Starting phenix.real_space_refine on Fri Feb 6 05:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cwr_45972/02_2026/9cwr_45972.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.098 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 108 5.16 5 C 13917 2.51 5 N 3811 2.21 5 O 4834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22670 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 6749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 6749 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 405} Link IDs: {'PTRANS': 56, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 1393 Unresolved non-hydrogen angles: 1792 Unresolved non-hydrogen dihedrals: 1134 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 25, 'TYR:plan': 21, 'ASN:plan1': 36, 'PHE:plan': 22, 'ASP:plan': 35, 'HIS:plan': 6, 'GLU:plan': 27, 'ARG:plan': 15, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 832 Chain: "B" Number of atoms: 6683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 6683 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 407} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 9 Unresolved non-hydrogen bonds: 1410 Unresolved non-hydrogen angles: 1813 Unresolved non-hydrogen dihedrals: 1149 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 25, 'TYR:plan': 19, 'ASN:plan1': 32, 'PHE:plan': 26, 'ASP:plan': 37, 'HIS:plan': 6, 'GLU:plan': 26, 'ARG:plan': 15, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 832 Chain: "C" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 6628 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 430} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Unresolved non-hydrogen bonds: 1466 Unresolved non-hydrogen angles: 1891 Unresolved non-hydrogen dihedrals: 1185 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'GLN:plan1': 26, 'TYR:plan': 20, 'ASN:plan1': 40, 'PHE:plan': 23, 'ASP:plan': 40, 'TRP:plan': 4, 'GLU:plan': 26, 'ARG:plan': 16, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 867 Chain: "K" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 349 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 349 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "I" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 349 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 69} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 2, 'HIS:plan': 4, 'ASP:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: "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: "Y" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 229 Classifications: {'water': 229} Link IDs: {None: 228} Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "C" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 212 Classifications: {'water': 212} Link IDs: {None: 211} Time building chain proxies: 6.17, per 1000 atoms: 0.27 Number of scatterers: 22670 At special positions: 0 Unit cell: (138, 139, 195, 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 108 16.00 O 4834 8.00 N 3811 7.00 C 13917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 62 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 245 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 62 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 245 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C 245 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1134 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 62 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1134 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A 282 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 282 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C 331 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6196 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 30.1% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.726A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.957A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 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: 3.646A 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 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.853A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.913A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1144 removed outlier: 3.840A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.532A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.971A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.534A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 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: 3.562A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.860A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 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 1033 removed outlier: 3.562A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 3.646A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.830A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.638A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.642A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.591A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.813A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.880A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 4.014A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 Processing helix chain 'K' and resid 26 through 49 removed outlier: 3.971A pdb=" N ILE K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 70 Processing helix chain 'G' and resid 2 through 22 removed outlier: 4.070A pdb=" N HIS G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 49 removed outlier: 3.521A pdb=" N THR G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU G 44 " --> pdb=" O THR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 70 Processing helix chain 'I' and resid 2 through 21 removed outlier: 3.624A pdb=" N VAL I 6 " --> pdb=" O LEU I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 49 removed outlier: 3.669A pdb=" N LEU I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 47 " --> pdb=" O MET I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.531A pdb=" N TRP A 65 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASN A 62 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR A 269 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 64 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 4.027A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 56 removed outlier: 3.916A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.682A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.926A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.402A 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: 4.119A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE A 565 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 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: 5.996A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.672A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.761A 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: 6.672A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.529A 