Starting phenix.real_space_refine on Wed May 28 08:21:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlw_27518/05_2025/8dlw_27518.cif" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.047 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 147 5.16 5 C 19254 2.51 5 N 4947 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30267 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" 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: "b" 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: "c" 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 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: "E" 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 Time building chain proxies: 15.92, per 1000 atoms: 0.53 Number of scatterers: 30267 At special positions: 0 Unit cell: (136, 141, 187, 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 147 16.00 O 5919 8.00 N 4947 7.00 C 19254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 S 2 " - " BMA S 3 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG Z 1 " - " FUC Z 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 343 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN E 17 " " NAG Y 1 " - " ASN E 122 " " NAG Z 1 " - " ASN E 343 " " NAG a 1 " - " ASN E 717 " " NAG b 1 " - " ASN E 801 " " NAG c 1 " - " ASN E1098 " " NAG d 1 " - " ASN E1134 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.5 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 66 sheets defined 23.4% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 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 349 through 353 removed outlier: 3.647A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.238A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.010A 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 removed outlier: 3.699A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.696A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (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: 3.644A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.227A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 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 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.020A 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 removed outlier: 3.706A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.697A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.612A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.925A pdb=" N TYR C 111 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.526A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.662A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.015A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.690A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.697A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.677A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.545A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.928A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.538A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.886A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.214A pdb=" N PHE A 43 " --> pdb=" O ARG E 567 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.542A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 4.288A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.719A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.954A 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: 4.325A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.161A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.671A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.511A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.609A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.939A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.554A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.790A pdb=" N LYS A 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.678A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.870A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.537A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 141 removed outlier: 4.289A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.710A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.348A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.157A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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: 6.505A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.760A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.949A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.552A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.655A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.667A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.916A pdb=" N TYR C 114 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.498A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.498A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.890A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.922A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.473A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 132 through 141 removed outlier: 4.271A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.717A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.167A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.682A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.509A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.931A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.545A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.661A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.657A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.895A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.610A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.125A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 3603 