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1411 time to fit residues: 44.8224 Evaluate side-chains 123 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 279 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 72 HIS A 755 GLN ** 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 ** C 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.024927 restraints weight = 517470.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.026453 restraints weight = 224640.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.027545 restraints weight = 134328.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.028313 restraints weight = 92796.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028906 restraints weight = 70445.754| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 26038 Z= 0.249 Angle : 0.685 11.389 35592 Z= 0.360 Chirality : 0.045 0.191 4230 Planarity : 0.005 0.044 4478 Dihedral : 5.806 58.906 4653 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 : 0.00 % 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: -0.14 (0.14), residues: 3141 helix: 0.20 (0.19), residues: 684 sheet: 0.11 (0.18), residues: 726 loop : -0.20 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 403 TYR 0.023 0.002 TYR L 86 PHE 0.024 0.002 PHE B 58 TRP 0.011 0.002 TRP C 436 HIS 0.018 0.002 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00487 (25938) covalent geometry : angle 0.67224 (35333) SS BOND : bond 0.00514 ( 41) SS BOND : angle 1.23144 ( 82) hydrogen bonds : bond 0.04812 ( 937) hydrogen bonds : angle 6.30137 ( 2637) link_BETA1-4 : bond 0.00498 ( 12) link_BETA1-4 : angle 1.49843 ( 36) link_NAG-ASN : bond 0.00370 ( 47) link_NAG-ASN : angle 1.93309 ( 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 167 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8664 (m-80) cc_final: 0.8274 (m-80) REVERT: H 82 MET cc_start: 0.1903 (mpp) cc_final: 0.1024 (mpp) REVERT: A 365 TYR cc_start: 0.9695 (m-80) cc_final: 0.9246 (m-80) REVERT: A 390 LEU cc_start: 0.9604 (mp) cc_final: 0.9393 (mp) REVERT: A 740 MET cc_start: 0.9745 (tpt) cc_final: 0.9506 (tpp) REVERT: A 861 LEU cc_start: 0.9750 (mt) cc_final: 0.9512 (tp) REVERT: A 902 MET cc_start: 0.9782 (mmp) cc_final: 0.9572 (mmm) REVERT: A 970 PHE cc_start: 0.9300 (m-10) cc_final: 0.8922 (m-10) REVERT: A 979 ASP cc_start: 0.9598 (t0) cc_final: 0.9341 (t0) REVERT: B 571 ASP cc_start: 0.8964 (m-30) cc_final: 0.8699 (m-30) REVERT: B 650 LEU cc_start: 0.9330 (tp) cc_final: 0.9100 (pp) REVERT: B 759 PHE cc_start: 0.9291 (m-10) cc_final: 0.9022 (m-10) REVERT: B 763 LEU cc_start: 0.9778 (mp) cc_final: 0.9422 (pp) REVERT: B 945 LEU cc_start: 0.9647 (mt) cc_final: 0.9374 (pp) REVERT: B 1002 GLN cc_start: 0.9765 (tt0) cc_final: 0.9383 (tm-30) REVERT: B 1004 LEU cc_start: 0.9735 (mt) cc_final: 0.9478 (mt) REVERT: B 1029 MET cc_start: 0.9628 (tmm) cc_final: 0.9428 (tmm) REVERT: B 1034 LEU cc_start: 0.9593 (mt) cc_final: 0.9243 (mt) REVERT: B 1067 TYR cc_start: 0.9377 (t80) cc_final: 0.9124 (t80) REVERT: C 55 PHE cc_start: 0.9237 (m-80) cc_final: 0.8601 (m-80) REVERT: C 365 TYR cc_start: 0.9611 (m-80) cc_final: 0.9289 (m-80) REVERT: C 900 MET cc_start: 0.9573 (mpp) cc_final: 0.9335 (mmp) REVERT: C 902 MET cc_start: 0.9601 (mmp) cc_final: 0.9311 (mmp) REVERT: C 1050 MET cc_start: 0.9268 (pmm) cc_final: 0.8991 (pmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1332 time to fit residues: 38.7398 Evaluate side-chains 118 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 189 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 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 = 0.044595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.028937 restraints weight = 441383.