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: 4.340A 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 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.725A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 37 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.370A pdb=" N PHE B 44 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 56 removed outlier: 7.718A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.689A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.978A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.635A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.608A pdb=" N VAL B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.786A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.161A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 56 removed outlier: 7.506A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.527A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.938A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.682A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.679A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.679A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.363A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 1250 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3638 1.27 - 1.40: 5375 1.40 - 1.54: 13172 1.54 - 1.68: 98 1.68 - 1.82: 132 Bond restraints: 22415 Sorted by residual: bond pdb=" C ASN A 717 " pdb=" O ASN A 717 " ideal model delta sigma weight residual 1.235 1.130 0.105 1.14e-02 7.69e+03 8.46e+01 bond pdb=" CA ASN A 717 " pdb=" CB ASN A 717 " ideal model delta sigma weight residual 1.535 1.494 0.041 1.32e-02 5.74e+03 9.57e+00 bond pdb=" C ASN A 717 " pdb=" N PHE A 718 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.23e-02 6.61e+03 9.47e+00 bond pdb=" CA ASN A 717 " pdb=" C ASN A 717 " ideal model delta sigma weight residual 1.525 1.494 0.031 1.34e-02 5.57e+03 5.45e+00 bond pdb=" C ARG C 273 " pdb=" N THR C 274 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.39e-02 5.18e+03 3.42e+00 ... (remaining 22410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 30419 1.73 - 3.47: 381 3.47 - 5.20: 35 5.20 - 6.94: 11 6.94 - 8.67: 4 Bond angle restraints: 30850 Sorted by residual: angle pdb=" N GLU B 281 " pdb=" CA GLU B 281 " pdb=" C GLU B 281 " ideal model delta sigma weight residual 112.38 118.76 -6.38 1.22e+00 6.72e-01 2.74e+01 angle pdb=" N ILE B 896 " pdb=" CA ILE B 896 " pdb=" C ILE B 896 " ideal model delta sigma weight residual 109.19 105.36 3.83 8.20e-01 1.49e+00 2.18e+01 angle pdb=" C ILE B 896 " pdb=" CA ILE B 896 " pdb=" CB ILE B 896 " ideal model delta sigma weight residual 109.33 113.13 -3.80 9.80e-01 1.04e+00 1.51e+01 angle pdb=" CA ASN A 717 " pdb=" CB ASN A 717 " pdb=" CG ASN A 717 " ideal model delta sigma weight residual 112.60 116.18 -3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CA ILE B 896 " pdb=" C ILE B 896 " pdb=" N PRO B 897 " ideal model delta sigma weight residual 116.57 119.93 -3.36 9.80e-01 1.04e+00 1.17e+01 ... (remaining 30845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 13616 17.49 - 34.98: 353 34.98 - 52.46: 68 52.46 - 69.95: 25 69.95 - 87.44: 12 Dihedral angle restraints: 14074 sinusoidal: 4537 harmonic: 9537 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 127.84 -34.84 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 125.16 -32.16 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CA LEU C 945 " pdb=" C LEU C 945 " pdb=" N GLY C 946 " pdb=" CA GLY C 946 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2951 0.045 - 0.090: 675 0.090 - 0.135: 296 0.135 - 0.180: 16 0.180 - 0.224: 3 Chirality restraints: 3941 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.14e+01 chirality pdb=" CA ARG C 273 " pdb=" N ARG C 273 " pdb=" C ARG C 273 " pdb=" CB ARG C 273 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3938 not shown) Planarity restraints: 4081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 273 " -0.406 9.50e-02 1.11e+02 1.82e-01 2.03e+01 pdb=" NE ARG C 273 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 273 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 273 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 273 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.047 2.00e-02 2.50e+03 3.79e-02 1.80e+01 pdb=" C7 NAG E 2 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.056 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.027 2.00e-02 2.50e+03 2.22e-02 6.16e+00 pdb=" C7 NAG E 1 " 0.002 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.036 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.008 2.00e-02 2.50e+03 ... (remaining 4078 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 10288 2.95 - 3.44: 20899 3.44 - 3.92: 38235 3.92 - 4.41: 41366 4.41 - 4.90: 67282 Nonbonded interactions: 178070 Sorted by model distance: nonbonded pdb=" O5 NAG C1303 " pdb=" O6 NAG C1303 " model vdw 2.459 2.432 nonbonded pdb=" N ASN A 717 " pdb=" O ASN A 717 " model vdw 2.523 2.496 nonbonded pdb=" O5 NAG A1303 " pdb=" O6 NAG A1303 " model vdw 2.531 2.432 nonbonded pdb=" O5 NAG E 2 " pdb=" O6 NAG E 2 " model vdw 2.550 2.432 nonbonded pdb=" O5 NAG F 2 " pdb=" O6 NAG F 2 " model vdw 2.563 2.432 ... (remaining 178065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 25 or (resid 27 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 51 or (resid 52 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or res \ id 62 or (resid 63 through 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 or resid 82 through 83 or (resid 84 and (name N or name CA or \ name C or name O or name CB )) or resid 85 or (resid 86 through 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 through 113 or (resid 1 \ 15 through 130 and (name N or name CA or name C or name O or name CB )) or resid \ 131 through 143 or resid 156 through 167 or (resid 168 through 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 or (resid 175 through \ 190 and (name N or name CA or name C or name O or name CB )) or resid 191 throug \ h 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or \ resid 204 through 236 or (resid 237 and (name N or name CA or name C or name O o \ r name CB )) or resid 238 through 273 or (resid 274 and (name N or name CA or na \ me C or name O or name CB )) or resid 275 through 279 or (resid 280 through 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 through 28 \ 3 or (resid 284 and (name N or name CA or name C or name O or name CB )) or resi \ d 285 or (resid 286 through 288 and (name N or name CA or name C or name O or na \ me CB )) or resid 289 through 301 or (resid 302 and (name N or name CA or name C \ or name O or name CB )) or resid 303 through 316 or (resid 317 and (name N or n \ ame CA or name C or name O or name CB )) or resid 318 through 550 or (resid 551 \ and (name N or name CA or name C or name O or name CB )) or resid 552 through 55 \ 9 or (resid 560 and (name N or name CA or name C or name O or name CB )) or resi \ d 561 or (resid 