Starting phenix.real_space_refine on Fri Mar 6 18:37:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.map" model { file = "/net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ly2_23582/03_2026/7ly2_23582.cif" } resolution = 2.5 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= 0.005 sd= 0.126 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 153 5.16 5 C 21183 2.51 5 N 5541 2.21 5 O 6567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s 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: 33444 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 4, 'TYR:plan': 9, 'HIS:plan': 1, 'TRP:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 240 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "B" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 4, 'TYR:plan': 9, 'HIS:plan': 1, 'TRP:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 240 Chain: "I" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "J" Number of atoms: 7994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 7994 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 56, 'TRANS': 984} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'ARG:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 95 Chain: "K" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 578 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'PHE:plan': 4, 'TYR:plan': 9, 'HIS:plan': 1, 'TRP:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 240 Chain: "O" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 535 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "R" 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: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: "U" 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: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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: "X" 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "J" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 7.88, per 1000 atoms: 0.24 Number of scatterers: 33444 At special positions: 0 Unit cell: (204.75, 190.05, 191.1, 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 153 16.00 O 6567 8.00 N 5541 7.00 C 21183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.13 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.11 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.13 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.06 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.04 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.02 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 361 " distance=2.02 Simple disulfide: pdb=" SG CYS J 379 " - pdb=" SG CYS J 432 " distance=2.13 Simple disulfide: pdb=" SG CYS J 391 " - pdb=" SG CYS J 525 " distance=2.05 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 488 " distance=2.03 Simple disulfide: pdb=" SG CYS J 538 " - pdb=" SG CYS J 590 " distance=2.02 Simple disulfide: pdb=" SG CYS J 617 " - pdb=" SG CYS J 649 " distance=2.04 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 760 " distance=2.11 Simple disulfide: pdb=" SG CYS J 743 " - pdb=" SG CYS J 749 " distance=2.11 Simple disulfide: pdb=" SG CYS J1032 " - pdb=" SG CYS J1043 " distance=2.01 Simple disulfide: pdb=" SG CYS J1082 " - pdb=" SG CYS J1126 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.06 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 87 " distance=2.04 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 P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 149 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG A1314 " - " ASN A 61 " " NAG A1315 " - " ASN A 234 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 149 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG B1314 " - " ASN B 61 " " NAG B1315 " - " ASN B 234 " " NAG J1301 " - " ASN J 17 " " NAG J1302 " - " ASN J 122 " " NAG J1303 " - " ASN J 165 " " NAG J1304 " - " ASN J 282 " " NAG J1305 " - " ASN J 149 " " NAG J1306 " - " ASN J 331 " " NAG J1307 " - " ASN J 603 " " NAG J1308 " - " ASN J 616 " " NAG J1309 " - " ASN J 657 " " NAG J1310 " - " ASN J 709 " " NAG J1311 " - " ASN J1074 " " NAG J1312 " - " ASN J1098 " " NAG J1313 " - " ASN J1134 " " NAG J1314 " - " ASN J 61 " " NAG J1315 " - " ASN J 234 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 717 " " NAG R 1 " - " ASN A 801 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN J 343 " " NAG W 1 " - " ASN J 717 " " NAG X 1 " - " ASN J 801 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8274 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 84 sheets defined 21.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 247 through 250 removed outlier: 3.806A pdb=" N THR A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.604A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.178A 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 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 1031 removed outlier: 4.818A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.524A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.807A pdb=" N THR B 250 " --> pdb=" O SER B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.604A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A 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 984 Processing helix chain 'B' and resid 985 through 1031 removed outlier: 4.818A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.525A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'J' and resid 247 through 250 removed outlier: 3.807A pdb=" N THR J 250 " --> pdb=" O SER J 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 247 through 250' Processing helix chain 'J' and resid 294 through 303 Processing helix chain 'J' and resid 338 through 343 Processing helix chain 'J' and resid 349 through 353 removed outlier: 3.604A pdb=" N TRP J 353 " --> pdb=" O VAL J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 370 Processing helix chain 'J' and resid 386 through 389 Processing helix chain 'J' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG J 408 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 502 through 505 Processing helix chain 'J' and resid 616 through 620 removed outlier: 3.726A pdb=" N VAL J 620 " --> pdb=" O CYS J 617 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 744 Processing helix chain 'J' and resid 746 through 754 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 758 through 783 removed outlier: 3.733A pdb=" N ASP J 775 " --> pdb=" O ALA J 771 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 Processing helix chain 'J' and resid 853 through 856 Processing helix chain 'J' and resid 866 through 885 Processing helix chain 'J' and resid 886 through 890 Processing helix chain 'J' and resid 897 through 908 Processing helix chain 'J' and resid 912 through 919 removed outlier: 4.055A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 919 through 940 Processing helix chain 'J' and resid 941 through 944 Processing helix chain 'J' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL J 951 " --> pdb=" O LYS J 947 " (cutoff:3.500A) Processing helix chain 'J' and resid 966 through 968 No H-bonds generated for 'chain 'J' and resid 966 through 968' Processing helix chain 'J' and resid 976 through 984 Processing helix chain 'J' and resid 985 through 1031 removed outlier: 4.818A pdb=" N VAL J 991 " --> pdb=" O PRO J 