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.030507 restraints weight = 203920.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.031601 restraints weight = 125650.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032398 restraints weight = 89561.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033002 restraints weight = 69076.086| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 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 = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26038 Z= 0.138 Angle : 0.559 10.176 35592 Z= 0.285 Chirality : 0.043 0.191 4230 Planarity : 0.004 0.037 4478 Dihedral : 5.259 59.363 4653 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 0.17 (0.15), residues: 3141 helix: 0.72 (0.19), residues: 679 sheet: 0.15 (0.18), residues: 760 loop : -0.05 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.017 0.001 TYR H 59 PHE 0.024 0.001 PHE A 559 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00280 (25938) covalent geometry : angle 0.54881 (35333) SS BOND : bond 0.00271 ( 41) SS BOND : angle 0.90355 ( 82) hydrogen bonds : bond 0.03735 ( 937) hydrogen bonds : angle 5.88407 ( 2637) link_BETA1-4 : bond 0.00176 ( 12) link_BETA1-4 : angle 1.14002 ( 36) link_NAG-ASN : bond 0.00242 ( 47) link_NAG-ASN : angle 1.60139 ( 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 172 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8578 (m-80) cc_final: 0.7975 (m-80) REVERT: A 365 TYR cc_start: 0.9664 (m-80) cc_final: 0.9266 (m-80) REVERT: A 718 PHE cc_start: 0.9887 (p90) cc_final: 0.9402 (p90) REVERT: A 740 MET cc_start: 0.9716 (tpt) cc_final: 0.9504 (tpp) REVERT: A 861 LEU cc_start: 0.9761 (mt) cc_final: 0.9541 (tp) REVERT: A 869 MET cc_start: 0.9737 (mpp) cc_final: 0.9440 (mpp) REVERT: A 902 MET cc_start: 0.9816 (mmp) cc_final: 0.9536 (mmm) REVERT: A 970 PHE cc_start: 0.9321 (m-10) cc_final: 0.8943 (m-10) REVERT: A 979 ASP cc_start: 0.9613 (t0) cc_final: 0.9343 (t0) REVERT: A 1004 LEU cc_start: 0.9676 (mm) cc_final: 0.9443 (mm) REVERT: A 1067 TYR cc_start: 0.9409 (t80) cc_final: 0.9168 (t80) REVERT: B 227 VAL cc_start: 0.8425 (t) cc_final: 0.8184 (t) REVERT: B 365 TYR cc_start: 0.9148 (m-10) cc_final: 0.8921 (m-10) REVERT: B 571 ASP cc_start: 0.8992 (m-30) cc_final: 0.8712 (m-30) REVERT: B 650 LEU cc_start: 0.9318 (tp) cc_final: 0.9049 (pp) REVERT: B 759 PHE cc_start: 0.9270 (m-10) cc_final: 0.8893 (m-10) REVERT: B 763 LEU cc_start: 0.9763 (mp) cc_final: 0.9454 (pp) REVERT: B 773 GLU cc_start: 0.9616 (pm20) cc_final: 0.9232 (pm20) REVERT: B 902 MET cc_start: 0.9644 (mmp) cc_final: 0.9374 (mmp) REVERT: B 1002 GLN cc_start: 0.9733 (tt0) cc_final: 0.9364 (tm-30) REVERT: B 1004 LEU cc_start: 0.9730 (mt) cc_final: 0.9464 (mt) REVERT: B 1005 GLN cc_start: 0.9474 (tm-30) cc_final: 0.9064 (tm-30) REVERT: B 1029 MET cc_start: 0.9636 (tmm) cc_final: 0.9409 (tmm) REVERT: B 1034 LEU cc_start: 0.9696 (mt) cc_final: 0.9400 (mt) REVERT: B 1067 TYR cc_start: 0.9351 (t80) cc_final: 0.9106 (t80) REVERT: C 55 PHE cc_start: 0.9226 (m-80) cc_final: 0.8600 (m-80) REVERT: C 277 LEU cc_start: 0.9729 (mm) cc_final: 0.9194 (tt) REVERT: C 365 TYR cc_start: 0.9652 (m-80) cc_final: 0.9323 (m-80) REVERT: C 902 MET cc_start: 0.9582 (mmp) cc_final: 0.9246 (mmm) REVERT: C 1050 MET cc_start: 0.9313 (pmm) cc_final: 0.8999 (pmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1420 time to fit residues: 42.5174 Evaluate side-chains 129 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 0.0770 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 129 optimal weight: 0.0670 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 784 GLN C 544 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.029907 restraints weight = 301161.