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: 14.46 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9335 1.34 - 1.46: 8087 1.46 - 1.59: 13355 1.59 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 30969 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" CG LEU B 916 " pdb=" CD2 LEU B 916 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 30964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 40688 2.56 - 5.12: 1305 5.12 - 7.67: 138 7.67 - 10.23: 16 10.23 - 12.79: 9 Bond angle restraints: 42156 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.50 -6.80 1.22e+00 6.72e-01 3.11e+01 angle pdb=" N PRO E 986 " pdb=" CA PRO E 986 " pdb=" C PRO E 986 " ideal model delta sigma weight residual 110.70 117.47 -6.77 1.22e+00 6.72e-01 3.08e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.96e+01 angle pdb=" CA TYR H 103 " pdb=" CB TYR H 103 " pdb=" CG TYR H 103 " ideal model delta sigma weight residual 113.90 122.95 -9.05 1.80e+00 3.09e-01 2.53e+01 angle pdb=" C GLY G 51 " pdb=" N ALA G 52 " pdb=" CA ALA G 52 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 ... (remaining 42151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 18604 21.33 - 42.67: 551 42.67 - 64.00: 132 64.00 - 85.34: 54 85.34 - 106.67: 24 Dihedral angle restraints: 19365 sinusoidal: 8436 harmonic: 10929 Sorted by residual: dihedral pdb=" CD1 TYR E 449 " pdb=" CE1 TYR E 449 " pdb=" CZ TYR E 449 " pdb=" OH TYR E 449 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CD1 TYR B 449 " pdb=" CE1 TYR B 449 " pdb=" CZ TYR B 449 " pdb=" OH TYR B 449 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" SG CYS A 131 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sinusoidal sigma weight residual 79.00 9.23 69.77 1 2.00e+01 2.50e-03 1.57e+01 ... (remaining 19362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4365 0.094 - 0.189: 547 0.189 - 0.283: 36 0.283 - 0.377: 5 0.377 - 0.472: 3 Chirality restraints: 4956 Sorted by residual: chirality pdb=" CG LEU E 916 " pdb=" CB LEU E 916 " pdb=" CD1 LEU E 916 " pdb=" CD2 LEU E 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.56e+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 -2.14 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 4953 not shown) Planarity restraints: 5391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.007 2.00e-02 2.50e+03 7.73e-02 1.20e+02 pdb=" CG TYR E 449 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " 0.107 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.108 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.110 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " -0.007 2.00e-02 2.50e+03 7.72e-02 1.19e+02 pdb=" CG TYR B 449 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " 0.108 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 356 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS E 356 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS E 356 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG E 357 " -0.020 2.00e-02 2.50e+03 ... (remaining 5388 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8035 2.81 - 3.33: 25392 3.33 - 3.86: 51390 3.86 - 4.38: 59345 4.38 - 4.90: 103153 Nonbonded interactions: 247315 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" O LEU E 54 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" OD2 ASP E 420 " model vdw 2.342 3.040 nonbonded pdb=" NE2 GLN B 493 " pdb=" OH TYR C 103 " model vdw 2.349 3.120 ... (remaining 247310 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.220 Set scattering table: 0.230 Process input model: 66.280 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 31095 Z= 0.311 Angle : 1.066 12.789 42486 Z= 0.599 Chirality : 0.063 0.472 4956 Planarity : 0.008 0.077 5340 Dihedral : 11.949 106.672 12213 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.13), residues: 3708 helix: 1.46 (0.18), residues: 669 sheet: 0.94 (0.15), residues: 1020 loop : 0.10 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 106 HIS 0.014 0.002 HIS B1048 PHE 0.039 0.003 PHE A 329 TYR 0.112 0.004 TYR E 449 ARG 0.013 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 51) link_NAG-ASN : angle 2.32511 ( 153) link_BETA1-4 : bond 0.01005 ( 24) link_BETA1-4 : angle 1.86206 ( 72) hydrogen bonds : bond 0.12045 ( 1314) hydrogen bonds : angle 7.69618 ( 3603) link_BETA1-6 : bond 0.00227 ( 3) link_BETA1-6 : angle 1.05996 ( 9) SS BOND : bond 0.00635 ( 48) SS BOND : angle 1.99911 ( 96) covalent geometry : bond 0.00665 (30969) covalent geometry : angle 1.05337 (42156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 419 time to evaluate : 3.492 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: C 11 VAL cc_start: 0.8725 (t) cc_final: 0.8137 (m) REVERT: C 12 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8572 (ttmm) REVERT: E 869 MET cc_start: 0.9311 (mtt) cc_final: 0.9083 (mtm) REVERT: F 46 GLU cc_start: 0.7868 (tt0) cc_final: 0.7537 (tt0) REVERT: F 67 ARG cc_start: 0.6421 (mtp180) cc_final: 0.6103 (ttp80) REVERT: G 38 GLN cc_start: 0.7495 (tt0) cc_final: 0.7126 (tm130) REVERT: L 83 ASP cc_start: 0.7673 (m-30) cc_final: 0.7054 (m-30) outliers start: 6 outliers final: 0 residues processed: 425 average time/residue: 1.5498 time to fit residues: 764.7151 Evaluate side-chains 229 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 337 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 185 ASN A 207 HIS A 762 GLN A 901 GLN A 907 ASN A 955 ASN A1010 GLN B 137 ASN B 185 ASN B 762 GLN B 901 GLN B 955 ASN B1010 GLN E 115 GLN E 185 ASN E 762 GLN E 901 GLN E1010 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058172 restraints weight = 72999.961| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.00 r_work: 0.2909 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31095 Z= 0.170 Angle : 0.643 9.920 42486 Z= 0.329 Chirality : 0.045 0.244 4956 Planarity : 0.005 0.049 5340 Dihedral : 7.210 68.251 5682 