562 and (name N or name CA or name C or name O or name CB )) or \ resid 563 through 575 or (resid 576 and (name N or name CA or name C or name O o \ r name CB )) or resid 577 through 595 or (resid 596 and (name N or name CA or na \ me C or name O or name CB )) or resid 597 through 604 or (resid 605 through 606 \ and (name N or name CA or name C or name O or name CB )) or resid 607 through 61 \ 4 or (resid 615 and (name N or name CA or name C or name O or name CB )) or resi \ d 616 through 640 or (resid 641 and (name N or name CA or name C or name O or na \ me CB )) or resid 642 through 662 or (resid 663 and (name N or name CA or name C \ or name O or name CB )) or resid 664 through 675 or resid 690 through 718 or (r \ esid 719 and (name N or name CA or name C or name O or name CB )) or resid 720 t \ hrough 722 or (resid 723 and (name N or name CA or name C or name O or name CB ) \ ) or resid 724 through 734 or (resid 735 through 737 and (name N or name CA or n \ ame C or name O or name CB )) or resid 738 through 753 or (resid 754 and (name N \ or name CA or name C or name O or name CB )) or resid 755 through 775 or (resid \ 776 and (name N or name CA or name C or name O or name CB )) or resid 777 throu \ gh 784 or (resid 785 through 786 and (name N or name CA or name C or name O or n \ ame CB )) or resid 787 through 789 or (resid 790 through 791 and (name N or name \ CA or name C or name O or name CB )) or resid 792 through 820 or (resid 821 and \ (name N or name CA or name C or name O or name CB )) or resid 822 through 823 o \ r (resid 824 through 855 and (name N or name CA or name C or name O or name CB ) \ ) or resid 856 through 866 or (resid 867 through 868 and (name N or name CA or n \ ame C or name O or name CB )) or resid 869 through 930 or (resid 931 and (name N \ or name CA or name C or name O or name CB )) or resid 932 through 936 or (resid \ 937 through 941 and (name N or name CA or name C or name O or name CB )) or res \ id 942 through 948 or (resid 949 through 950 and (name N or name CA or name C or \ name O or name CB )) or resid 951 through 976 or (resid 977 through 985 and (na \ me N or name CA or name C or name O or name CB )) or resid 986 through 990 or (r \ esid 991 and (name N or name CA or name C or name O or name CB )) or resid 992 t \ hrough 1009 or (resid 1010 and (name N or name CA or name C or name O or name CB \ )) or resid 1011 through 1040 or (resid 1041 and (name N or name CA or name C o \ r name O or name CB )) or resid 1042 through 1071 or (resid 1072 through 1073 an \ d (name N or name CA or name C or name O or name CB )) or resid 1074 through 108 \ 3 or (resid 1084 and (name N or name CA or name C or name O or name CB )) or res \ id 1085 or (resid 1086 through 1087 and (name N or name CA or name C or name O o \ r name CB )) or resid 1088 through 1124 or (resid 1125 and (name N or name CA or \ name C or name O or name CB )) or resid 1126 through 1127 or (resid 1128 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1129 through 1138 or \ (resid 1139 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 140 through 1307)) selection = (chain 'B' and (resid 15 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 64 or (resid 65 and (name N or nam \ e CA or name C or name O or name CB )) or resid 66 or resid 82 through 143 or re \ sid 156 through 175 or resid 188 through 199 or (resid 200 and (name N or name C \ A or name C or name O or name CB )) or resid 201 through 202 or (resid 203 and ( \ name N or name CA or name C or name O or name CB )) or resid 204 through 210 or \ resid 217 through 223 or (resid 224 and (name N or name CA or name C or name O o \ r name CB )) or resid 225 or (resid 226 through 229 and (name N or name CA or na \ me C or name O or name CB )) or resid 230 through 236 or (resid 237 and (name N \ or name CA or name C or name O or name CB )) or resid 238 through 239 or (resid \ 240 through 244 and (name N or name CA or name C or name O or name CB )) or resi \ d 245 through 279 or (resid 280 through 281 and (name N or name CA or name C or \ name O or name CB )) or resid 282 through 283 or (resid 284 and (name N or name \ CA or name C or name O or name CB )) or resid 285 through 316 or (resid 317 and \ (name N or name CA or name C or name O or name CB )) or resid 318 through 342 or \ (resid 343 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 539 or (resid 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 550 or (resid 551 and (name N or name CA o \ r name C or name O or name CB )) or resid 552 through 559 or (resid 560 and (nam \ e N or name CA or name C or name O or name CB )) or resid 561 or (resid 562 and \ (name N or name CA or name C or name O or name CB )) or resid 563 or (resid 564 \ and (name N or name CA or name C or name O or name CB )) or resid 565 through 57 \ 5 or (resid 576 and (name N or name CA or name C or name O or name CB )) or resi \ d 577 through 587 or (resid 588 and (name N or name CA or name C or name O or na \ me CB )) or resid 589 through 604 or (resid 605 through 606 and (name N or name \ CA or name C or name O or name CB )) or resid 607 through 614 or (resid 615 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 623 or \ (resid 624 through 630 and (name N or name CA or name C or name O or name CB )) \ or resid 631 through 640 or (resid 641 and (name N or name CA or name C or name \ O or name CB )) or resid 642 through 662 or (resid 663 and (name N or name CA o \ r name C or name O or name CB )) or resid 664 through 697 or (resid 698 and (nam \ e N or name CA or name C or name O or name CB )) or resid 699 through 722 or (re \ sid 723 and (name N or name CA or name C or name O or name CB )) or resid 724 th \ rough 734 or (resid 735 through 737 and (name N or name CA or name C or name O o \ r name CB )) or resid 738 through 753 or (resid 754 and (name N or name CA or na \ me C or name O or name CB )) or resid 755 through 790 or (resid 791 and (name N \ or name CA or name C or name O or name CB )) or resid 792 through 807 or (resid \ 808 and (name N or name CA or name C or name O or name CB )) or resid 809 throug \ h 812 or (resid 813 through 814 and (name N or name CA or name C or name O or na \ me CB )) or resid 815 through 823 or (resid 824 through 855 and (name N or name \ CA or name C or name O or name CB )) or resid 856 through 857 or (resid 858 thro \ ugh 859 and (name N or name CA or name C or name O or name CB )) or resid 860 th \ rough 959 or (resid 960 and (name N or name CA or name C or name O or name CB )) \ or resid 961 through 966 or (resid 967 and (name N or name CA or name C or name \ O or name CB )) or resid 968 through 973 or (resid 974 and (name N or name CA o \ r name C or name O or name CB )) or resid 975 through 976 or (resid 977 through \ 985 and (name N or name CA or name C or name O or name CB )) or resid 986 throug \ h 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB )) o \ r resid 1042 through 1054 or (resid 1055 through 1056 and (name N or