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.571A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.525A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'O' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.707A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.470A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.266A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 565 " --> pdb=" O PHE J 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.562A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.646A pdb=" N ALA A 701 " --> pdb=" O ILE J 788 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS J 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN A 703 " --> pdb=" O LYS J 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.795A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 114 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.472A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.707A pdb=" N ALA J 575 " --> pdb=" O GLY J 566 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU J 324 " --> pdb=" O ASN J 540 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN J 542 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE J 326 " --> pdb=" O ASN J 542 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.470A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.258A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.561A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.795A pdb=" N LYS B 790 " --> pdb=" O ASN J 703 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.777A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.500A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.500A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TYR C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 34 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'J' and resid 28 through 30 removed outlier: 8.049A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA J 264 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR J 95 " --> pdb=" O ALA J 264 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 84 through 85 removed outlier: 12.470A pdb=" N PHE J 135 " --> pdb=" O PHE J 238 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N THR J 240 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN J 137 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LEU J 242 " --> pdb=" O ASN J 137 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU J 244 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU J 141 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS J 136 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER J 161 " --> pdb=" O CYS J 136 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP J 138 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL J 159 " --> pdb=" O ASP J 138 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE J 140 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE J 157 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY J 142 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 84 through 85 removed outlier: 6.315A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE J 312 " --> pdb=" O THR J 599 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR J 599 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN J 314 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL J 597 " --> pdb=" O GLN J 314 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY J 594 " --> pdb=" O GLN J 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 354 through 358 removed outlier: 3.763A pdb=" N ASN J 394 " --> pdb=" O GLU J 516 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.578A pdb=" N CYS J 361 " --> pdb=" O CYS J 525 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'J' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.561A pdb=" N ILE J 670 " --> pdb=" O ILE J 666 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER J 711 " --> pdb=" O THR J1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR J1076 " --> pdb=" O SER J 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA J 713 " --> pdb=" O ASN J1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN J1074 " --> pdb=" O ALA J 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU J1072 " --> pdb=" O PRO J 715 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.483A pdb=" N SER J 711 " --> pdb=" O THR J1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR J1076 " --> pdb=" O SER J 711 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA J 713 " --> pdb=" O ASN J1074 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASN J1074 " --> pdb=" O ALA J 713 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLU J1072 " --> pdb=" O PRO J 715 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE J1095 " --> pdb=" O ALA J1078 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.428A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 1120 through 1125 removed outlier: 4.778A pdb=" N ALA J1087 " --> pdb=" O SER J1123 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI2, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.501A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.690A pdb=" N GLU M 10 " --> pdb=" O THR M 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR M 114 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AI8, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.715A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.060A pdb=" N TYR N 108 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP O 34 " --> pdb=" O VAL O 46 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.471A pdb=" N VAL O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 18 through 23 1586 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8130 1.33 - 1.46: 9368 1.46 - 1.58: 16471 1.58 - 1.71: 0 1.71 - 1.84: 198 Bond restraints: 34167 Sorted by residual: bond pdb=" N GLU A 619 " pdb=" CA GLU A 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" N GLU J 619 " pdb=" CA GLU J 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.13e+01 bond pdb=" N GLU B 619 " pdb=" CA GLU B 619 " ideal model delta sigma weight residual 1.455 1.501 -0.046 1.37e-02 5.33e+03 1.12e+01 bond pdb=" C5 NAG B1314 " pdb=" O5 NAG B1314 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CG ASP C 83 " pdb=" OD2 ASP C 83 " ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.42e+00 ... (remaining 34162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 44460 2.43 - 4.86: 1676 4.86 - 7.30: 494 7.30 - 9.73: 32 9.73 - 12.16: 3 Bond angle restraints: 46665 Sorted by residual: angle pdb=" C GLN O 6 " pdb=" N PRO O 7 " pdb=" CA PRO O 7 " ideal model delta sigma weight residual 119.66 125.99 -6.33 7.30e-01 1.88e+00 7.52e+01 angle pdb=" C GLN I 6 " pdb=" N PRO I 7 " pdb=" CA PRO I 7 " ideal model delta sigma weight residual 119.66 125.98 -6.32 7.30e-01 1.88e+00 7.51e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.98 -6.32 7.30e-01 1.88e+00 7.50e+01 angle pdb=" C THR J 791 " pdb=" N PRO J 792 " pdb=" CA PRO J 792 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.20e-01 1.93e+00 7.37e+01 angle pdb=" C THR B 791 " pdb=" N PRO B 792 " pdb=" CA PRO B 792 " ideal model delta sigma weight residual 119.66 125.81 -6.15 7.20e-01 1.93e+00 7.29e+01 ... (remaining 46660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 20334 21.31 - 42.63: 540 42.63 - 63.94: 