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.031291 restraints weight = 160214.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032281 restraints weight = 105050.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032972 restraints weight = 77311.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033475 restraints weight = 61653.412| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- 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: 19 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26038 Z= 0.110 Angle : 0.540 9.662 35592 Z= 0.275 Chirality : 0.043 0.185 4230 Planarity : 0.003 0.041 4478 Dihedral : 4.903 59.458 4653 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.04 % Allowed : 0.63 % 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: 0.29 (0.15), residues: 3141 helix: 0.84 (0.20), residues: 688 sheet: 0.22 (0.18), residues: 766 loop : 0.03 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.017 0.001 TYR H 59 PHE 0.024 0.001 PHE B 782 TRP 0.011 0.001 TRP C 436 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00227 (25938) covalent geometry : angle 0.53112 (35333) SS BOND : bond 0.00220 ( 41) SS BOND : angle 0.84528 ( 82) hydrogen bonds : bond 0.03611 ( 937) hydrogen bonds : angle 5.68442 ( 2637) link_BETA1-4 : bond 0.00230 ( 12) link_BETA1-4 : angle 1.09928 ( 36) link_NAG-ASN : bond 0.00230 ( 47) link_NAG-ASN : angle 1.49438 ( 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 175 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8482 (m-80) cc_final: 0.7993 (m-80) REVERT: A 365 TYR cc_start: 0.9663 (m-80) cc_final: 0.9260 (m-80) REVERT: A 718 PHE cc_start: 0.9882 (p90) cc_final: 0.9460 (p90) REVERT: A 902 MET cc_start: 0.9764 (mmp) cc_final: 0.9456 (mmp) REVERT: A 970 PHE cc_start: 0.9279 (m-10) cc_final: 0.9069 (m-10) REVERT: A 979 ASP cc_start: 0.9625 (t0) cc_final: 0.9361 (t0) REVERT: A 1004 LEU cc_start: 0.9656 (mm) cc_final: 0.9311 (mt) REVERT: B 227 VAL cc_start: 0.8445 (t) cc_final: 0.8202 (t) REVERT: B 365 TYR cc_start: 0.9164 (m-10) cc_final: 0.8900 (m-10) REVERT: B 571 ASP cc_start: 0.8930 (m-30) cc_final: 0.8670 (m-30) REVERT: B 650 LEU cc_start: 0.9277 (tp) cc_final: 0.8970 (pp) REVERT: B 763 LEU cc_start: 0.9751 (mp) cc_final: 0.9247 (pp) REVERT: B 902 MET cc_start: 0.9650 (mmp) cc_final: 0.9414 (mmp) REVERT: B 1002 GLN cc_start: 0.9781 (tt0) cc_final: 0.9480 (tm-30) REVERT: B 1004 LEU cc_start: 0.9738 (mt) cc_final: 0.9429 (pp) REVERT: B 1029 MET cc_start: 0.9659 (tmm) cc_final: 0.9376 (tmm) REVERT: B 1034 LEU cc_start: 0.9705 (mt) cc_final: 0.9416 (mt) REVERT: B 1067 TYR cc_start: 0.9332 (t80) cc_final: 0.9072 (t80) REVERT: C 55 PHE cc_start: 0.9173 (m-80) cc_final: 0.8485 (m-80) REVERT: C 277 LEU cc_start: 0.9733 (mm) cc_final: 0.9227 (tt) REVERT: C 365 TYR cc_start: 0.9667 (m-80) cc_final: 0.9342 (m-80) REVERT: C 759 PHE cc_start: 0.9505 (m-80) cc_final: 0.9237 (m-80) REVERT: C 902 MET cc_start: 0.9580 (mmp) cc_final: 0.9229 (mmm) REVERT: C 1050 MET cc_start: 0.9346 (pmm) cc_final: 0.9032 (pmm) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.1263 time to fit residues: 38.9769 Evaluate side-chains 127 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 9.9990 chunk 190 optimal weight: 0.0470 chunk 9 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 275 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.029337 restraints weight = 422427.