name CA or \ name C or name O or name CB )) or resid 1057 through 1071 or (resid 1072 through \ 1073 and (name N or name CA or name C or name O or name CB )) or resid 1074 thr \ ough 1124 or (resid 1125 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1126 through 1137 or (resid 1138 through 1139 and (name N or name CA \ or name C or name O or name CB )) or resid 1140 through 1307)) selection = (chain 'C' and (resid 15 through 25 or resid 27 through 40 or (resid 41 through \ 42 and (name N or name CA or name C or name O or name CB )) or resid 43 through \ 62 or (resid 63 through 65 and (name N or name CA or name C or name O or name CB \ )) or resid 66 or resid 82 through 85 or (resid 86 through 88 and (name N or na \ me CA or name C or name O or name CB )) or resid 89 through 113 or (resid 115 th \ rough 130 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 132 or (resid 133 through 135 and (name N or name CA or name C or name O \ or name CB )) or resid 136 through 174 or (resid 175 through 190 and (name N or \ name CA or name C or name O or name CB )) or resid 191 through 210 or resid 217 \ through 225 or (resid 226 through 229 and (name N or name CA or name C or name \ O or name CB )) or resid 230 through 247 or resid 264 through 273 or (resid 274 \ and (name N or name CA or name C or name O or name CB )) or resid 275 through 29 \ 7 or (resid 298 and (name N or name CA or name C or name O or name CB )) or resi \ d 299 through 536 or (resid 537 and (name N or name CA or name C or name O or na \ me CB )) or resid 538 through 539 or (resid 540 and (name N or name CA or name C \ or name O or name CB )) or resid 541 through 572 or (resid 573 through 576 and \ (name N or name CA or name C or name O or name CB )) or resid 577 through 595 or \ (resid 596 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 7 through 628 or (resid 629 through 630 and (name N or name CA or name C or name \ O or name CB )) or resid 631 through 672 or (resid 673 and (name N or name CA o \ r name C or name O or name CB )) or resid 674 through 675 or resid 690 through 7 \ 03 or (resid 704 and (name N or name CA or name C or name O or name CB )) or res \ id 705 through 718 or (resid 719 and (name N or name CA or name C or name O or n \ ame CB )) or resid 720 through 784 or (resid 785 through 786 and (name N or name \ CA or name C or name O or name CB )) or resid 787 through 825 or (resid 826 thr \ ough 855 and (name N or name CA or name C or name O or name CB )) or resid 856 t \ hrough 857 or (resid 858 through 859 and (name N or name CA or name C or name O \ or name CB )) or resid 860 through 930 or (resid 931 and (name N or name CA or n \ ame C or name O or name CB )) or resid 932 through 1044 or (resid 1045 and (name \ N or name CA or name C or name O or name CB )) or resid 1046 through 1127 or (r \ esid 1128 and (name N or name CA or name C or name O or name CB )) or resid 1129 \ through 1137 or (resid 1138 through 1139 and (name N or name CA or name C or na \ me O or name CB )) or resid 1140 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } 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: 9.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.820 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.003 0.105 22521 Z= 0.169 Angle : 0.539 10.321 31126 Z= 0.285 Chirality : 0.044 0.224 3941 Planarity : 0.005 0.182 4036 Dihedral : 9.348 87.441 7752 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.88 % Allowed : 2.59 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3228 helix: 2.35 (0.17), residues: 834 sheet: 0.52 (0.20), residues: 640 loop : -0.43 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 273 TYR 0.021 0.001 TYR B1067 PHE 0.019 0.001 PHE C 898 TRP 0.007 0.001 TRP C 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00336 (22415) covalent geometry : angle 0.52086 (30850) SS BOND : bond 0.00179 ( 42) SS BOND : angle 0.65859 ( 84) hydrogen bonds : bond 0.17561 ( 1208) hydrogen bonds : angle 8.26156 ( 3453) link_BETA1-4 : bond 0.01220 ( 19) link_BETA1-4 : angle 1.63038 ( 57) link_NAG-ASN : bond 0.00572 ( 45) link_NAG-ASN : angle 1.86494 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7633 (m-80) cc_final: 0.7283 (m-80) REVERT: A 191 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 207 HIS cc_start: 0.7799 (m-70) cc_final: 0.7392 (m-70) REVERT: A 328 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6877 (mmm-85) REVERT: A 607 GLN cc_start: 0.8712 (mt0) cc_final: 0.8512 (mt0) REVERT: A 755 GLN cc_start: 0.7668 (mt0) cc_final: 0.6754 (mp10) REVERT: A 773 GLU cc_start: 0.8420 (tt0) cc_final: 0.8198 (tt0) REVERT: A 780 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8323 (tt0) REVERT: A 998 THR cc_start: 0.8562 (m) cc_final: 0.8313 (p) REVERT: B 37 VAL cc_start: 0.7502 (t) cc_final: 0.7242 (p) REVERT: B 206 LYS cc_start: 0.7690 (tptm) cc_final: 0.6920 (tppt) REVERT: B 780 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8202 (pt0) REVERT: B 808 ASP cc_start: 0.7755 (t0) cc_final: 0.7435 (t0) REVERT: B 1107 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8706 (mtt90) REVERT: B 1125 ASN cc_start: 0.8488 (p0) cc_final: 0.8239 (p0) REVERT: C 206 LYS cc_start: 0.8484 (tptm) cc_final: 0.8010 (tppp) REVERT: C 304 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8002 (mtmm) REVERT: C 565 PHE cc_start: 0.8119 (p90) cc_final: 0.7625 (p90) REVERT: C 755 GLN cc_start: 0.7621 (mt0) cc_final: 0.6665 (mp10) REVERT: C 773 GLU cc_start: 0.8609 (tt0) cc_final: 0.8214 (tt0) REVERT: C 933 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7720 (mmtm) REVERT: C 1005 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (tp-100) REVERT: C 1029 MET cc_start: 0.9385 (tpp) cc_final: 0.8987 (tpp) REVERT: C 1113 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8633 (mt0) outliers start: 13 outliers final: 4 residues processed: 229 average time/residue: 0.6048 time to fit residues: 157.9507 Evaluate side-chains 188 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 755 GLN A1113 GLN B 207 HIS ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN C 607 GLN C 703 ASN C 755 GLN C 992 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.211120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146388 restraints weight = 21880.372| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.08 r_work: 0.3373 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 22521 Z= 0.148 Angle : 0.557 14.994 31126 Z= 0.284 Chirality : 0.045 0.331 3941 Planarity : 0.004 0.036 4036 Dihedral : 4.892 59.382 4745 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.70 % Allowed : 5.58 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3228 helix: 2.49 (0.17), residues: 875 sheet: 0.68 (0.19), residues: 663 loop : -0.41 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1014 TYR 0.024 0.002 TYR B1067 PHE 0.018 0.001 PHE C 898 TRP 0.009 0.001 TRP A 633 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00319 (22415) covalent geometry : angle 0.52414 (30850) SS BOND : bond 0.00267 ( 42) SS BOND : angle 1.61963 ( 84) hydrogen bonds : bond 0.04673 ( 1208) hydrogen bonds : angle 5.97206 ( 3453) link_BETA1-4 : bond 0.00409 ( 19) link_BETA1-4 : angle 1.28392 ( 57) link_NAG-ASN : bond 0.00421 ( 45) link_NAG-ASN : angle 2.55319 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 PHE cc_start: 0.7714 (m-80) cc_final: 0.7415 (m-80) REVERT: A 207 HIS cc_start: 0.7915 (m-70) cc_final: 0.7489 (m-70) REVERT: A 269 TYR cc_start: 0.7999 (m-80) cc_final: 0.7471 (m-80) REVERT: A 328 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7156 (mmm-85) REVERT: A 755 GLN cc_start: 0.7675 (mt0) cc_final: 0.6766 (mp10) REVERT: A 773 GLU cc_start: 0.8410 (tt0) cc_final: 0.8189 (tt0) REVERT: A 998 THR cc_start: 0.8597 (m) cc_final: 0.8379 (p) REVERT: A 1113 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: B 37 VAL cc_start: 0.7602 (t) cc_final: 0.7391 (p) REVERT: B 92 PHE cc_start: 0.7645 (t80) cc_final: 0.7359 (t80) REVERT: B 206 LYS cc_start: 0.7604 (tptm) cc_final: 0.7316 (tppt) REVERT: B 808 ASP cc_start: 0.7814 (t0) cc_final: 0.7420 (t0) REVERT: B 977 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8609 (mp) REVERT: B 1107 ARG cc_start: 0.8930 (mtt180) cc_final: 0.8682 (mtt90) REVERT: B 1125 ASN cc_start: 0.8471 (p0) cc_final: 0.8251 (p0) REVERT: C 298 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: C 304 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8057 (mtmm) REVERT: C 565 PHE cc_start: 0.8031 (p90) cc_final: 0.7566 (p90) REVERT: C 755 GLN cc_start: 0.7589 (mt0) cc_final: 0.6883 (mp10) REVERT: C 765 ARG cc_start: 0.8580 (ttm110) cc_final: 0.8323 (ttm110) REVERT: C 773 GLU cc_start: 0.8560 (tt0) cc_final: 0.8207 (tt0) REVERT: C 933 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7780 (mmtm) REVERT: C 1029 MET cc_start: 0.9244 (tpp) cc_final: 0.8880 (tpp) outliers start: 25 outliers final: 9 residues processed: 208 average time/residue: 0.6004 time to fit residues: 142.8913 Evaluate side-chains 194 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 94 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 222 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 755 GLN B 762 GLN C 607 GLN C 703 ASN C 787 GLN C 992 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.211886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147347 restraints weight = 21984.955| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.08 r_work: 0.3387 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22521 Z= 0.120 Angle : 0.516 14.145 31126 Z= 0.261 Chirality : 0.044 0.277 3941 Planarity : 0.004 0.036 4036 Dihedral : 4.388 55.484 4740 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.80 % Favored : 98.17 % Rotamer: Outliers : 1.70 % Allowed : 6.54 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3228 helix: 2.71 (0.17), residues: 879 sheet: 0.72 (0.19), residues: 655 loop : -0.38 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1014 TYR 0.022 0.001 TYR B1067 PHE 0.017 0.001 PHE C 898 TRP 0.007 0.001 TRP A 633 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00255 (22415) covalent geometry : angle 0.48529 (30850) SS BOND : bond 0.00227 ( 42) SS BOND : angle 1.28299 ( 84) hydrogen bonds : bond 0.04129 ( 1208) hydrogen bonds : angle 5.52543 ( 3453) link_BETA1-4 : bond 0.00347 ( 19) link_BETA1-4 : angle 1.21128 ( 57) link_NAG-ASN : bond 0.00302 ( 45) link_NAG-ASN : angle 2.42902 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7891 (m-70) cc_final: 0.7469 (m-70) REVERT: A 269 TYR cc_start: 0.8039 (m-80) cc_final: 0.7528 (m-80) REVERT: A 755 GLN cc_start: 0.7644 (mt0) cc_final: 0.6696 (mp10) REVERT: A 773 GLU cc_start: 0.8337 (tt0) cc_final: 0.8132 (tt0) REVERT: A 998 THR cc_start: 0.8594 (m) cc_final: 0.8380 (p) REVERT: A 1113 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: B 37 VAL cc_start: 0.7572 (t) cc_final: 0.7357 (p) REVERT: B 92 PHE cc_start: 0.7639 (t80) cc_final: 0.7395 (t80) REVERT: B 206 LYS cc_start: 0.7558 (tptm) cc_final: 0.7248 (tppt) REVERT: B 624 ILE cc_start: 0.8684 (mt) cc_final: 0.8360 (mt) REVERT: B 780 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8223 (pt0) REVERT: B 808 ASP cc_start: 0.7829 (t0) cc_final: 0.7427 (t0) REVERT: B 1107 ARG cc_start: 0.8914 (mtt180) cc_final: 0.8680 (mtt90) REVERT: B 1113 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: C 298 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: C 304 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8066 (mtmm) REVERT: C 565 PHE cc_start: 0.7999 (p90) cc_final: 0.7504 (p90) REVERT: C 603 ASN cc_start: 0.7726 (t0) cc_final: 0.7457 (t0) REVERT: C 755 GLN cc_start: 0.7554 (mt0) cc_final: 0.6854 (mp10) REVERT: C 773 GLU cc_start: 0.8554 (tt0) cc_final: 0.8233 (tt0) REVERT: C 933 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7791 (mmtm) REVERT: C 1029 MET cc_start: 0.9230 (tpp) cc_final: 0.8867 (tpp) outliers start: 25 outliers final: 11 residues processed: 204 average time/residue: 0.6179 time to fit residues: 144.8953 Evaluate side-chains 198 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 232 optimal weight: 40.0000 chunk 151 optimal weight: 0.0770 chunk 258 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 overall best weight: 0.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 755 GLN B 762 GLN B 787 GLN C 87 ASN C 703 ASN C 787 GLN C 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.211572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146511 restraints weight = 21893.932| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.11 r_work: 0.3377 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22521 Z= 0.139 Angle : 0.522 13.510 31126 Z= 0.267 Chirality : 0.044 0.167 3941 Planarity : 0.004 0.036 4036 Dihedral : 4.349 55.690 4740 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 1.77 % Allowed : 7.35 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3228 helix: 2.73 (0.17), residues: 880 sheet: 0.75 (0.19), residues: 649 loop : -0.38 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.023 0.002 TYR B1067 PHE 0.019 0.001 PHE C 898 TRP 0.008 0.001 TRP A 633 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00306 (22415) covalent geometry : angle 0.49476 (30850) SS BOND : bond 0.00176 ( 42) SS BOND : angle 1.29994 ( 84) hydrogen bonds : bond 0.04201 ( 1208) hydrogen bonds : angle 5.42006 ( 3453) link_BETA1-4 : bond 0.00378 ( 19) link_BETA1-4 : angle 1.23793 ( 57) link_NAG-ASN : bond 0.00486 ( 45) link_NAG-ASN : angle 2.27078 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7868 (m-70) cc_final: 0.7420 (m-70) REVERT: A 269 TYR cc_start: 0.8053 (m-80) cc_final: 0.7505 (m-80) REVERT: A 328 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: A 773 GLU cc_start: 0.8342 (tt0) cc_final: 0.8126 (tt0) REVERT: A 998 THR cc_start: 0.8589 (m) cc_final: 0.8377 (p) REVERT: A 1113 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: B 37 VAL cc_start: 0.7584 (t) cc_final: 0.7368 (p) REVERT: B 92 PHE cc_start: 0.7600 (t80) cc_final: 0.7325 (t80) REVERT: B 206 LYS