117 63.94 - 85.25: 48 85.25 - 106.57: 18 Dihedral angle restraints: 21057 sinusoidal: 8160 harmonic: 12897 Sorted by residual: dihedral pdb=" C ASN B 616 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C ASN A 616 " pdb=" N ASN A 616 " pdb=" CA ASN A 616 " pdb=" CB ASN A 616 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C ASN J 616 " pdb=" N ASN J 616 " pdb=" CA ASN J 616 " pdb=" CB ASN J 616 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 ... (remaining 21054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4418 0.082 - 0.164: 845 0.164 - 0.245: 215 0.245 - 0.327: 66 0.327 - 0.409: 6 Chirality restraints: 5550 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.66e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.61e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.61e+01 ... (remaining 5547 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 92 " -0.041 2.00e-02 2.50e+03 2.11e-02 8.89e+00 pdb=" CG TYR D 92 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 92 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 92 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR D 92 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 92 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 92 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 92 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 92 " 0.040 2.00e-02 2.50e+03 2.09e-02 8.76e+00 pdb=" CG TYR K 92 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR K 92 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR K 92 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR K 92 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR K 92 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR K 92 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 92 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 92 " 0.040 2.00e-02 2.50e+03 2.09e-02 8.74e+00 pdb=" CG TYR C 92 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 92 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 92 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 92 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 92 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR C 92 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 92 " 0.028 2.00e-02 2.50e+03 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 14720 2.92 - 3.42: 29784 3.42 - 3.91: 57829 3.91 - 4.41: 64870 4.41 - 4.90: 107136 Nonbonded interactions: 274339 Sorted by model distance: nonbonded pdb=" OD1 ASN B 331 " pdb=" O5 NAG B1306 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASN J 331 " pdb=" O5 NAG J1306 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASN A 331 " pdb=" O5 NAG A1306 " model vdw 2.427 3.040 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.437 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.437 3.120 ... (remaining 274334 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.410 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.011 0.103 34290 Z= 0.615 Angle : 1.252 12.162 46980 Z= 0.841 Chirality : 0.075 0.409 5550 Planarity : 0.005 0.027 6018 Dihedral : 11.258 106.565 12621 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.33 % 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: 0.74 (0.12), residues: 4392 helix: 0.46 (0.19), residues: 669 sheet: 0.75 (0.13), residues: 1314 loop : 0.49 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.041 0.005 TYR D 92 PHE 0.020 0.003 PHE A 898 TRP 0.026 0.005 TRP E 106 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01091 (34167) covalent geometry : angle 1.23667 (46665) SS BOND : bond 0.03693 ( 54) SS BOND : angle 3.05154 ( 108) hydrogen bonds : bond 0.15109 ( 1478) hydrogen bonds : angle 8.34709 ( 4020) link_BETA1-4 : bond 0.05532 ( 12) link_BETA1-4 : angle 2.40339 ( 36) link_BETA1-6 : bond 0.04578 ( 3) link_BETA1-6 : angle 1.93059 ( 9) link_NAG-ASN : bond 0.05330 ( 54) link_NAG-ASN : angle 2.48273 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 637 time to evaluate : 1.185 Fit side-chains REVERT: A 29 THR cc_start: 0.7968 (t) cc_final: 0.7659 (p) REVERT: A 369 TYR cc_start: 0.8494 (t80) cc_final: 0.8263 (t80) REVERT: A 755 GLN cc_start: 0.8253 (mt0) cc_final: 0.8004 (mt0) REVERT: E 34 MET cc_start: 0.8392 (tpp) cc_final: 0.7854 (tpp) REVERT: E 48 MET cc_start: 0.8258 (mtp) cc_final: 0.8018 (mtm) REVERT: E 93 VAL cc_start: 0.7936 (t) cc_final: 0.7731 (p) REVERT: B 227 VAL cc_start: 0.8109 (p) cc_final: 0.7841 (m) REVERT: B 369 TYR cc_start: 0.8548 (t80) cc_final: 0.8338 (t80) REVERT: B 725 GLU cc_start: 0.7358 (tt0) cc_final: 0.6929 (tm-30) REVERT: B 755 GLN cc_start: 0.8245 (mt0) cc_final: 0.7948 (mt0) REVERT: B 1029 MET cc_start: 0.8738 (tpp) cc_final: 0.8454 (tpp) REVERT: C 103 THR cc_start: 0.7482 (p) cc_final: 0.7073 (t) REVERT: F 34 MET cc_start: 0.8398 (tpp) cc_final: 0.8099 (tpp) REVERT: F 70 MET cc_start: 0.8330 (mtt) cc_final: 0.8097 (mtt) REVERT: F 95 TYR cc_start: 0.8565 (m-80) cc_final: 0.8284 (m-80) REVERT: J 29 THR cc_start: 0.7957 (t) cc_final: 0.7576 (p) REVERT: J 318 PHE cc_start: 0.7675 (t80) cc_final: 0.7430 (t80) REVERT: J 523 THR cc_start: 0.8347 (p) cc_final: 0.8128 (p) REVERT: J 1050 MET cc_start: 0.8914 (ptm) cc_final: 0.8644 (ptp) REVERT: K 103 THR cc_start: 0.7434 (p) cc_final: 0.7109 (t) outliers start: 6 outliers final: 0 residues processed: 642 average time/residue: 0.6968 time to fit residues: 529.7227 Evaluate side-chains 398 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 30.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 271 GLN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 641 ASN A 644 GLN A 675 GLN A 762 GLN A 901 GLN A 935 GLN A1101 HIS A1113 GLN A1125 ASN D 38 GLN B 52 GLN B 271 GLN B 394 ASN B 540 ASN B 580 GLN B 644 GLN B 779 GLN B 804 GLN B 901 GLN B 955 ASN B 957 GLN B1011 GLN B1101 HIS B1113 GLN J 394 ASN J 580 GLN J 644 GLN J 675 GLN J 762 GLN J 901 GLN J1002 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1113 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.193579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165725 restraints weight = 33628.225| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 0.98 r_work: 0.3486 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34290 Z= 0.159 Angle : 0.613 9.728 46980 Z= 0.316 Chirality : 0.046 0.235 5550 Planarity : 0.004 0.033 6018 Dihedral : 6.654 68.424 6171 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.13 % Allowed : 7.78 % Favored : 90.