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.22 % Allowed : 6.44 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 3708 helix: 2.35 (0.20), residues: 666 sheet: 0.92 (0.15), residues: 1017 loop : 0.09 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 106 HIS 0.004 0.001 HIS E1048 PHE 0.020 0.001 PHE B 133 TYR 0.026 0.002 TYR B1138 ARG 0.008 0.001 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 51) link_NAG-ASN : angle 1.94358 ( 153) link_BETA1-4 : bond 0.00600 ( 24) link_BETA1-4 : angle 1.42898 ( 72) hydrogen bonds : bond 0.04694 ( 1314) hydrogen bonds : angle 6.22319 ( 3603) link_BETA1-6 : bond 0.00144 ( 3) link_BETA1-6 : angle 1.40317 ( 9) SS BOND : bond 0.00327 ( 48) SS BOND : angle 0.82033 ( 96) covalent geometry : bond 0.00379 (30969) covalent geometry : angle 0.63001 (42156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.9362 (p) cc_final: 0.9161 (m) REVERT: B 227 VAL cc_start: 0.9341 (p) cc_final: 0.9113 (m) REVERT: B 319 ARG cc_start: 0.8542 (ttm110) cc_final: 0.7979 (ttm-80) REVERT: B 940 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8088 (m) REVERT: C 10 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6764 (tm-30) REVERT: C 12 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8725 (ttmm) REVERT: C 41 PRO cc_start: 0.8426 (Cg_exo) cc_final: 0.8174 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8414 (tt0) cc_final: 0.8169 (tt0) REVERT: D 62 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8081 (ttm170) REVERT: D 78 ARG cc_start: 0.7999 (tmm-80) cc_final: 0.7720 (ptm-80) REVERT: E 227 VAL cc_start: 0.9305 (p) cc_final: 0.9073 (m) REVERT: F 19 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8800 (ttmm) REVERT: F 46 GLU cc_start: 0.8538 (tt0) cc_final: 0.7942 (tt0) REVERT: F 81 MET cc_start: 0.7947 (tmm) cc_final: 0.7689 (tmm) REVERT: F 85 ARG cc_start: 0.7365 (ttp80) cc_final: 0.7111 (ttp80) REVERT: G 27 GLN cc_start: 0.8463 (mp10) cc_final: 0.8178 (mp10) REVERT: G 55 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8176 (ttm110) REVERT: G 88 TYR cc_start: 0.8658 (m-80) cc_final: 0.8232 (m-80) REVERT: H 12 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8068 (mtmm) REVERT: H 19 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8429 (ttmm) REVERT: H 82 GLU cc_start: 0.7802 (tp30) cc_final: 0.7600 (tp30) REVERT: H 87 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8482 (mtm-85) REVERT: L 5 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8087 (pmm) REVERT: L 27 GLN cc_start: 0.9049 (mt0) cc_final: 0.8685 (mp10) REVERT: L 38 GLN cc_start: 0.7310 (tm130) cc_final: 0.5775 (tm-30) REVERT: L 62 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7898 (ttm170) REVERT: L 70 THR cc_start: 0.9219 (p) cc_final: 0.8846 (t) REVERT: L 83 ASP cc_start: 0.7075 (m-30) cc_final: 0.6832 (m-30) outliers start: 71 outliers final: 23 residues processed: 299 average time/residue: 1.4902 time to fit residues: 520.2063 Evaluate side-chains 246 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 78 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 256 optimal weight: 4.9990 chunk 357 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 353 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 115 GLN E 137 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055107 restraints weight = 73361.846| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.01 r_work: 0.2828 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31095 Z= 0.234 Angle : 0.659 8.972 42486 Z= 0.330 Chirality : 0.046 0.251 4956 Planarity : 0.005 0.069 5340 Dihedral : 5.949 58.056 5682 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.41 % Allowed : 7.22 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 3708 helix: 2.38 (0.20), residues: 663 sheet: 0.88 (0.15), residues: 996 loop : 0.05 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 106 HIS 0.006 0.001 HIS E1064 PHE 0.017 0.002 PHE E 898 TYR 0.027 0.002 TYR E1067 ARG 0.006 0.001 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 51) link_NAG-ASN : angle 2.33059 ( 153) link_BETA1-4 : bond 0.00475 ( 24) link_BETA1-4 : angle 1.39002 ( 72) hydrogen bonds : bond 0.04829 ( 1314) hydrogen bonds : angle 5.90943 ( 3603) link_BETA1-6 : bond 0.00245 ( 3) link_BETA1-6 : angle 1.54608 ( 9) SS BOND : bond 0.00358 ( 48) SS BOND : angle 0.75804 ( 96) covalent geometry : bond 0.00536 (30969) covalent geometry : angle 0.64253 (42156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 247 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9615 (mtt) cc_final: 0.9405 (mtm) REVERT: B 227 VAL cc_start: 0.9424 (p) cc_final: 0.9215 (m) REVERT: B 237 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8408 (mtp85) REVERT: C 10 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 12 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8804 (ttmm) REVERT: C 41 PRO cc_start: 0.8599 (Cg_exo) cc_final: 0.8368 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8484 (tt0) cc_final: 0.7794 (pt0) REVERT: C 48 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8390 (mtp) REVERT: D 46 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.8492 (ptt90) REVERT: D 62 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8189 (ttm170) REVERT: D 78 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7798 (ptm-80) REVERT: E 242 LEU cc_start: 0.8881 (mp) cc_final: 0.8191 (tp) REVERT: E 790 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9086 (mtmt) REVERT: F 19 LYS cc_start: 0.9133 (ttmm) cc_final: 0.8901 (ttmm) REVERT: F 38 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7319 (ptm160) REVERT: F 46 GLU cc_start: 0.8669 (tt0) cc_final: 0.8136 (tt0) REVERT: F 98 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7472 (ttt180) REVERT: G 5 MET cc_start: 0.8386 (pmm) cc_final: 0.8117 (pmm) REVERT: G 27 GLN cc_start: 0.8246 (mp10) cc_final: 0.8001 (mp10) REVERT: G 46 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8476 (ptt90) REVERT: G 48 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8707 (mm) REVERT: G 55 ARG cc_start: 0.8481 (ttm110) cc_final: 0.8150 (ttm110) REVERT: G 80 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7529 (mm-30) REVERT: G 88 TYR cc_start: 0.8506 (m-80) cc_final: 0.8072 (m-80) REVERT: G 104 LYS cc_start: 0.8649 (tptt) cc_final: 0.7809 (tmmt) REVERT: H 12 LYS cc_start: 0.8759 (mmmm) cc_final: 0.8237 (mmmm) REVERT: H 23 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8422 (tptp) REVERT: H 70 MET cc_start: 0.8769 (mtt) cc_final: 0.8564 (mtt) REVERT: H 81 MET cc_start: 0.8522 (tmm) cc_final: 0.8290 (tpp) REVERT: H 87 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8459 (mtm-85) REVERT: L 3 VAL cc_start: 0.9439 (t) cc_final: 0.9186 (p) REVERT: L 13 LEU cc_start: 0.8103 (tp) cc_final: 0.7877 (tt) REVERT: L 48 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8447 (mm) REVERT: L 84 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: L 105 VAL cc_start: 0.8212 (p) cc_final: 0.7973 (m) outliers start: 77 outliers final: 30 residues processed: 286 average time/residue: 1.5438 time to fit residues: 517.9892 Evaluate side-chains 256 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 84 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 263 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 282 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 368 optimal weight: 10.0000 chunk 366 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056398 restraints weight = 73592.178| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.00 r_work: 0.2865 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31095 Z= 0.126 Angle : 0.572 8.007 42486 Z= 0.288 Chirality : 0.043 0.152 4956 Planarity : 0.004 0.053 5340 Dihedral : 5.075 52.881 5682 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 8.26 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 3708 helix: 2.53 (0.19), residues: 663 sheet: 0.83 (0.15), residues: 1026 loop : 0.03 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 106 HIS 0.002 0.001 HIS A1048 PHE 0.023 0.001 PHE B 133 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 51) link_NAG-ASN : angle 1.83707 ( 153) link_BETA1-4 : bond 0.00518 ( 24) link_BETA1-4 : angle 1.30359 ( 72) hydrogen bonds : bond 0.04094 ( 1314) hydrogen bonds : angle 5.61578 ( 3603) link_BETA1-6 : bond 0.00103 ( 3) link_BETA1-6 : angle 1.40847 ( 9) SS BOND : bond 0.00243 ( 48) SS BOND : angle 0.76531 ( 96) covalent geometry : bond 0.00280 (30969) covalent geometry : angle 0.55951 (42156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9593 (mtt) cc_final: 0.9386 (mtm) REVERT: A 940 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8100 (m) REVERT: B 237 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8443 (mtp85) REVERT: B 319 ARG cc_start: 0.8571 (ttm110) cc_final: 0.8191 (ttm-80) REVERT: C 10 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7131 (tm-30) REVERT: C 19 LYS cc_start: 0.9028 (ttmm) cc_final: 0.8714 (ttmm) REVERT: C 46 GLU cc_start: 0.8498 (tt0) cc_final: 0.8287 (tt0) REVERT: C 82 GLU cc_start: 0.8842 (tp30) cc_final: 0.8622 (tp30) REVERT: E 227 VAL cc_start: 0.9429 (p) cc_final: 0.9218 (m) REVERT: E 242 LEU cc_start: 0.8850 (mp) cc_final: 0.8205 (tp) REVERT: E 790 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9073 (mtmt) REVERT: F 10 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7174 (tm-30) REVERT: F 46 GLU cc_start: 0.8640 (tt0) cc_final: 0.8135 (tt0) REVERT: F 87 ARG cc_start: 0.8840 (ttp80) cc_final: 0.8192 (tmm-80) REVERT: F 98 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7583 (ttt180) REVERT: G 27 GLN cc_start: 0.8404 (mp10) cc_final: 0.7974 (mp10) REVERT: G 48 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8609 (mm) REVERT: G 55 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8154 (ttm110) REVERT: G 62 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7976 (ttm170) REVERT: G 80 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7201 (mp0) REVERT: G 88 TYR cc_start: 0.8512 (m-80) cc_final: 0.8097 (m-80) REVERT: G 104 LYS cc_start: 0.8618 (tptt) cc_final: 0.7875 (tmmt) REVERT: H 23 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8500 (tptp) REVERT: L 48 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8450 (mm) outliers start: 60 outliers final: 27 residues processed: 282 average time/residue: 1.5586 time to fit residues: 512.5676 Evaluate side-chains 249 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 102 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 357 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 262 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.084561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053899 restraints weight = 73149.197| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.99 r_work: 0.2797 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31095 Z= 0.261 Angle : 0.641 7.746 42486 Z= 0.323 Chirality : 0.045 0.200 4956 Planarity : 0.005 0.070 5340 Dihedral : 4.956 46.477 5682 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.13 % Allowed : 8.72 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 3708 helix: 2.43 (0.20), residues: 663 sheet: 0.67 (0.15), residues: 1008 loop : 0.00 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 106 HIS 0.007 0.001 HIS E1064 PHE 0.018 0.002 PHE E 898 TYR 0.027 0.002 TYR E1067 ARG 0.008 0.001 ARG H 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 51) link_NAG-ASN : angle 1.96173 ( 153) link_BETA1-4 : bond 0.00447 ( 24) link_BETA1-4 : angle 1.28120 ( 72) hydrogen bonds : bond 0.04816 ( 1314) hydrogen bonds : angle 5.72374 ( 3603) link_BETA1-6 : bond 0.00273 ( 3) link_BETA1-6 : angle 1.64152 ( 9) SS BOND : bond 0.00358 ( 48) SS BOND : angle 0.74746 ( 96) covalent geometry : bond 0.00601 (30969) covalent geometry : angle 0.62918 (42156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9651 (mtt) cc_final: 0.9431 (mtm) REVERT: B 237 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8461 (mtp85) REVERT: B 319 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8218 (ttm-80) REVERT: C 10 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 19 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8856 (ttmm) REVERT: C 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8259 (tt0) REVERT: C 48 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: C 82 GLU cc_start: 0.8896 (tp30) cc_final: 0.8659 (tp30) REVERT: D 62 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7959 (ttp-110) REVERT: D 71 ASP cc_start: 0.8786 (m-30) cc_final: 0.8520 (p0) REVERT: E 227 VAL cc_start: 0.9418 (p) cc_final: 0.9186 (m) REVERT: E 242 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8165 (tp) REVERT: F 10 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7159 (tm-30) REVERT: F 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8094 (tt0) REVERT: F 87 ARG cc_start: 0.8854 (ttp80) cc_final: 0.7967 (tmm-80) REVERT: F 89 ASP cc_start: 0.9092 (t0) cc_final: 0.8887 (t70) REVERT: F 98 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7386 (ttt180) REVERT: G 27 GLN cc_start: 0.8455 (mp10) cc_final: 0.8032 (mp10) REVERT: G 46 ARG cc_start: 0.8966 (ptt90) cc_final: 0.8754 (ptt90) REVERT: G 48 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8659 (mm) REVERT: G 55 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8139 (ttm110) REVERT: G 80 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7356 (mm-30) REVERT: G 88 TYR cc_start: 0.8536 (m-80) cc_final: 0.8128 (m-80) REVERT: H 12 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8252 (mtmm) REVERT: H 46 GLU cc_start: 0.8654 (tt0) cc_final: 0.8381 (tt0) REVERT: L 46 ARG cc_start: 0.8939 (ptt90) cc_final: 0.8645 (ptt90) REVERT: L 48 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8586 (mm) REVERT: L 78 ARG cc_start: 0.8480 (pmm-80) cc_final: 0.8034 (pmm150) REVERT: L 80 GLU cc_start: 0.6751 (mp0) cc_final: 0.6476 (mp0) outliers start: 68 outliers final: 29 residues processed: 259 average time/residue: 1.5917 time to fit residues: 483.6230 Evaluate side-chains 245 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 226 optimal weight: 50.0000 chunk 142 optimal weight: 0.7980 chunk 338 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 316 optimal weight: 0.8980 chunk 315 optimal weight: 0.6980 chunk 148 optimal weight: 0.0870 chunk 172 optimal weight: 0.5980 chunk 326 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.086284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056029 restraints weight = 72991.612| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.98 r_work: 0.2855 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31095 Z= 0.117 Angle : 0.573 10.958 42486 Z= 0.287 Chirality : 0.043 0.162 4956 Planarity : 0.004 0.055 5340 Dihedral : 4.581 40.067 5682 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.91 % Allowed : 9.04 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 3708 helix: 2.66 (0.19), residues: 666 sheet: 0.62 (0.15), residues: 1020 loop : 0.04 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 106 HIS 0.002 0.001 HIS A1048 PHE 0.016 0.001 PHE A 133 TYR 0.017 0.001 TYR A1067 ARG 0.013 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 51) link_NAG-ASN : angle 1.74958 ( 153) link_BETA1-4 : bond 0.00544 ( 24) link_BETA1-4 : angle 1.14918 ( 72) hydrogen bonds : bond 0.03951 ( 1314) hydrogen bonds : angle 5.47613 ( 3603) link_BETA1-6 : bond 0.00039 ( 3) link_BETA1-6 : angle 1.38493 ( 9) SS BOND : bond 0.00219 ( 48) SS BOND : angle 0.70112 ( 96) covalent geometry : bond 0.00257 (30969) covalent geometry : angle 0.56211 (42156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 869 MET cc_start: 0.9626 (mtt) cc_final: 0.9389 (mtm) REVERT: A 940 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8150 (m) REVERT: A 1094 VAL cc_start: 0.9398 (m) cc_final: 0.9164 (p) REVERT: B 237 ARG cc_start: 0.8866 (ttm170) cc_final: 0.8447 (mtp85) REVERT: B 242 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8212 (tp) REVERT: B 319 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8221 (ttm-80) REVERT: C 10 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6850 (tm-30) REVERT: C 19 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8632 (ttmm) REVERT: C 23 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8604 (tptm) REVERT: C 48 MET cc_start: 0.8665 (mtp) cc_final: 0.8413 (mtp) REVERT: C 82 GLU cc_start: 0.8732 (tp30) cc_final: 0.8530 (tp30) REVERT: D 62 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.8089 (ttp-110) REVERT: D 71 ASP cc_start: 0.8829 (m-30) cc_final: 0.8572 (p0) REVERT: D 78 ARG cc_start: 0.7731 (ptm-80) cc_final: 0.7347 (ptm-80) REVERT: E 242 LEU cc_start: 0.8799 (mp) cc_final: 0.8235 (tp) REVERT: E 935 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8692 (mm-40) REVERT: F 10 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6865 (tm-30) REVERT: F 46 GLU cc_start: 0.8636 (tt0) cc_final: 0.8110 (tt0) REVERT: F 87 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8060 (tmm-80) REVERT: F 89 ASP cc_start: 0.9093 (t0) cc_final: 0.8890 (t70) REVERT: F 98 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7720 (ttt180) REVERT: G 4 MET cc_start: 0.8428 (mmm) cc_final: 0.7823 (mmm) REVERT: G 27 GLN cc_start: 0.8487 (mp10) cc_final: 0.8081 (mp10) REVERT: G 43 GLN cc_start: 0.8843 (pt0) cc_final: 0.8293 (pm20) REVERT: G 46 ARG cc_start: 0.8966 (ptt90) cc_final: 0.8745 (ptt90) REVERT: G 48 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8710 (mm) REVERT: G 55 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8181 (ttm110) REVERT: G 62 ARG cc_start: 0.8338 (ttm170) cc_final: 0.8022 (ttp80) REVERT: G 80 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7222 (mp0) REVERT: G 83 ASP cc_start: 0.7523 (m-30) cc_final: 0.7024 (m-30) REVERT: G 88 TYR cc_start: 0.8483 (m-80) cc_final: 0.8085 (m-80) REVERT: G 104 LYS cc_start: 0.8580 (tptt) cc_final: 0.7877 (tmmt) REVERT: H 12 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8203 (mtmm) REVERT: H 13 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7710 (mmtt) REVERT: H 23 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8673 (tptm) REVERT: H 46 GLU cc_start: 0.8673 (tt0) cc_final: 0.8424 (tt0) REVERT: H 85 ARG cc_start: 0.8439 (ttp80) cc_final: 0.7968 (ttp80) REVERT: H 87 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8198 (mtm-85) REVERT: L 48 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8538 (mm) REVERT: L 78 ARG cc_start: 0.8654 (pmm-80) cc_final: 0.8171 (pmm150) outliers start: 61 outliers final: 26 residues processed: 269 average time/residue: 1.6469 time to fit residues: 511.9821 Evaluate side-chains 248 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 321 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 360 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN G 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054930 restraints weight = 73620.048| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.98 r_work: 0.2824 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31095 Z= 0.181 Angle : 0.594 8.995 42486 Z= 0.300 Chirality : 0.043 0.182 4956 Planarity : 0.004 0.057 5340 Dihedral : 4.477 35.869 5682 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.66 % Allowed : 9.72 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3708 helix: 2.64 (0.19), residues: 666 sheet: 0.59 (0.15), residues: 1038 loop : 0.06 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 106 HIS 0.004 0.001 HIS E1064 PHE 0.015 0.001 PHE E 898 TYR 0.022 0.001 TYR E1067 ARG 0.014 0.001 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 51) link_NAG-ASN : angle 1.80857 ( 153) link_BETA1-4 : bond 0.00483 ( 24) link_BETA1-4 : angle 1.16400 ( 72) hydrogen bonds : bond 0.04279 ( 1314) hydrogen bonds : angle 5.50278 ( 3603) link_BETA1-6 : bond 0.00107 ( 3) link_BETA1-6 : angle 1.50477 ( 9) SS BOND : bond 0.00259 ( 48) SS BOND : angle 0.67017 ( 96) covalent geometry : bond 0.00415 (30969) covalent geometry : angle 0.58274 (42156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7929 (tp) REVERT: A 869 MET cc_start: 0.9600 (mtt) cc_final: 0.9386 (mtm) REVERT: B 237 ARG cc_start: 0.8892 (ttm170) cc_final: 0.8481 (mtp85) REVERT: B 242 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8232 (tp) REVERT: B 319 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8236 (ttm-80) REVERT: B 869 MET cc_start: 0.9628 (mtt) cc_final: 0.9426 (mtt) REVERT: C 10 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7000 (tm-30) REVERT: C 19 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8789 (ttmm) REVERT: C 48 MET cc_start: 0.8674 (mtp) cc_final: 0.8444 (mtp) REVERT: C 82 GLU cc_start: 0.8712 (tp30) cc_final: 0.8497 (tp30) REVERT: D 71 ASP cc_start: 0.8850 (m-30) cc_final: 0.8613 (p0) REVERT: D 78 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7147 (ptm-80) REVERT: E 242 LEU cc_start: 0.8804 (mp) cc_final: 0.8237 (tp) REVERT: F 10 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6745 (tm-30) REVERT: F 46 GLU cc_start: 0.8638 (tt0) cc_final: 0.8425 (tt0) REVERT: F 98 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7430 (ttt180) REVERT: G 24 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7124 (mtm-85) REVERT: G 27 GLN cc_start: 0.8519 (mp10) cc_final: 0.8111 (mp10) REVERT: G 48 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8766 (mm) REVERT: G 80 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7317 (mp0) REVERT: G 88 TYR cc_start: 0.8468 (m-80) cc_final: 0.8090 (m-80) REVERT: G 104 LYS cc_start: 0.8584 (tptt) cc_final: 0.7907 (tmmt) REVERT: H 12 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8266 (mtmm) REVERT: H 13 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7711 (mmtt) REVERT: H 23 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8606 (tptm) REVERT: H 85 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8057 (ttp80) REVERT: L 5 MET cc_start: 0.8339 (pmm) cc_final: 0.7695 (pmm) REVERT: L 27 GLN cc_start: 0.9256 (pt0) cc_final: 0.9027 (pm20) REVERT: L 48 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8485 (mm) REVERT: L 78 ARG cc_start: 0.8652 (pmm-80) cc_final: 0.8201 (pmm150) outliers start: 53 outliers final: 27 residues processed: 246 average time/residue: 1.6912 time to fit residues: 480.7874 Evaluate side-chains 245 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 51 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 349 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 252 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 324 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.086203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056040 restraints weight = 73324.546| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.98 r_work: 0.2856 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31095 Z= 0.119 Angle : 0.574 9.205 42486 Z= 0.290 Chirality : 0.043 0.165 4956 Planarity : 0.004 0.056 5340 Dihedral : 4.299 36.831 5682 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.50 % Allowed : 9.97 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3708 helix: 2.73 (0.19), residues: 666 sheet: 0.59 (0.16), residues: 1026 loop : 0.05 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 106 HIS 0.002 0.000 HIS A1048 PHE 0.014 0.001 PHE A 133 TYR 0.022 0.001 TYR A 28 ARG 0.014 0.001 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 51) link_NAG-ASN : angle 1.71353 ( 153) link_BETA1-4 : bond 0.00521 ( 24) link_BETA1-4 : angle 1.11482 ( 72) hydrogen bonds : bond 0.03873 ( 1314) hydrogen bonds : angle 5.37538 ( 3603) link_BETA1-6 : bond 0.00030 ( 3) link_BETA1-6 : angle 1.39484 ( 9) SS BOND : bond 0.00201 ( 48) SS BOND : angle 