cc_start: 0.7525 (tptm) cc_final: 0.7213 (tppt) REVERT: B 624 ILE cc_start: 0.8595 (mt) cc_final: 0.8273 (mt) REVERT: B 780 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8251 (pt0) REVERT: B 808 ASP cc_start: 0.7834 (t0) cc_final: 0.7421 (t0) REVERT: B 1107 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8694 (mtt90) REVERT: B 1113 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: C 269 TYR cc_start: 0.7844 (m-10) cc_final: 0.7597 (m-80) REVERT: C 298 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: C 304 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8047 (mtmm) REVERT: C 565 PHE cc_start: 0.8005 (p90) cc_final: 0.7531 (p90) REVERT: C 603 ASN cc_start: 0.7833 (t0) cc_final: 0.7608 (t0) REVERT: C 755 GLN cc_start: 0.7579 (mt0) cc_final: 0.6862 (mp10) REVERT: C 765 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8316 (ttm110) REVERT: C 773 GLU cc_start: 0.8581 (tt0) cc_final: 0.8249 (tt0) REVERT: C 933 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7797 (mmtm) REVERT: C 1029 MET cc_start: 0.9226 (tpp) cc_final: 0.8838 (tpp) outliers start: 26 outliers final: 14 residues processed: 199 average time/residue: 0.5775 time to fit residues: 132.4292 Evaluate side-chains 200 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 322 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 317 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 302 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1113 GLN B 755 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 607 GLN C 703 ASN C 787 GLN C 992 GLN C1108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.205040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136861 restraints weight = 20967.427| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.72 r_work: 0.3061 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22521 Z= 0.208 Angle : 0.583 13.260 31126 Z= 0.300 Chirality : 0.046 0.224 3941 Planarity : 0.004 0.038 4036 Dihedral : 4.680 56.700 4740 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.21 % Rotamer: Outliers : 2.04 % Allowed : 7.76 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3228 helix: 2.56 (0.17), residues: 880 sheet: 0.70 (0.19), residues: 657 loop : -0.45 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 905 TYR 0.025 0.002 TYR B1067 PHE 0.026 0.002 PHE C 898 TRP 0.011 0.002 TRP A 633 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00475 (22415) covalent geometry : angle 0.55640 (30850) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.46888 ( 84) hydrogen bonds : bond 0.04838 ( 1208) hydrogen bonds : angle 5.57121 ( 3453) link_BETA1-4 : bond 0.00413 ( 19) link_BETA1-4 : angle 1.38446 ( 57) link_NAG-ASN : bond 0.00384 ( 45) link_NAG-ASN : angle 2.33181 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7921 (m-70) cc_final: 0.7430 (m-70) REVERT: A 269 TYR cc_start: 0.8220 (m-80) cc_final: 0.7755 (m-80) REVERT: A 328 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7520 (mmm-85) REVERT: A 773 GLU cc_start: 0.8649 (tt0) cc_final: 0.8378 (tt0) REVERT: A 1113 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: B 92 PHE cc_start: 0.7753 (t80) cc_final: 0.7499 (t80) REVERT: B 206 LYS cc_start: 0.7698 (tptm) cc_final: 0.7366 (tppt) REVERT: B 780 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8350 (pt0) REVERT: B 808 ASP cc_start: 0.7943 (t0) cc_final: 0.7587 (t0) REVERT: B 1107 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8834 (mtt90) REVERT: C 206 LYS cc_start: 0.8604 (tptm) cc_final: 0.8273 (tptm) REVERT: C 298 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8509 (mt-10) REVERT: C 304 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8168 (mtmm) REVERT: C 537 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7749 (mmtp) REVERT: C 565 PHE cc_start: 0.8150 (p90) cc_final: 0.7644 (p90) REVERT: C 755 GLN cc_start: 0.7821 (mt0) cc_final: 0.6810 (mp10) REVERT: C 765 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8460 (ttm110) REVERT: C 773 GLU cc_start: 0.8875 (tt0) cc_final: 0.8453 (tt0) REVERT: C 787 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: C 933 LYS cc_start: 0.8516 (mtmt) cc_final: 0.7849 (mmtm) REVERT: C 1029 MET cc_start: 0.9336 (tpp) cc_final: 0.8888 (tpp) outliers start: 30 outliers final: 14 residues processed: 197 average time/residue: 0.6113 time to fit residues: 137.8555 Evaluate side-chains 194 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 282 optimal weight: 0.7980 chunk 319 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 242 optimal weight: 30.0000 chunk 297 optimal weight: 0.8980 chunk 240 optimal weight: 40.0000 chunk 294 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 190 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 271 GLN B 755 GLN B 787 GLN C 607 GLN C 703 ASN C 787 GLN C 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.211421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144368 restraints weight = 21900.136| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.40 r_work: 0.3358 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22521 Z= 0.134 Angle : 0.524 12.851 31126 Z= 0.267 Chirality : 0.044 0.210 3941 Planarity : 0.004 0.038 4036 Dihedral : 4.438 56.184 4740 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 8.71 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3228 helix: 2.72 (0.17), residues: 880 sheet: 0.79 (0.19), residues: 641 loop : -0.41 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.022 0.002 TYR B1067 PHE 0.020 0.001 PHE C 898 TRP 0.008 0.001 TRP A 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00295 (22415) covalent geometry : angle 0.49624 (30850) SS BOND : bond 0.00272 ( 42) SS BOND : angle 1.33889 ( 84) hydrogen bonds : bond 0.04140 ( 1208) hydrogen bonds : angle 5.30752 ( 3453) link_BETA1-4 : bond 0.00372 ( 19) link_BETA1-4 : angle 1.25155 ( 57) link_NAG-ASN : bond 0.00450 ( 45) link_NAG-ASN : angle 2.26780 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7883 (m-70) cc_final: 0.7399 (m-70) REVERT: A 328 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7550 (mmm-85) REVERT: A 773 GLU cc_start: 0.8435 (tt0) cc_final: 0.8204 (tt0) REVERT: A 1113 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: B 37 VAL cc_start: 0.7616 (t) cc_final: 0.7371 (p) REVERT: B 92 PHE cc_start: 0.7677 (t80) cc_final: 0.7400 (t80) REVERT: B 206 LYS cc_start: 0.7629 (tptm) cc_final: 0.7367 (tppt) REVERT: B 780 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8251 (pt0) REVERT: B 808 ASP cc_start: 0.7894 (t0) cc_final: 0.7467 (t0) REVERT: B 1107 ARG cc_start: 0.8962 (mtt180) cc_final: 0.8734 (mtt90) REVERT: C 298 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: C 304 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8087 (mtmm) REVERT: C 537 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7566 (mmtp) REVERT: C 565 PHE cc_start: 0.8064 (p90) cc_final: 0.7592 (p90) REVERT: C 603 ASN cc_start: 0.7749 (t0) cc_final: 0.7463 (t0) REVERT: C 622 VAL cc_start: 0.8542 (t) cc_final: 0.8236 (m) REVERT: C 755 GLN cc_start: 0.7615 (mt0) cc_final: 0.6875 (mp10) REVERT: C 765 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8373 (ttm110) REVERT: C 773 GLU cc_start: 0.8685 (tt0) cc_final: 0.8342 (tt0) REVERT: C 787 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: C 933 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7843 (mmtm) REVERT: C 1029 MET cc_start: 0.9255 (tpp) cc_final: 0.8815 (tpp) outliers start: 23 outliers final: 13 residues processed: 198 average time/residue: 0.6316 time to fit residues: 143.7189 Evaluate side-chains 193 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 0.4980 chunk 224 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B 271 GLN B 755 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 607 GLN C 703 ASN C 787 GLN C 992 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.212247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150015 restraints weight = 21977.649| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.91 r_work: 0.3416 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22521 Z= 0.128 Angle : 0.518 12.615 31126 Z= 0.265 Chirality : 0.044 0.207 3941 Planarity : 0.004 0.038 4036 Dihedral : 4.328 55.928 4740 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 1.43 % Allowed : 8.92 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.14), residues: 3228 helix: 2.79 (0.17), residues: 880 sheet: 0.82 (0.19), residues: 635 loop : -0.39 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.022 0.001 TYR B1067 PHE 0.019 0.001 PHE C 898 TRP 0.008 0.001 TRP A 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00282 (22415) covalent geometry : angle 0.48951 (30850) SS BOND : bond 0.00194 ( 42) SS BOND : angle 1.62057 ( 84) hydrogen bonds : bond 0.04019 ( 1208) hydrogen bonds : angle 5.21660 ( 3453) link_BETA1-4 : bond 0.00389 ( 19) link_BETA1-4 : angle 1.22952 ( 57) link_NAG-ASN : bond 0.00298 ( 45) link_NAG-ASN : angle 2.20058 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7980 (m-70) cc_final: 0.7497 (m-70) REVERT: A 269 TYR cc_start: 0.7976 (m-80) cc_final: 0.7425 (m-80) REVERT: A 328 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: A 773 GLU cc_start: 0.8338 (tt0) cc_final: 0.8123 (tt0) REVERT: A 1113 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8259 (mt0) REVERT: B 37 VAL cc_start: 0.7631 (t) cc_final: 0.7426 (p) REVERT: B 92 PHE cc_start: 0.7635 (t80) cc_final: 0.7375 (t80) REVERT: B 206 LYS cc_start: 0.7599 (tptm) cc_final: 0.7382 (tppt) REVERT: B 780 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8245 (pt0) REVERT: B 808 ASP cc_start: 0.7908 (t0) cc_final: 0.7507 (t0) REVERT: B 1107 ARG cc_start: 0.8939 (mtt180) cc_final: 0.8719 (mtt90) REVERT: C 206 LYS cc_start: 0.8553 (tptm) cc_final: 0.8232 (tptm) REVERT: C 298 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: C 304 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8097 (mtmm) REVERT: C 537 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7564 (mmtp) REVERT: C 565 PHE cc_start: 0.8015 (p90) cc_final: 0.7565 (p90) REVERT: C 603 ASN cc_start: 0.7748 (t0) cc_final: 0.7485 (t0) REVERT: C 755 GLN cc_start: 0.7561 (mt0) cc_final: 0.6903 (mp10) REVERT: C 765 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8261 (ttm110) REVERT: C 773 GLU cc_start: 0.8584 (tt0) cc_final: 0.8268 (tt0) REVERT: C 787 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: C 933 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7816 (mmtm) REVERT: C 1029 MET cc_start: 0.9218 (tpp) cc_final: 0.8784 (tpp) outliers start: 21 outliers final: 12 residues processed: 191 average time/residue: 0.6221 time to fit residues: 136.4002 Evaluate side-chains 194 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 6 optimal weight: 7.9990 chunk 305 optimal weight: 0.3980 chunk 146 optimal weight: 40.0000 chunk 38 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 271 GLN B 755 GLN B 787 GLN C 703 ASN C 787 GLN C 992 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.211740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.149394 restraints weight = 21828.165| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.90 r_work: 0.3401 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22521 Z= 0.159 Angle : 0.546 10.778 31126 Z= 0.280 Chirality : 0.045 0.208 3941 Planarity : 0.004 0.037 4036 Dihedral : 4.426 56.251 4740 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.29 % Favored : 97.61 % Rotamer: Outliers : 1.77 % Allowed : 8.71 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.06 (0.14), residues: 3228 helix: 2.73 (0.17), residues: 880 sheet: 0.81 (0.19), residues: 639 loop : -0.42 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.023 0.002 TYR B1067 PHE 0.021 0.002 PHE B 643 TRP 0.009 0.001 TRP A 633 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00356 (22415) covalent geometry : angle 0.52126 (30850) SS BOND : bond 0.00184 ( 42) SS BOND : angle 1.64626 ( 84) hydrogen bonds : bond 0.04280 ( 1208) hydrogen bonds : angle 5.27807 ( 3453) link_BETA1-4 : bond 0.00379 ( 19) link_BETA1-4 : angle 1.27428 ( 57) link_NAG-ASN : bond 0.00667 ( 45) link_NAG-ASN : angle 2.07057 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7985 (m-70) cc_final: 0.7519 (m-70) REVERT: A 269 TYR cc_start: 0.7984 (m-80) cc_final: 0.7448 (m-80) REVERT: A 328 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: A 773 GLU cc_start: 0.8362 (tt0) cc_final: 0.8137 (tt0) REVERT: A 1113 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: B 780 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8265 (pt0) REVERT: B 808 ASP cc_start: 0.7917 (t0) cc_final: 0.7526 (t0) REVERT: B 1107 ARG cc_start: 0.8946 (mtt180) cc_final: 0.8726 (mtt90) REVERT: C 206 LYS cc_start: 0.8550 (tptm) cc_final: 0.8219 (tptm) REVERT: C 298 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: C 304 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8101 (mtmm) REVERT: C 537 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7588 (mmtp) REVERT: C 565 PHE cc_start: 0.8040 (p90) cc_final: 0.7592 (p90) REVERT: C 603 ASN cc_start: 0.7780 (t0) cc_final: 0.7517 (t0) REVERT: C 622 VAL cc_start: 0.8564 (t) cc_final: 0.8313 (m) REVERT: C 755 GLN cc_start: 0.7596 (mt0) cc_final: 0.6937 (mp10) REVERT: C 765 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8258 (ttm110) REVERT: C 773 GLU cc_start: 0.8597 (tt0) cc_final: 0.8221 (tt0) REVERT: C 933 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7854 (mmtm) REVERT: C 1029 MET cc_start: 0.9233 (tpp) cc_final: 0.8780 (tpp) outliers start: 26 outliers final: 13 residues processed: 195 average time/residue: 0.6291 time to fit residues: 140.6938 Evaluate side-chains 193 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 chunk 252 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 155 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 282 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 755 GLN C 607 GLN C 703 ASN C 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.213053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150719 