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 4392 helix: 2.06 (0.21), residues: 627 sheet: 0.91 (0.14), residues: 1260 loop : 0.75 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1039 TYR 0.024 0.002 TYR J1067 PHE 0.013 0.002 PHE A 32 TRP 0.016 0.002 TRP F 36 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00349 (34167) covalent geometry : angle 0.59144 (46665) SS BOND : bond 0.00285 ( 54) SS BOND : angle 1.09757 ( 108) hydrogen bonds : bond 0.04845 ( 1478) hydrogen bonds : angle 6.17650 ( 4020) link_BETA1-4 : bond 0.00595 ( 12) link_BETA1-4 : angle 1.93578 ( 36) link_BETA1-6 : bond 0.00058 ( 3) link_BETA1-6 : angle 1.66845 ( 9) link_NAG-ASN : bond 0.00410 ( 54) link_NAG-ASN : angle 2.52165 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 453 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7686 (m-10) cc_final: 0.7414 (m-10) REVERT: A 81 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6906 (t0) REVERT: A 126 VAL cc_start: 0.7060 (t) cc_final: 0.6697 (p) REVERT: A 583 GLU cc_start: 0.7723 (tt0) cc_final: 0.7330 (pt0) REVERT: A 675 GLN cc_start: 0.7323 (mm-40) cc_final: 0.7061 (mm110) REVERT: A 725 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: A 755 GLN cc_start: 0.8553 (mt0) cc_final: 0.8299 (mt0) REVERT: A 814 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6954 (ttpt) REVERT: A 921 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8402 (mttp) REVERT: A 1010 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: E 34 MET cc_start: 0.8838 (tpp) cc_final: 0.8371 (tpp) REVERT: B 32 PHE cc_start: 0.7617 (m-10) cc_final: 0.7395 (m-10) REVERT: B 81 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7112 (t0) REVERT: B 121 ASN cc_start: 0.7219 (m-40) cc_final: 0.6936 (m110) REVERT: B 227 VAL cc_start: 0.8332 (p) cc_final: 0.7998 (m) REVERT: B 755 GLN cc_start: 0.8553 (mt0) cc_final: 0.8190 (mt0) REVERT: B 787 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: B 945 LEU cc_start: 0.8406 (mm) cc_final: 0.8151 (mt) REVERT: B 1010 GLN cc_start: 0.8499 (mm110) cc_final: 0.8269 (mm-40) REVERT: B 1017 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 1029 MET cc_start: 0.8839 (tpp) cc_final: 0.8510 (tpp) REVERT: B 1050 MET cc_start: 0.9047 (ptm) cc_final: 0.8839 (ptp) REVERT: C 13 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7219 (pp) REVERT: C 103 THR cc_start: 0.8028 (p) cc_final: 0.7541 (t) REVERT: F 34 MET cc_start: 0.8823 (tpp) cc_final: 0.8552 (tpp) REVERT: F 95 TYR cc_start: 0.8623 (m-80) cc_final: 0.8380 (m-80) REVERT: J 29 THR cc_start: 0.7979 (t) cc_final: 0.7724 (t) REVERT: J 32 PHE cc_start: 0.7451 (m-10) cc_final: 0.7173 (m-10) REVERT: J 125 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6620 (p0) REVERT: J 740 MET cc_start: 0.8497 (tpt) cc_final: 0.8264 (tpt) REVERT: J 787 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: J 814 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6220 (mtmt) REVERT: J 820 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: K 13 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6866 (pp) REVERT: K 103 THR cc_start: 0.7860 (p) cc_final: 0.7280 (t) REVERT: M 87 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.6319 (mtp180) outliers start: 68 outliers final: 18 residues processed: 491 average time/residue: 0.6513 time to fit residues: 383.4104 Evaluate side-chains 427 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 395 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain J residue 125 ASN Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 591 SER Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 814 LYS Chi-restraints excluded: chain J residue 820 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 146 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 377 optimal weight: 2.9990 chunk 132 optimal weight: 40.0000 chunk 220 optimal weight: 0.0370 chunk 134 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 370 optimal weight: 0.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 271 GLN A 394 ASN A 804 GLN A 935 GLN A1101 HIS A1113 GLN D 38 GLN B 52 GLN B 271 GLN B 394 ASN B 957 GLN B1101 HIS J 394 ASN J 675 GLN J 804 GLN J1101 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163211 restraints weight = 33292.243| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 0.97 r_work: 0.3452 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34290 Z= 0.182 Angle : 0.610 8.769 46980 Z= 0.312 Chirality : 0.046 0.353 5550 Planarity : 0.004 0.039 6018 Dihedral : 5.913 59.819 6171 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.63 % Allowed : 8.75 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 4392 helix: 2.08 (0.20), residues: 627 sheet: 0.75 (0.14), residues: 1296 loop : 0.70 (0.13), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.024 0.002 TYR J1067 PHE 0.020 0.002 PHE J 898 TRP 0.016 0.002 TRP M 36 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00405 (34167) covalent geometry : angle 0.59366 (46665) SS BOND : bond 0.00455 ( 54) SS BOND : angle 0.92217 ( 108) hydrogen bonds : bond 0.04694 ( 1478) hydrogen bonds : angle 5.88328 ( 4020) link_BETA1-4 : bond 0.00581 ( 12) link_BETA1-4 : angle 1.74061 ( 36) link_BETA1-6 : bond 0.00063 ( 3) link_BETA1-6 : angle 1.51267 ( 9) link_NAG-ASN : bond 0.00523 ( 54) link_NAG-ASN : angle 2.22914 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 403 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6952 (t0) REVERT: A 356 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8571 (tmtp) REVERT: A 583 GLU cc_start: 0.7830 (tt0) cc_final: 0.7360 (pt0) REVERT: A 675 GLN cc_start: 0.7294 (mm-40) cc_final: 0.7044 (mm110) REVERT: A 725 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: A 755 GLN cc_start: 0.8520 (mt0) cc_final: 0.8240 (mt0) REVERT: A 1010 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: D 80 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: E 34 MET cc_start: 0.8881 (tpp) cc_final: 0.8377 (tpp) REVERT: E 87 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.5906 (mtp85) REVERT: B 32 PHE cc_start: 0.7812 (m-10) cc_final: 0.7583 (m-10) REVERT: B 129 LYS cc_start: 0.7835 (mtpm) cc_final: 0.7224 (mppt) REVERT: B 227 VAL cc_start: 0.8343 (p) cc_final: 0.7984 (m) REVERT: B 787 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: B 814 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6732 (mtmt) REVERT: B 1017 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 1050 MET cc_start: 0.9142 (ptm) cc_final: 0.8906 (ptp) REVERT: B 1113 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: C 13 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7196 (pp) REVERT: C 103 THR cc_start: 0.8182 (p) cc_final: 0.7783 (t) REVERT: J 29 THR cc_start: 0.7881 (t) cc_final: 0.7610 (t) REVERT: J 190 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7374 (mmm-85) REVERT: J 787 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: J 814 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6400 (mtmt) REVERT: K 13 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6965 (pp) REVERT: K 103 THR cc_start: 0.7835 (p) cc_final: 0.7432 (t) REVERT: M 87 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6295 (mtp180) outliers start: 84 outliers final: 37 residues processed: 448 average time/residue: 0.6606 time to fit residues: 354.5511 Evaluate side-chains 430 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 379 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain J residue 125 ASN Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 657 ASN Chi-restraints excluded: chain J residue 731 MET Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 814 LYS Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 241 optimal weight: 0.9980 chunk 362 optimal weight: 0.9980 chunk 290 optimal weight: 50.0000 chunk 323 optimal weight: 0.1980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 354 ASN A1101 HIS A1113 GLN B 52 GLN B 394 ASN B 804 GLN B 957 GLN B1101 HIS J 394 ASN J 540 ASN J 675 GLN J 762 GLN J 955 ASN J1011 GLN J1101 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.192696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164876 restraints weight = 33131.156| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.94 r_work: 0.3487 