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.030764 restraints weight = 203752.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.031773 restraints weight = 129303.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.032461 restraints weight = 94081.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.032954 restraints weight = 75040.950| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 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 = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 26038 Z= 0.242 Angle : 0.653 9.694 35592 Z= 0.339 Chirality : 0.044 0.230 4230 Planarity : 0.004 0.039 4478 Dihedral : 5.375 59.972 4653 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.38 (0.19), residues: 702 sheet: 0.10 (0.18), residues: 732 loop : -0.14 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1000 TYR 0.024 0.002 TYR C1067 PHE 0.019 0.002 PHE A 559 TRP 0.009 0.001 TRP H 47 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00476 (25938) covalent geometry : angle 0.64153 (35333) SS BOND : bond 0.00479 ( 41) SS BOND : angle 0.98688 ( 82) hydrogen bonds : bond 0.03987 ( 937) hydrogen bonds : angle 6.01208 ( 2637) link_BETA1-4 : bond 0.00375 ( 12) link_BETA1-4 : angle 1.59813 ( 36) link_NAG-ASN : bond 0.00406 ( 47) link_NAG-ASN : angle 1.84270 ( 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 145 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8514 (m-80) cc_final: 0.7963 (m-80) REVERT: A 365 TYR cc_start: 0.9653 (m-80) cc_final: 0.9210 (m-80) REVERT: A 390 LEU cc_start: 0.9661 (mp) cc_final: 0.9445 (mp) REVERT: A 740 MET cc_start: 0.9717 (tpt) cc_final: 0.9457 (tpp) REVERT: A 756 TYR cc_start: 0.9489 (m-10) cc_final: 0.9120 (m-80) REVERT: A 902 MET cc_start: 0.9810 (mmp) cc_final: 0.9502 (mmp) REVERT: A 970 PHE cc_start: 0.9452 (m-10) cc_final: 0.9074 (m-10) REVERT: A 979 ASP cc_start: 0.9682 (t0) cc_final: 0.9428 (t0) REVERT: A 1004 LEU cc_start: 0.9681 (mm) cc_final: 0.9413 (mm) REVERT: B 365 TYR cc_start: 0.9219 (m-10) cc_final: 0.8957 (m-10) REVERT: B 759 PHE cc_start: 0.9157 (m-10) cc_final: 0.8941 (m-10) REVERT: B 763 LEU cc_start: 0.9753 (mp) cc_final: 0.9526 (pp) REVERT: B 902 MET cc_start: 0.9670 (mmp) cc_final: 0.9459 (mmp) REVERT: B 1002 GLN cc_start: 0.9829 (tt0) cc_final: 0.9595 (tm-30) REVERT: B 1004 LEU cc_start: 0.9674 (mt) cc_final: 0.9356 (mt) REVERT: B 1034 LEU cc_start: 0.9708 (mt) cc_final: 0.9441 (mt) REVERT: B 1067 TYR cc_start: 0.9286 (t80) cc_final: 0.9079 (t80) REVERT: C 365 TYR cc_start: 0.9689 (m-80) cc_final: 0.9365 (m-80) REVERT: C 902 MET cc_start: 0.9592 (mmp) cc_final: 0.9297 (mmp) REVERT: C 1050 MET cc_start: 0.9381 (pmm) cc_final: 0.9050 (pmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1288 time to fit residues: 33.1111 Evaluate side-chains 106 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.2980 chunk 222 optimal weight: 0.0370 chunk 275 optimal weight: 10.0000 chunk 316 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 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 = 0.3010 r_free = 0.3010 target = 0.045646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.029600 restraints weight = 384594.