0.64880 ( 96) covalent geometry : bond 0.00265 (30969) covalent geometry : angle 0.56375 (42156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 1094 VAL cc_start: 0.9367 (m) cc_final: 0.9149 (p) REVERT: B 237 ARG cc_start: 0.8888 (ttm170) cc_final: 0.8541 (mtp85) REVERT: B 242 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 319 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8244 (ttm-80) REVERT: B 869 MET cc_start: 0.9619 (mtt) cc_final: 0.9385 (mtt) REVERT: C 19 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8745 (ttmm) REVERT: C 48 MET cc_start: 0.8667 (mtp) cc_final: 0.8436 (mtp) REVERT: C 82 GLU cc_start: 0.8600 (tp30) cc_final: 0.8353 (tp30) REVERT: D 71 ASP cc_start: 0.8829 (m-30) cc_final: 0.8603 (p0) REVERT: D 78 ARG cc_start: 0.7929 (ptm-80) cc_final: 0.7214 (ptm-80) REVERT: E 231 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8123 (pp) REVERT: E 242 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8241 (tp) REVERT: E 935 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: F 10 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 12 LYS cc_start: 0.8336 (ptmm) cc_final: 0.8064 (ptmm) REVERT: F 46 GLU cc_start: 0.8632 (tt0) cc_final: 0.8406 (tt0) REVERT: F 98 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7531 (ttt180) REVERT: G 27 GLN cc_start: 0.8552 (mp10) cc_final: 0.8144 (mp10) REVERT: G 43 GLN cc_start: 0.8874 (pt0) cc_final: 0.8628 (pm20) REVERT: G 80 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7411 (mp0) REVERT: G 88 TYR cc_start: 0.8456 (m-80) cc_final: 0.8034 (m-80) REVERT: G 104 LYS cc_start: 0.8605 (tptt) cc_final: 0.7978 (tmmt) REVERT: H 12 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8237 (mtmm) REVERT: H 23 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8623 (tptm) REVERT: H 85 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8165 (ttp80) REVERT: L 43 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: L 48 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8532 (mm) REVERT: L 55 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8306 (ttm-80) REVERT: L 78 ARG cc_start: 0.8627 (pmm-80) cc_final: 0.8256 (pmm150) REVERT: L 98 THR cc_start: 0.9017 (m) cc_final: 0.8643 (p) outliers start: 48 outliers final: 22 residues processed: 256 average time/residue: 1.6446 time to fit residues: 486.4122 Evaluate side-chains 245 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 0 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 323 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054919 restraints weight = 73383.425| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.98 r_work: 0.2825 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31095 Z= 0.182 Angle : 0.602 8.550 42486 Z= 0.303 Chirality : 0.044 0.185 4956 Planarity : 0.004 0.065 5340 Dihedral : 4.324 36.020 5682 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.34 % Allowed : 10.19 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3708 helix: 2.69 (0.19), residues: 666 sheet: 0.58 (0.15), residues: 1035 loop : 0.06 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 106 HIS 0.004 0.001 HIS E1064 PHE 0.041 0.001 PHE E 168 TYR 0.022 0.001 TYR E1067 ARG 0.015 0.001 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 51) link_NAG-ASN : angle 1.77245 ( 153) link_BETA1-4 : bond 0.00479 ( 24) link_BETA1-4 : angle 1.13097 ( 72) hydrogen bonds : bond 0.04217 ( 1314) hydrogen bonds : angle 5.45566 ( 3603) link_BETA1-6 : bond 0.00106 ( 3) link_BETA1-6 : angle 1.48131 ( 9) SS BOND : bond 0.00250 ( 48) SS BOND : angle 0.66167 ( 96) covalent geometry : bond 0.00419 (30969) covalent geometry : angle 0.59126 (42156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7959 (tp) REVERT: B 237 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8505 (mtp85) REVERT: B 242 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 319 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8258 (ttm-80) REVERT: B 869 MET cc_start: 0.9615 (mtt) cc_final: 0.9376 (mtt) REVERT: C 19 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8785 (ttmm) REVERT: C 48 MET cc_start: 0.8662 (mtp) cc_final: 0.8432 (mtp) REVERT: C 82 GLU cc_start: 0.8496 (tp30) cc_final: 0.8258 (tp30) REVERT: D 62 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7758 (ttp-110) REVERT: D 71 ASP cc_start: 0.8837 (m-30) cc_final: 0.8606 (p0) REVERT: D 78 ARG cc_start: 0.7792 (ptm-80) cc_final: 0.7543 (ptm-80) REVERT: E 242 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8198 (tp) REVERT: E 319 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8270 (mtp-110) REVERT: F 10 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6930 (tm-30) REVERT: F 12 LYS cc_start: 0.8409 (ptmm) cc_final: 0.8138 (ptmm) REVERT: F 98 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7388 (ttt180) REVERT: G 4 MET cc_start: 0.8507 (mmm) cc_final: 0.8012 (mmm) REVERT: G 27 GLN cc_start: 0.8538 (mp10) cc_final: 0.8117 (mp10) REVERT: G 43 GLN cc_start: 0.8863 (pt0) cc_final: 0.8607 (pm20) REVERT: G 63 PHE cc_start: 0.8513 (m-80) cc_final: 0.8311 (m-80) REVERT: G 80 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7591 (mp0) REVERT: G 88 TYR cc_start: 0.8467 (m-80) cc_final: 0.8054 (m-80) REVERT: H 12 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8354 (mtmm) REVERT: H 13 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7537 (mmtt) REVERT: H 46 GLU cc_start: 0.8528 (tt0) cc_final: 0.8147 (tt0) REVERT: H 85 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8134 (ttp80) REVERT: H 87 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8325 (mtm-85) REVERT: L 43 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8719 (pm20) REVERT: L 48 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8559 (mm) REVERT: L 55 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8264 (ttm-80) REVERT: L 78 ARG cc_start: 0.8675 (pmm-80) cc_final: 0.8339 (pmm150) outliers start: 43 