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34290 Z= 0.123 Angle : 0.534 7.927 46980 Z= 0.273 Chirality : 0.044 0.201 5550 Planarity : 0.004 0.036 6018 Dihedral : 4.987 46.158 6171 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.16 % Allowed : 9.88 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.13), residues: 4392 helix: 2.36 (0.20), residues: 627 sheet: 0.87 (0.14), residues: 1290 loop : 0.71 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 34 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE A 898 TRP 0.013 0.001 TRP E 106 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (34167) covalent geometry : angle 0.51985 (46665) SS BOND : bond 0.00268 ( 54) SS BOND : angle 0.75603 ( 108) hydrogen bonds : bond 0.03962 ( 1478) hydrogen bonds : angle 5.50532 ( 4020) link_BETA1-4 : bond 0.00559 ( 12) link_BETA1-4 : angle 1.65436 ( 36) link_BETA1-6 : bond 0.00163 ( 3) link_BETA1-6 : angle 1.33194 ( 9) link_NAG-ASN : bond 0.00470 ( 54) link_NAG-ASN : angle 1.95436 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 404 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8567 (tmtp) REVERT: A 498 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: A 546 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 583 GLU cc_start: 0.7618 (tt0) cc_final: 0.7199 (pt0) REVERT: A 675 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6981 (mm110) REVERT: A 725 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: A 755 GLN cc_start: 0.8544 (mt0) cc_final: 0.8263 (mt0) REVERT: D 55 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.8091 (ttm-80) REVERT: E 34 MET cc_start: 0.8774 (tpp) cc_final: 0.8268 (tpp) REVERT: E 87 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5919 (mtp85) REVERT: B 32 PHE cc_start: 0.7859 (m-10) cc_final: 0.7604 (m-10) REVERT: B 129 LYS cc_start: 0.7845 (mtpm) cc_final: 0.7146 (mppt) REVERT: B 725 GLU cc_start: 0.8342 (tt0) cc_final: 0.7826 (tm-30) REVERT: B 787 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7714 (mt0) REVERT: B 814 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6818 (ttpp) REVERT: B 990 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7354 (tm-30) REVERT: B 1017 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 1050 MET cc_start: 0.9056 (ptm) cc_final: 0.8829 (ptp) REVERT: B 1113 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: C 13 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7209 (pp) REVERT: C 62 ARG cc_start: 0.7357 (ptp90) cc_final: 0.7055 (ptp90) REVERT: C 103 THR cc_start: 0.8023 (p) cc_final: 0.7696 (t) REVERT: J 29 THR cc_start: 0.7797 (t) cc_final: 0.7521 (t) REVERT: J 129 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7058 (mtpm) REVERT: J 787 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: J 1113 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: K 13 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6953 (pp) REVERT: K 103 THR cc_start: 0.7730 (p) cc_final: 0.7512 (t) outliers start: 69 outliers final: 29 residues processed: 436 average time/residue: 0.6815 time to fit residues: 353.3300 Evaluate side-chains 426 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 385 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 657 ASN Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 237 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 349 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 394 ASN B 957 GLN B1101 HIS ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN J 675 GLN J 804 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.161107 restraints weight = 32975.377| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 0.93 r_work: 0.3433 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34290 Z= 0.226 Angle : 0.652 24.358 46980 Z= 0.327 Chirality : 0.063 3.055 5550 Planarity : 0.004 0.044 6018 Dihedral : 5.266 52.419 6171 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.04 % Allowed : 9.69 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.13), residues: 4392 helix: 2.06 (0.20), residues: 627 sheet: 0.68 (0.13), residues: 1344 loop : 0.67 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.028 0.002 TYR K 92 PHE 0.024 0.002 PHE B 898 TRP 0.017 0.002 TRP M 36 HIS 0.013 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00515 (34167) covalent geometry : angle 0.62618 (46665) SS BOND : bond 0.00492 ( 54) SS BOND : angle 0.90175 ( 108) hydrogen bonds : bond 0.04783 ( 1478) hydrogen bonds : angle 5.76622 ( 4020) link_BETA1-4 : bond 0.00514 ( 12) link_BETA1-4 : angle 1.63121 ( 36) link_BETA1-6 : bond 0.00239 ( 3) link_BETA1-6 : angle 1.76877 ( 9) link_NAG-ASN : bond 0.00438 ( 54) link_NAG-ASN : angle 2.99425 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 401 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7816 (m-10) cc_final: 0.7543 (m-10) REVERT: A 356 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8531 (tmtp) REVERT: A 498 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 546 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 725 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 1010 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: A 1113 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: D 103 THR cc_start: 0.8071 (p) cc_final: 0.7564 (t) REVERT: E 34 MET cc_start: 0.8857 (tpp) cc_final: 0.8373 (tpp) REVERT: E 87 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6046 (mtp85) REVERT: B 32 PHE cc_start: 0.7918 (m-10) cc_final: 0.7672 (m-10) REVERT: B 112 SER cc_start: 0.7179 (p) cc_final: 0.6930 (m) REVERT: B 121 ASN cc_start: 0.7426 (m-40) cc_final: 0.7140 (m110) REVERT: B 227 VAL cc_start: 0.8228 (p) cc_final: 0.7848 (m) REVERT: B 528 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7772 (mtmt) REVERT: B 725 GLU cc_start: 0.8403 (tt0) cc_final: 0.7894 (tm-30) REVERT: B 776 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8070 (ttpp) REVERT: B 787 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 814 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6733 (mtmt) REVERT: B 990 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7526 (tm-30) REVERT: B 1017 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8067 (tm-30) REVERT: B 1050 MET cc_start: 0.9170 (ptm) cc_final: 0.8910 (ptp) REVERT: B 1113 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: C 13 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7062 (pp) REVERT: C 64 SER cc_start: 0.8039 (p) cc_final: 0.7685 (m) REVERT: C 103 THR cc_start: 0.8165 (p) cc_final: 0.7889 (t) REVERT: J 29 THR cc_start: 0.7897 (t) cc_final: 0.7647 (t) REVERT: J 787 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: J 1113 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: K 13 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7052 (pp) outliers start: 97 outliers final: 45 residues processed: 450 average time/residue: 0.6821 time to fit residues: 365.5048 Evaluate side-chains 448 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 387 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 125 ASN Chi-restraints excluded: chain J residue 236 THR Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 405 ASP Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 560 LEU Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 902 MET Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 36 optimal weight: 0.3980 chunk 172 optimal weight: 3.9990 chunk 383 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 402 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 432 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 137 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 675 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN A1135 ASN B 271 GLN B 394 ASN B 957 GLN B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN ** J 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.190860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162445 restraints weight = 33123.662| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 0.97 r_work: 0.3453 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34290 Z= 0.133 Angle : 0.582 18.743 46980 Z= 0.288 Chirality : 0.051 1.335 5550 Planarity : 0.004 0.041 6018 Dihedral : 5.018 57.272 6171 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.16 % Allowed : 11.04 % Favored : 86.