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031093 restraints weight = 184778.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.032155 restraints weight = 116149.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.032903 restraints weight = 83518.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.033441 restraints weight = 65326.380| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 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 = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26038 Z= 0.101 Angle : 0.541 9.100 35592 Z= 0.274 Chirality : 0.043 0.216 4230 Planarity : 0.003 0.044 4478 Dihedral : 4.861 58.201 4653 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.93 (0.20), residues: 694 sheet: 0.17 (0.18), residues: 747 loop : 0.04 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1000 TYR 0.018 0.001 TYR H 59 PHE 0.021 0.001 PHE B 759 TRP 0.012 0.001 TRP C 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00212 (25938) covalent geometry : angle 0.53226 (35333) SS BOND : bond 0.00217 ( 41) SS BOND : angle 0.78724 ( 82) hydrogen bonds : bond 0.03411 ( 937) hydrogen bonds : angle 5.58148 ( 2637) link_BETA1-4 : bond 0.00313 ( 12) link_BETA1-4 : angle 1.07577 ( 36) link_NAG-ASN : bond 0.00238 ( 47) link_NAG-ASN : angle 1.47725 ( 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 159 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8532 (m-80) cc_final: 0.8034 (m-80) REVERT: A 365 TYR cc_start: 0.9616 (m-80) cc_final: 0.9163 (m-80) REVERT: A 740 MET cc_start: 0.9668 (tpt) cc_final: 0.9465 (tpp) REVERT: A 902 MET cc_start: 0.9825 (mmp) cc_final: 0.9489 (mmp) REVERT: A 979 ASP cc_start: 0.9677 (t0) cc_final: 0.9414 (t0) REVERT: A 1004 LEU cc_start: 0.9759 (mm) cc_final: 0.9470 (mm) REVERT: B 227 VAL cc_start: 0.8611 (t) cc_final: 0.8392 (t) REVERT: B 365 TYR cc_start: 0.9168 (m-10) cc_final: 0.8904 (m-80) REVERT: B 731 MET cc_start: 0.8850 (tmm) cc_final: 0.8603 (tmm) REVERT: B 763 LEU cc_start: 0.9721 (mp) cc_final: 0.9445 (pp) REVERT: B 902 MET cc_start: 0.9658 (mmp) cc_final: 0.9435 (mmp) REVERT: B 1004 LEU cc_start: 0.9687 (mt) cc_final: 0.9373 (mt) REVERT: B 1029 MET cc_start: 0.9627 (tmm) cc_final: 0.9383 (tmm) REVERT: B 1034 LEU cc_start: 0.9708 (mt) cc_final: 0.9352 (mt) REVERT: B 1067 TYR cc_start: 0.9313 (t80) cc_final: 0.9032 (t80) REVERT: C 55 PHE cc_start: 0.9122 (m-80) cc_final: 0.8387 (m-80) REVERT: C 365 TYR cc_start: 0.9637 (m-80) cc_final: 0.9318 (m-80) REVERT: C 697 MET cc_start: 0.8223 (ppp) cc_final: 0.7984 (ppp) REVERT: C 902 MET cc_start: 0.9550 (mmp) cc_final: 0.9196 (mmp) REVERT: C 913 GLN cc_start: 0.9613 (pt0) cc_final: 0.9295 (pm20) REVERT: C 1050 MET cc_start: 0.9306 (pmm) cc_final: 0.8981 (pmm) REVERT: C 1067 TYR cc_start: 0.9526 (t80) cc_final: 0.9288 (t80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1404 time to fit residues: 38.5538 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 : 0.808 ------------------------------------------------------------------------------- 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: 5.9990 chunk 132 optimal weight: 10.0000 chunk 64 optimal weight: 0.0470 chunk 253 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** H 76 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 = 0.2999 r_free = 0.2999 target = 0.045515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.029521 restraints weight = 408339.