restraints weight = 22053.803| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.01 r_work: 0.3423 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 22521 Z= 0.111 Angle : 0.515 16.025 31126 Z= 0.259 Chirality : 0.045 0.617 3941 Planarity : 0.004 0.039 4036 Dihedral : 4.326 55.408 4740 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 1.16 % Allowed : 9.05 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 3228 helix: 2.84 (0.17), residues: 880 sheet: 0.91 (0.19), residues: 646 loop : -0.37 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 905 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE B 643 TRP 0.007 0.001 TRP A 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00241 (22415) covalent geometry : angle 0.47968 (30850) SS BOND : bond 0.00180 ( 42) SS BOND : angle 1.44001 ( 84) hydrogen bonds : bond 0.03752 ( 1208) hydrogen bonds : angle 5.07213 ( 3453) link_BETA1-4 : bond 0.00358 ( 19) link_BETA1-4 : angle 1.18152 ( 57) link_NAG-ASN : bond 0.00305 ( 45) link_NAG-ASN : angle 2.56977 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7953 (m-70) cc_final: 0.7488 (m-70) REVERT: A 269 TYR cc_start: 0.7993 (m-80) cc_final: 0.7428 (m-80) REVERT: A 773 GLU cc_start: 0.8310 (tt0) cc_final: 0.8100 (tt0) REVERT: A 1113 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 37 VAL cc_start: 0.7608 (t) cc_final: 0.7401 (p) REVERT: B 624 ILE cc_start: 0.8630 (mt) cc_final: 0.8307 (mt) REVERT: B 643 PHE cc_start: 0.8527 (t80) cc_final: 0.8257 (t80) REVERT: B 808 ASP cc_start: 0.7900 (t0) cc_final: 0.7502 (t0) REVERT: B 945 LEU cc_start: 0.8407 (mm) cc_final: 0.8083 (mt) REVERT: B 1107 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8697 (mtt90) REVERT: C 298 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: C 304 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8079 (mtmm) REVERT: C 537 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7542 (mmtp) REVERT: C 565 PHE cc_start: 0.8004 (p90) cc_final: 0.7496 (p90) REVERT: C 603 ASN cc_start: 0.7856 (t0) cc_final: 0.7610 (t0) REVERT: C 622 VAL cc_start: 0.8539 (t) cc_final: 0.8303 (m) REVERT: C 755 GLN cc_start: 0.7467 (mt0) cc_final: 0.6829 (mp10) REVERT: C 765 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8229 (ttm110) REVERT: C 773 GLU cc_start: 0.8556 (tt0) cc_final: 0.8241 (tt0) REVERT: C 933 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7795 (mmtm) REVERT: C 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8816 (tpp) outliers start: 17 outliers final: 9 residues processed: 189 average time/residue: 0.6318 time to fit residues: 137.1398 Evaluate side-chains 191 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 123 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 chunk 293 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 755 GLN C 703 ASN C 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136680 restraints weight = 21094.880| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.61 r_work: 0.3100 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22521 Z= 0.150 Angle : 0.540 11.766 31126 Z= 0.276 Chirality : 0.045 0.330 3941 Planarity : 0.004 0.037 4036 Dihedral : 4.544 58.884 4740 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.49 % Rotamer: Outliers : 0.95 % Allowed : 9.46 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.14), residues: 3228 helix: 2.76 (0.17), residues: 879 sheet: 0.83 (0.19), residues: 643 loop : -0.40 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.023 0.002 TYR B1067 PHE 0.020 0.002 PHE A 898 TRP 0.009 0.001 TRP A 633 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00337 (22415) covalent geometry : angle 0.51115 (30850) SS BOND : bond 0.00181 ( 42) SS BOND : angle 1.56066 ( 84) hydrogen bonds : bond 0.04195 ( 1208) hydrogen bonds : angle 5.19312 ( 3453) link_BETA1-4 : bond 0.00367 ( 19) link_BETA1-4 : angle 1.25173 ( 57) link_NAG-ASN : bond 0.00398 ( 45) link_NAG-ASN : angle 2.29686 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.7993 (m-70) cc_final: 0.7491 (m-70) REVERT: A 269 TYR cc_start: 0.8151 (m-80) cc_final: 0.7624 (m-80) REVERT: A 773 GLU cc_start: 0.8592 (tt0) cc_final: 0.8314 (tt0) REVERT: A 1113 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8456 (mt0) REVERT: B 643 PHE cc_start: 0.8523 (t80) cc_final: 0.8312 (t80) REVERT: B 780 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8313 (pt0) REVERT: B 808 ASP cc_start: 0.7964 (t0) cc_final: 0.7578 (t0) REVERT: B 1107 ARG cc_start: 0.9024 (mtt180) cc_final: 0.8806 (mtt90) REVERT: C 206 LYS cc_start: 0.8608 (tptm) cc_final: 0.8271 (tptm) REVERT: C 298 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: C 304 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8140 (mtmm) REVERT: C 537 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7723 (mmtp) REVERT: C 565 PHE cc_start: 0.8134 (p90) cc_final: 0.7671 (p90) REVERT: C 603 ASN cc_start: 0.7961 (t0) cc_final: 0.7721 (t0) REVERT: C 622 VAL cc_start: 0.8518 (t) cc_final: 0.8172 (m) REVERT: C 755 GLN cc_start: 0.7705 (mt0) cc_final: 0.6797 (mp10) REVERT: C 765 ARG cc_start: 0.8739 (ttm110) cc_final: 0.8379 (ttm110) REVERT: C 773 GLU cc_start: 0.8834 (tt0) cc_final: 0.8412 (tt0) REVERT: C 933 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7838 (mmtm) REVERT: C 1029 MET cc_start: 0.9292 (tpp) cc_final: 0.8867 (tpp) outliers start: 14 outliers final: 9 residues processed: 189 average time/residue: 0.6279 time to fit residues: 136.0968 Evaluate side-chains 190 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 262 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 270 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 755 GLN C 703 ASN C 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.213216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150819 restraints weight = 22032.149| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.01 r_work: 0.3426 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22521 Z= 0.108 Angle : 0.495 10.675 31126 Z= 0.252 Chirality : 0.044 0.249 3941 Planarity : 0.004 0.039 4036 Dihedral : 4.232 55.121 4740 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.67 % Favored : 98.27 % Rotamer: Outliers : 0.82 % Allowed : 9.67 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3228 helix: 2.90 (0.17), residues: 875 sheet: 0.94 (0.19), residues: 648 loop : -0.35 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 905 TYR 0.021 0.001 TYR B1067 PHE 0.017 0.001 PHE C 898 TRP 0.006 0.001 TRP A 633 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00235 (22415) covalent geometry : angle 0.46937 (30850) SS BOND : bond 0.00169 ( 42) SS BOND : angle 1.33964 ( 84) hydrogen bonds : bond 0.03691 ( 1208) hydrogen bonds : angle 4.99706 ( 3453) link_BETA1-4 : bond 0.00350 ( 19) link_BETA1-4 : angle 1.16535 ( 57) link_NAG-ASN : bond 0.00299 ( 45) link_NAG-ASN : angle 2.08598 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12174.43 seconds wall clock time: 206 minutes 35.88 seconds (12395.88 seconds total)