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.13), residues: 4392 helix: 2.28 (0.20), residues: 627 sheet: 0.75 (0.14), residues: 1284 loop : 0.66 (0.13), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 62 TYR 0.021 0.001 TYR J1067 PHE 0.018 0.001 PHE B 898 TRP 0.018 0.001 TRP E 106 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00290 (34167) covalent geometry : angle 0.55032 (46665) SS BOND : bond 0.00293 ( 54) SS BOND : angle 0.69178 ( 108) hydrogen bonds : bond 0.04130 ( 1478) hydrogen bonds : angle 5.53263 ( 4020) link_BETA1-4 : bond 0.00569 ( 12) link_BETA1-4 : angle 1.48577 ( 36) link_BETA1-6 : bond 0.00037 ( 3) link_BETA1-6 : angle 1.46506 ( 9) link_NAG-ASN : bond 0.00412 ( 54) link_NAG-ASN : angle 3.16665 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 399 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8542 (tmtp) REVERT: A 498 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: A 546 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7805 (tt) REVERT: A 725 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: E 34 MET cc_start: 0.8791 (tpp) cc_final: 0.8251 (tpp) REVERT: E 87 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6082 (mtp85) REVERT: B 32 PHE cc_start: 0.7915 (m-10) cc_final: 0.7703 (m-10) REVERT: B 112 SER cc_start: 0.7142 (p) cc_final: 0.6928 (m) REVERT: B 121 ASN cc_start: 0.7427 (m-40) cc_final: 0.7129 (m110) REVERT: B 227 VAL cc_start: 0.8216 (p) cc_final: 0.7847 (m) REVERT: B 528 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7736 (mtmt) REVERT: B 725 GLU cc_start: 0.8369 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 787 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: B 814 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6731 (mtmt) REVERT: B 990 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7511 (tm-30) REVERT: B 1017 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 1050 MET cc_start: 0.9104 (ptm) cc_final: 0.8856 (ptp) REVERT: B 1113 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: C 13 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7030 (pp) REVERT: C 62 ARG cc_start: 0.7250 (ptp90) cc_final: 0.7044 (ptp90) REVERT: C 64 SER cc_start: 0.7946 (p) cc_final: 0.7636 (m) REVERT: F 120 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7586 (tt) REVERT: J 29 THR cc_start: 0.7894 (t) cc_final: 0.7639 (t) REVERT: J 126 VAL cc_start: 0.6749 (t) cc_final: 0.6465 (p) REVERT: J 190 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7531 (mmm-85) REVERT: J 415 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8322 (p) REVERT: J 787 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: J 1113 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: K 13 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6991 (pp) outliers start: 69 outliers final: 34 residues processed: 439 average time/residue: 0.6796 time to fit residues: 354.9946 Evaluate side-chains 437 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 388 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 49 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 388 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 675 GLN A 804 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN B1011 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159658 restraints weight = 33119.478| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 0.98 r_work: 0.3408 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34290 Z= 0.238 Angle : 0.652 16.442 46980 Z= 0.331 Chirality : 0.049 0.795 5550 Planarity : 0.004 0.044 6018 Dihedral : 5.272 57.372 6171 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.79 % Allowed : 10.85 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4392 helix: 1.78 (0.20), residues: 639 sheet: 0.68 (0.13), residues: 1341 loop : 0.55 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1039 TYR 0.028 0.002 TYR K 92 PHE 0.024 0.002 PHE B 898 TRP 0.017 0.002 TRP E 106 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00545 (34167) covalent geometry : angle 0.63073 (46665) SS BOND : bond 0.00519 ( 54) SS BOND : angle 0.93733 ( 108) hydrogen bonds : bond 0.04858 ( 1478) hydrogen bonds : angle 5.77570 ( 4020) link_BETA1-4 : bond 0.00552 ( 12) link_BETA1-4 : angle 1.54057 ( 36) link_BETA1-6 : bond 0.00310 ( 3) link_BETA1-6 : angle 1.83098 ( 9) link_NAG-ASN : bond 0.00526 ( 54) link_NAG-ASN : angle 2.70348 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 398 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7828 (m-10) cc_final: 0.7539 (m-10) REVERT: A 356 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8656 (tmtp) REVERT: A 498 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: A 546 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 725 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 776 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: A 814 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6955 (ttpt) REVERT: A 1010 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: A 1125 ASN cc_start: 0.7762 (p0) cc_final: 0.7556 (p0) REVERT: D 103 THR cc_start: 0.8149 (p) cc_final: 0.7743 (t) REVERT: E 34 MET cc_start: 0.8891 (tpp) cc_final: 0.8402 (tpp) REVERT: E 87 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6007 (mtp85) REVERT: B 32 PHE cc_start: 0.7954 (m-10) cc_final: 0.7647 (m-10) REVERT: B 112 SER cc_start: 0.7008 (p) cc_final: 0.6777 (m) REVERT: B 121 ASN cc_start: 0.7347 (m-40) cc_final: 0.7052 (m110) REVERT: B 129 LYS cc_start: 0.7936 (mtpm) cc_final: 0.7322 (mtpt) REVERT: B 227 VAL cc_start: 0.8222 (p) cc_final: 0.7775 (m) REVERT: B 528 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7782 (mtmt) REVERT: B 725 GLU cc_start: 0.8395 (tt0) cc_final: 0.7885 (tm-30) REVERT: B 787 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: B 814 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6810 (mtmt) REVERT: B 1017 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 1050 MET cc_start: 0.9166 (ptm) cc_final: 0.8926 (ptp) REVERT: B 1091 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8290 (mtt-85) REVERT: B 1113 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: C 13 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7087 (pp) REVERT: C 64 SER cc_start: 0.8111 (p) cc_final: 0.7762 (m) REVERT: F 73 ASP cc_start: 0.8241 (t70) cc_final: 0.8020 (t70) REVERT: F 120 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7561 (tt) REVERT: J 29 THR cc_start: 0.8055 (t) cc_final: 0.7836 (t) REVERT: J 126 VAL cc_start: 0.6777 (t) cc_final: 0.6464 (p) REVERT: J 190 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7581 (mmm-85) REVERT: J 415 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8339 (p) REVERT: J 787 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: J 1113 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: K 13 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7156 (pp) outliers start: 89 outliers final: 41 residues processed: 449 average time/residue: 0.6812 time to fit residues: 363.9544 Evaluate side-chains 449 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain J residue 125 ASN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 902 MET Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 157 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 348 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 438 optimal weight: 40.0000 chunk 358 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 437 optimal weight: 30.