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.031007 restraints weight = 193718.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.032058 restraints weight = 121281.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.032790 restraints weight = 87104.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.033293 restraints weight = 68563.780| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 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 = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4463 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= 0.136 Angle : 0.560 9.720 35592 Z= 0.286 Chirality : 0.043 0.281 4230 Planarity : 0.003 0.043 4478 Dihedral : 4.794 55.708 4653 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.96 (0.20), residues: 685 sheet: 0.18 (0.18), residues: 752 loop : 0.03 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1091 TYR 0.015 0.001 TYR H 59 PHE 0.018 0.001 PHE B 559 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00277 (25938) covalent geometry : angle 0.54448 (35333) SS BOND : bond 0.00342 ( 41) SS BOND : angle 1.01753 ( 82) hydrogen bonds : bond 0.03452 ( 937) hydrogen bonds : angle 5.57555 ( 2637) link_BETA1-4 : bond 0.00248 ( 12) link_BETA1-4 : angle 1.18670 ( 36) link_NAG-ASN : bond 0.00257 ( 47) link_NAG-ASN : angle 1.99875 ( 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 147 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.943 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: 0.8527 (m-80) cc_final: 0.8027 (m-80) REVERT: A 365 TYR cc_start: 0.9623 (m-80) cc_final: 0.9115 (m-80) REVERT: A 740 MET cc_start: 0.9669 (tpt) cc_final: 0.9458 (tpp) REVERT: A 902 MET cc_start: 0.9823 (mmp) cc_final: 0.9519 (mmp) REVERT: A 979 ASP cc_start: 0.9684 (t0) cc_final: 0.9425 (t0) REVERT: A 1004 LEU cc_start: 0.9718 (mm) cc_final: 0.9509 (mm) REVERT: B 365 TYR cc_start: 0.9179 (m-10) cc_final: 0.8909 (m-80) REVERT: B 867 ASP cc_start: 0.9428 (p0) cc_final: 0.9216 (p0) REVERT: B 902 MET cc_start: 0.9648 (mmp) cc_final: 0.9429 (mmp) REVERT: B 1004 LEU cc_start: 0.9664 (mt) cc_final: 0.9386 (mt) REVERT: B 1029 MET cc_start: 0.9632 (tmm) cc_final: 0.9387 (tmm) REVERT: B 1034 LEU cc_start: 0.9706 (mt) cc_final: 0.9379 (mt) REVERT: B 1067 TYR cc_start: 0.9266 (t80) cc_final: 0.9010 (t80) REVERT: C 277 LEU cc_start: 0.9708 (mm) cc_final: 0.9236 (tt) REVERT: C 365 TYR cc_start: 0.9646 (m-80) cc_final: 0.9336 (m-80) REVERT: C 697 MET cc_start: 0.8347 (ppp) cc_final: 0.8141 (ppp) REVERT: C 902 MET cc_start: 0.9549 (mmp) cc_final: 0.9236 (mmp) REVERT: C 1050 MET cc_start: 0.9344 (pmm) cc_final: 0.8985 (pmm) REVERT: C 1067 TYR cc_start: 0.9500 (t80) cc_final: 0.9274 (t80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1289 time to fit residues: 33.3300 Evaluate side-chains 123 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 1.9990 chunk 313 optimal weight: 2.9990 chunk 288 optimal weight: 0.3980 chunk 238 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 294 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 207 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.029365 restraints weight = 491624.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.031003 restraints weight = 210254.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.032155 restraints weight = 125972.