outliers final: 25 residues processed: 246 average time/residue: 1.6667 time to fit residues: 473.3966 Evaluate side-chains 247 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 269 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 209 optimal weight: 4.9990 chunk 330 optimal weight: 0.1980 chunk 291 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 205 optimal weight: 30.0000 chunk 208 optimal weight: 3.9990 chunk 21 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.086241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056162 restraints weight = 73023.791| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.98 r_work: 0.2861 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31095 Z= 0.117 Angle : 0.584 8.951 42486 Z= 0.293 Chirality : 0.043 0.183 4956 Planarity : 0.004 0.068 5340 Dihedral : 4.198 36.861 5682 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.91 % Allowed : 10.91 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3708 helix: 2.77 (0.19), residues: 666 sheet: 0.62 (0.16), residues: 1023 loop : 0.07 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 106 HIS 0.002 0.000 HIS A1048 PHE 0.037 0.001 PHE E 168 TYR 0.026 0.001 TYR E 28 ARG 0.018 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 51) link_NAG-ASN : angle 1.67626 ( 153) link_BETA1-4 : bond 0.00532 ( 24) link_BETA1-4 : angle 1.08716 ( 72) hydrogen bonds : bond 0.03811 ( 1314) hydrogen bonds : angle 5.33334 ( 3603) link_BETA1-6 : bond 0.00042 ( 3) link_BETA1-6 : angle 1.37763 ( 9) SS BOND : bond 0.00192 ( 48) SS BOND : angle 0.64476 ( 96) covalent geometry : bond 0.00262 (30969) covalent geometry : angle 0.57487 (42156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8558 (mp) cc_final: 0.8038 (tp) REVERT: A 1094 VAL cc_start: 0.9341 (m) cc_final: 0.9128 (p) REVERT: B 237 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8513 (mtp85) REVERT: B 242 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 319 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8257 (ttm-80) REVERT: C 19 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8746 (ttmm) REVERT: C 48 MET cc_start: 0.8646 (mtp) cc_final: 0.8428 (mtp) REVERT: C 82 GLU cc_start: 0.8432 (tp30) cc_final: 0.8194 (tp30) REVERT: D 43 GLN cc_start: 0.8375 (mt0) cc_final: 0.7926 (mp10) REVERT: D 62 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7802 (ttp-110) REVERT: D 71 ASP cc_start: 0.8849 (m-30) cc_final: 0.8619 (p0) REVERT: D 78 ARG cc_start: 0.7777 (ptm-80) cc_final: 0.7543 (ptm-80) REVERT: E 242 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8260 (tp) REVERT: E 319 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8257 (mtp-110) REVERT: E 1094 VAL cc_start: 0.9342 (m) cc_final: 0.9075 (p) REVERT: F 10 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6842 (tm-30) REVERT: F 12 LYS cc_start: 0.8557 (ptmm) cc_final: 0.8287 (ptmm) REVERT: F 98 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7713 (ttt180) REVERT: F 120 LEU cc_start: 0.8865 (mp) cc_final: 0.8660 (tp) REVERT: G 4 MET cc_start: 0.8465 (mmm) cc_final: 0.7995 (mmm) REVERT: G 27 GLN cc_start: 0.8571 (mp10) cc_final: 0.8171 (mp10) REVERT: G 43 GLN cc_start: 0.8909 (pt0) cc_final: 0.8652 (pm20) REVERT: G 55 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7919 (ttm110) REVERT: G 62 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7609 (ttp80) REVERT: G 63 PHE cc_start: 0.8459 (m-80) cc_final: 0.7802 (m-80) REVERT: G 80 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7594 (mp0) REVERT: G 88 TYR cc_start: 0.8441 (m-80) cc_final: 0.8063 (m-80) REVERT: G 104 LYS cc_start: 0.8578 (tptt) cc_final: 0.7804 (tmmt) REVERT: H 10 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7477 (pp20) REVERT: H 12 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8021 (mtpm) REVERT: H 85 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8206 (ttp80) REVERT: H 87 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8347 (mtm-85) REVERT: L 43 GLN cc_start: 0.8994 (pm20) cc_final: 0.8726 (pm20) REVERT: L 48 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8537 (mm) REVERT: L 55 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8450 (ttm-80) REVERT: L 78 ARG cc_start: 0.8748 (pmm-80) cc_final: 0.8453 (pmm150) REVERT: L 98 THR cc_start: 0.9090 (m) cc_final: 0.8868 (p) outliers start: 29 outliers final: 19 residues processed: 245 average time/residue: 1.7130 time to fit residues: 483.9392 Evaluate side-chains 243 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 278 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 313 optimal weight: 0.5980 chunk 137 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055050 restraints weight = 73216.608| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.98 r_work: 0.2831 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31095 Z= 0.165 Angle : 0.598 8.778 42486 Z= 0.301 Chirality : 0.043 0.180 4956 Planarity : 0.004 0.073 5340 Dihedral : 4.229 35.963 5682 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.97 % Allowed : 10.76 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3708 helix: 2.54 (0.19), residues: 690 sheet: 0.64 (0.16), residues: 999 loop : 0.02 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 106 HIS 0.004 0.001 HIS E1064 PHE 0.035 0.001 PHE E 168 TYR 0.021 0.001 TYR E1067 ARG 0.017 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 51) link_NAG-ASN : angle 1.73965 ( 153) link_BETA1-4 : bond 0.00482 ( 24) link_BETA1-4 : angle 1.10612 ( 72) hydrogen bonds : bond 0.04132 ( 1314) hydrogen bonds : angle 5.39165 ( 3603) link_BETA1-6 : bond 0.00045 ( 3) link_BETA1-6 : angle 1.47684 ( 9) SS BOND : bond 0.00232 ( 48) SS BOND : angle 0.66412 ( 96) covalent geometry : bond 0.00378 (30969) covalent geometry : angle 0.58784 (42156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35142.15 seconds wall clock time: 603 minutes 40.03 seconds (36220.03 seconds total)