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 804 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN D 38 GLN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN ** J 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160979 restraints weight = 33058.190| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 0.96 r_work: 0.3425 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34290 Z= 0.176 Angle : 0.601 12.683 46980 Z= 0.304 Chirality : 0.046 0.377 5550 Planarity : 0.004 0.040 6018 Dihedral : 5.065 47.888 6171 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.48 % Allowed : 11.41 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.13), residues: 4392 helix: 1.63 (0.20), residues: 669 sheet: 0.75 (0.14), residues: 1278 loop : 0.48 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.025 0.002 TYR K 92 PHE 0.022 0.002 PHE B 898 TRP 0.018 0.002 TRP E 106 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00397 (34167) covalent geometry : angle 0.58026 (46665) SS BOND : bond 0.00372 ( 54) SS BOND : angle 0.79034 ( 108) hydrogen bonds : bond 0.04461 ( 1478) hydrogen bonds : angle 5.64906 ( 4020) link_BETA1-4 : bond 0.00548 ( 12) link_BETA1-4 : angle 1.44958 ( 36) link_BETA1-6 : bond 0.00143 ( 3) link_BETA1-6 : angle 1.66859 ( 9) link_NAG-ASN : bond 0.00547 ( 54) link_NAG-ASN : angle 2.60502 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7794 (m-10) cc_final: 0.7546 (m-10) REVERT: A 356 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8620 (tmtp) REVERT: A 498 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: A 546 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (tt) REVERT: A 725 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 814 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6942 (ttpt) REVERT: A 1010 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: A 1113 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: D 103 THR cc_start: 0.8069 (p) cc_final: 0.7724 (t) REVERT: E 34 MET cc_start: 0.8845 (tpp) cc_final: 0.8317 (tpp) REVERT: E 87 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6046 (mtp85) REVERT: B 32 PHE cc_start: 0.7941 (m-10) cc_final: 0.7668 (m-10) REVERT: B 121 ASN cc_start: 0.7359 (m-40) cc_final: 0.7095 (m110) REVERT: B 129 LYS cc_start: 0.7922 (mtpm) cc_final: 0.7315 (mtpt) REVERT: B 227 VAL cc_start: 0.8215 (p) cc_final: 0.7793 (m) REVERT: B 528 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7785 (mtmt) REVERT: B 725 GLU cc_start: 0.8373 (tt0) cc_final: 0.7868 (tm-30) REVERT: B 776 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8019 (ttpp) REVERT: B 787 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: B 814 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6790 (mtmt) REVERT: B 1017 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 1050 MET cc_start: 0.9110 (ptm) cc_final: 0.8865 (ptp) REVERT: B 1113 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: C 13 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7072 (pp) REVERT: C 64 SER cc_start: 0.8130 (p) cc_final: 0.7782 (m) REVERT: F 120 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7565 (tt) REVERT: J 29 THR cc_start: 0.8001 (t) cc_final: 0.7773 (t) REVERT: J 126 VAL cc_start: 0.6881 (t) cc_final: 0.6546 (p) REVERT: J 190 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7568 (mmm-85) REVERT: J 415 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8304 (p) REVERT: J 787 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: J 1113 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: K 13 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7042 (pp) outliers start: 79 outliers final: 42 residues processed: 445 average time/residue: 0.6628 time to fit residues: 352.1220 Evaluate side-chains 452 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 391 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 560 LEU Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 902 MET Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 804 GLN A 955 ASN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN J 804 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159197 restraints weight = 32961.810| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 0.99 r_work: 0.3408 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 34290 Z= 0.214 Angle : 0.627 8.739 46980 Z= 0.319 Chirality : 0.047 0.306 5550 Planarity : 0.004 0.041 6018 Dihedral : 5.182 54.220 6171 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.35 % Allowed : 11.60 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % 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: 0.92 (0.13), residues: 4392 helix: 1.51 (0.20), residues: 669 sheet: 0.72 (0.13), residues: 1338 loop : 0.42 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.027 0.002 TYR K 92 PHE 0.023 0.002 PHE B 898 TRP 0.018 0.002 TRP E 106 HIS 0.008 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00489 (34167) covalent geometry : angle 0.61033 (46665) SS BOND : bond 0.00474 ( 54) SS BOND : angle 0.90881 ( 108) hydrogen bonds : bond 0.04694 ( 1478) hydrogen bonds : angle 5.71918 ( 4020) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 1.46159 ( 36) link_BETA1-6 : bond 0.00270 ( 3) link_BETA1-6 : angle 1.81693 ( 9) link_NAG-ASN : bond 0.00508 ( 54) link_NAG-ASN : angle 2.30643 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 398 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7741 (m-10) cc_final: 0.7474 (m-10) REVERT: A 356 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8624 (tmtp) REVERT: A 498 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: A 546 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 619 GLU cc_start: 0.7500 (mp0) cc_final: 0.7235 (mp0) REVERT: A 725 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: A 814 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6928 (ttpt) REVERT: A 1010 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: A 1113 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7783 (mt0) REVERT: D 103 THR cc_start: 0.8163 (p) cc_final: 0.7873 (t) REVERT: E 34 MET cc_start: 0.8873 (tpp) cc_final: 0.8381 (tpp) REVERT: E 87 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.5978 (mtp85) REVERT: B 32 PHE cc_start: 0.7942 (m-10) cc_final: 0.7606 (m-10) REVERT: B 121 ASN cc_start: 0.7403 (m-40) cc_final: 0.7145 (m110) REVERT: B 129 LYS cc_start: 0.7924 (mtpm) cc_final: 0.7336 (mtpt) REVERT: B 227 VAL cc_start: 0.8228 (p) cc_final: 0.7777 (m) REVERT: B 528 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7811 (mtmt) REVERT: B 725 GLU cc_start: 0.8444 (tt0) cc_final: 0.7925 (tm-30) REVERT: B 776 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8033 (ttpp) REVERT: B 787 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: B 814 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6767 (mtmt) REVERT: B 1017 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 1050 MET cc_start: 0.9131 (ptm) cc_final: 0.8889 (ptp) REVERT: B 1113 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7669 (mp10) REVERT: C 13 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7114 (pp) REVERT: C 64 SER cc_start: 0.8108 (p) cc_final: 0.7770 (m) REVERT: F 120 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7540 (tt) REVERT: J 29 THR cc_start: 0.8016 (t) cc_final: 0.7796 (t) REVERT: J 126 VAL cc_start: 0.6862 (t) cc_final: 0.6589 (p) REVERT: J 415 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8308 (p) REVERT: J 787 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: J 1017 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: J 1113 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: K 13 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7095 (pp) outliers start: 75 outliers final: 47 residues processed: 441 average time/residue: 0.6694 time to fit residues: 350.9571 Evaluate side-chains 457 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 390 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 582 LEU Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 820 ASP Chi-restraints excluded: chain J residue 821 LEU Chi-restraints excluded: chain J residue 902 MET Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1017 GLU Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 275 optimal weight: 30.0000 chunk 253 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 291 optimal weight: 0.1980 chunk 430 optimal weight: 6.9990 chunk 198 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162036 restraints weight = 33214.412| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 0.98 r_work: 0.3447 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34290 Z= 0.125 Angle : 0.548 10.442 46980 Z= 0.278 Chirality : 0.044 0.269 5550 Planarity : 0.004 0.040 6018 Dihedral : 4.702 34.666 6171 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.69 % Allowed : 12.51 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 4392 helix: 1.80 (0.20), residues: 669 sheet: 0.83 (0.14), residues: 1248 loop : 0.50 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 62 TYR 0.021 0.001 TYR J1067 PHE 0.019 0.001 PHE C 84 TRP 0.017 0.002 TRP E 106 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (34167) covalent geometry : angle 0.53306 (46665) SS BOND : bond 0.00277 ( 54) SS BOND : angle 0.75905 ( 108) hydrogen bonds : bond 0.03980 ( 1478) hydrogen bonds : angle 5.45942 ( 4020) link_BETA1-4 : bond 0.00584 ( 12) link_BETA1-4 : angle 1.36824 ( 36) link_BETA1-6 : bond 0.00055 ( 3) link_BETA1-6 : angle 1.51483 ( 9) link_NAG-ASN : bond 0.00453 ( 54) link_NAG-ASN : angle 2.10649 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 407 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7701 (tt) REVERT: A 619 GLU cc_start: 0.7453 (mp0) cc_final: 0.7200 (mp0) REVERT: A 725 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: D 103 THR cc_start: 0.7941 (p) cc_final: 0.7638 (t) REVERT: E 34 MET cc_start: 0.8824 (tpp) cc_final: 0.8334 (tpp) REVERT: E 87 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5984 (mtp85) REVERT: B 32 PHE cc_start: 0.7918 (m-10) cc_final: 0.7693 (m-10) REVERT: B 121 ASN cc_start: 0.7359 (m-40) cc_final: 0.7082 (m110) REVERT: B 129 LYS cc_start: 0.7933 (mtpm) cc_final: 0.7338 (mtpt) REVERT: B 227 VAL cc_start: 0.8200 (p) cc_final: 0.7737 (m) REVERT: B 239 GLN cc_start: 0.8041 (tt0) cc_final: 0.7808 (mt0) REVERT: B 725 GLU cc_start: 0.8448 (tt0) cc_final: 0.7923 (tm-30) REVERT: B 787 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: B 814 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6986 (ttpp) REVERT: B 1017 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 1050 MET cc_start: 0.9066 (ptm) cc_final: 0.8825 (ptp) REVERT: B 1113 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7687 (mp10) REVERT: C 13 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7080 (pp) REVERT: C 64 SER cc_start: 0.8164 (p) cc_final: 0.7869 (m) REVERT: F 56 SER cc_start: 0.8304 (m) cc_final: 0.7936 (p) REVERT: F 120 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7561 (tt) REVERT: J 29 THR cc_start: 0.7991 (t) cc_final: 0.7754 (t) REVERT: J 415 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8269 (p) REVERT: J 428 ASP cc_start: 0.8127 (p0) cc_final: 0.7927 (p0) REVERT: J 483 VAL cc_start: 0.8893 (t) cc_final: 0.8607 (p) REVERT: J 787 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: J 902 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8541 (tpp) REVERT: J 1017 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8300 (mt-10) REVERT: J 1113 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: K 13 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7027 (pp) outliers start: 54 outliers final: 30 residues processed: 440 average time/residue: 0.6856 time to fit residues: 359.7406 Evaluate side-chains 437 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain J residue 52 GLN Chi-restraints excluded: chain J residue 393 THR Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 787 GLN Chi-restraints excluded: chain J residue 902 MET Chi-restraints excluded: chain J residue 967 SER Chi-restraints excluded: chain J residue 1113 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain M residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 394 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 804 GLN A 957 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 675 GLN ** J1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160859 restraints weight = 33020.658| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.00 r_work: 0.3425 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34290 Z= 0.161 Angle : 0.585 11.086 46980 Z= 0.296 Chirality : 0.045 0.254 5550 Planarity : 0.004 0.040 6018 Dihedral : 5.070 91.321 6171 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.60 % Allowed : 12.76 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.13), residues: 4392 helix: 1.76 (0.20), residues: 669 sheet: 0.85 (0.14), residues: 1248 loop : 0.48 (0.13), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 62 TYR 0.023 0.002 TYR K 92 PHE 0.023 0.002 PHE J 168 TRP 0.018 0.002 TRP E 106 HIS 0.007 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (34167) covalent geometry : angle 0.56821 (46665) SS BOND : bond 0.00355 ( 54) SS BOND : angle 0.76048 ( 108) hydrogen bonds : bond 0.04250 ( 1478) hydrogen bonds : angle 5.51523 ( 4020) link_BETA1-4 : bond 0.00567 ( 12) link_BETA1-4 : angle 1.38149 ( 36) link_BETA1-6 : bond 0.00119 ( 3) link_BETA1-6 : angle 1.68550 ( 9) link_NAG-ASN : bond 0.00403 ( 54) link_NAG-ASN : angle 2.27919 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15692.07 seconds wall clock time: 266 minutes 13.41 seconds (15973.41 seconds total)