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.032956 restraints weight = 88295.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.033512 restraints weight = 68092.371| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 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 = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26038 Z= 0.099 Angle : 0.537 8.283 35592 Z= 0.272 Chirality : 0.043 0.289 4230 Planarity : 0.003 0.044 4478 Dihedral : 4.551 50.728 4653 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.44 (0.15), residues: 3141 helix: 1.06 (0.20), residues: 687 sheet: 0.25 (0.18), residues: 764 loop : 0.10 (0.16), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.024 0.001 TYR A 873 PHE 0.019 0.001 PHE B 782 TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00208 (25938) covalent geometry : angle 0.52619 (35333) SS BOND : bond 0.00251 ( 41) SS BOND : angle 0.99555 ( 82) hydrogen bonds : bond 0.03277 ( 937) hydrogen bonds : angle 5.42225 ( 2637) link_BETA1-4 : bond 0.00294 ( 12) link_BETA1-4 : angle 1.03817 ( 36) link_NAG-ASN : bond 0.00219 ( 47) link_NAG-ASN : angle 1.62452 ( 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 164 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8526 (m-80) cc_final: 0.8052 (m-80) REVERT: A 365 TYR cc_start: 0.9596 (m-80) cc_final: 0.9081 (m-80) REVERT: A 902 MET cc_start: 0.9833 (mmp) cc_final: 0.9412 (mmp) REVERT: A 970 PHE cc_start: 0.9244 (m-10) cc_final: 0.8852 (m-10) REVERT: A 979 ASP cc_start: 0.9687 (t0) cc_final: 0.9421 (t0) REVERT: A 1004 LEU cc_start: 0.9710 (mm) cc_final: 0.9479 (mm) REVERT: B 227 VAL cc_start: 0.8586 (t) cc_final: 0.8382 (t) REVERT: B 365 TYR cc_start: 0.9099 (m-10) cc_final: 0.8858 (m-80) REVERT: B 731 MET cc_start: 0.8904 (tmm) cc_final: 0.8532 (tmm) REVERT: B 867 ASP cc_start: 0.9404 (p0) cc_final: 0.9176 (p0) REVERT: B 902 MET cc_start: 0.9642 (mmp) cc_final: 0.9405 (mmp) REVERT: B 1004 LEU cc_start: 0.9650 (mt) cc_final: 0.9360 (mt) REVERT: B 1029 MET cc_start: 0.9616 (tmm) cc_final: 0.9370 (tmm) REVERT: B 1034 LEU cc_start: 0.9718 (mt) cc_final: 0.9364 (mt) REVERT: B 1067 TYR cc_start: 0.9277 (t80) cc_final: 0.8997 (t80) REVERT: C 277 LEU cc_start: 0.9721 (mm) cc_final: 0.9239 (tt) REVERT: C 365 TYR cc_start: 0.9621 (m-80) cc_final: 0.9309 (m-80) REVERT: C 902 MET cc_start: 0.9567 (mmp) cc_final: 0.9257 (mmp) REVERT: C 913 GLN cc_start: 0.9595 (pt0) cc_final: 0.9283 (pm20) REVERT: C 960 ASN cc_start: 0.9735 (m110) cc_final: 0.9499 (m110) REVERT: C 1050 MET cc_start: 0.9332 (pmm) cc_final: 0.8985 (pmm) REVERT: C 1067 TYR cc_start: 0.9478 (t80) cc_final: 0.9276 (t80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1349 time to fit residues: 39.3315 Evaluate side-chains 128 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 2.9990 chunk 244 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 234 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.029094 restraints weight = 394088.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.030418 restraints weight = 198159.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.031350 restraints weight = 127903.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.031981 restraints weight = 94348.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.032424 restraints weight = 75948.811| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 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 = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 26038 Z= 0.293 Angle : 0.732 10.518 35592 Z= 0.378 Chirality : 0.045 0.309 4230 Planarity : 0.004 0.043 4478 Dihedral : 5.391 47.931 4653 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.09 (0.15), residues: 3141 helix: 0.41 (0.20), residues: 697 sheet: -0.01 (0.18), residues: 756 loop : -0.18 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE A1052 TRP 0.013 0.002 TRP B 64 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00575 (25938) covalent geometry : angle 0.71732 (35333) SS BOND : bond 0.00410 ( 41) SS BOND : angle 1.37793 ( 82) hydrogen bonds : bond 0.04190 ( 937) hydrogen bonds : angle 6.01747 ( 2637) link_BETA1-4 : bond 0.00501 ( 12) link_BETA1-4 : angle 1.82060 ( 36) link_NAG-ASN : bond 0.00501 ( 47) link_NAG-ASN : angle 2.11048 ( 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 131 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 TYR cc_start: 0.8566 (m-80) cc_final: 0.8090 (m-10) REVERT: A 756 TYR cc_start: 0.9461 (m-10) cc_final: 0.9103 (m-80) REVERT: A 902 MET cc_start: 0.9833 (mmp) cc_final: 0.9518 (mmp) REVERT: A 979 ASP cc_start: 0.9704 (t0) cc_final: 0.9460 (t0) REVERT: B 365 TYR cc_start: 0.9256 (m-10) cc_final: 0.8982 (m-80) REVERT: B 731 MET cc_start: 0.8802 (tmm) cc_final: 0.8557 (tmm) REVERT: B 1004 LEU cc_start: 0.9671 (mt) cc_final: 0.9384 (mt) REVERT: B 1029 MET cc_start: 0.9656 (tmm) cc_final: 0.9419 (tmm) REVERT: B 1034 LEU cc_start: 0.9700 (mt) cc_final: 0.9399 (mt) REVERT: B 1050 MET cc_start: 0.9223 (pmm) cc_final: 0.8953 (pmm) REVERT: B 1067 TYR cc_start: 0.9223 (t80) cc_final: 0.9018 (t80) REVERT: C 365 TYR cc_start: 0.9655 (m-80) cc_final: 0.9328 (m-80) REVERT: C 902 MET cc_start: 0.9569 (mmp) cc_final: 0.9182 (mmp) REVERT: C 1050 MET cc_start: 0.9408 (pmm) cc_final: 0.8986 (pmm) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1423 time to fit residues: 32.3122 Evaluate side-chains 87 residues out of total 2778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 0.3980 chunk 176 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2981 r_free = 0.2981 target = 0.045688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.029436 restraints weight = 396400.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.030857 restraints weight = 192224.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.031851 restraints weight = 121920.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.032510 restraints weight = 88779.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032990 restraints weight = 70833.845| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26038 Z= 0.143 Angle : 0.581 9.914 35592 Z= 0.296 Chirality : 0.044 0.310 4230 Planarity : 0.004 0.045 4478 Dihedral : 5.042 50.452 4653 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 0.14 (0.15), residues: 3141 helix: 0.92 (0.20), residues: 684 sheet: -0.04 (0.18), residues: 776 loop : -0.08 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.017 0.001 TYR A 873 PHE 0.017 0.001 PHE A 782 TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00293 (25938) covalent geometry : angle 0.56764 (35333) SS BOND : bond 0.00290 ( 41) SS BOND : angle 1.31499 ( 82) hydrogen bonds : bond 0.03521 ( 937) hydrogen bonds : angle 5.67257 ( 2637) link_BETA1-4 : bond 0.00275 ( 12) link_BETA1-4 : angle 1.26410 ( 36) link_NAG-ASN : bond 0.00242 ( 47) link_NAG-ASN : angle 1.78037 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.45 seconds wall clock time: 69 minutes 58.16 seconds (4198.16 seconds total)