Starting phenix.real_space_refine on Mon Jul 28 10:36:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.map" model { file = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2025/7qcl_13896.cif" } resolution = 3.36 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= -0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 140 5.16 5 C 6064 2.51 5 N 1437 2.21 5 O 2241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9884 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4177 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 501} Chain breaks: 3 Chain: "B" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4177 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 501} Chain breaks: 3 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 171 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 4, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" 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: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} 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: "M" 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: "N" 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: "O" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 146 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "Q" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.46, per 1000 atoms: 0.96 Number of scatterers: 9884 At special positions: 0 Unit cell: (128.14, 113.52, 197.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 140 16.00 O 2241 8.00 N 1437 7.00 C 6064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A4352 " - pdb=" SG CYS A4386 " distance=2.03 Simple disulfide: pdb=" SG CYS A4379 " - pdb=" SG CYS B4379 " distance=2.29 Simple disulfide: pdb=" SG CYS A4381 " - pdb=" SG CYS A4422 " distance=2.06 Simple disulfide: pdb=" SG CYS A4399 " - pdb=" SG CYS A4423 " distance=2.01 Simple disulfide: pdb=" SG CYS A4407 " - pdb=" SG CYS A4428 " distance=2.01 Simple disulfide: pdb=" SG CYS A4430 " - pdb=" SG CYS A4576 " distance=2.02 Simple disulfide: pdb=" SG CYS A4432 " - pdb=" SG CYS A4573 " distance=2.03 Simple disulfide: pdb=" SG CYS A4454 " - pdb=" SG CYS A4612 " distance=2.03 Simple disulfide: pdb=" SG CYS A4478 " - pdb=" SG CYS A4486 " distance=2.02 Simple disulfide: pdb=" SG CYS A4584 " - pdb=" SG CYS A4595 " distance=2.03 Simple disulfide: pdb=" SG CYS A4638 " - pdb=" SG CYS A4673 " distance=2.03 Simple disulfide: pdb=" SG CYS A4644 " - pdb=" SG CYS A4668 " distance=2.03 Simple disulfide: pdb=" SG CYS A4655 " - pdb=" SG CYS A4692 " distance=2.03 Simple disulfide: pdb=" SG CYS A4682 " - pdb=" SG CYS A4709 " distance=2.04 Simple disulfide: pdb=" SG CYS A4698 " - pdb=" SG CYS A4722 " distance=2.03 Simple disulfide: pdb=" SG CYS A4713 " - pdb=" SG CYS A4746 " distance=2.03 Simple disulfide: pdb=" SG CYS A4730 " - pdb=" SG CYS A4766 " distance=2.18 Simple disulfide: pdb=" SG CYS A4748 " - pdb=" SG CYS A4762 " distance=2.03 Simple disulfide: pdb=" SG CYS A4768 " - pdb=" SG CYS A4791 " distance=2.03 Simple disulfide: pdb=" SG CYS A4786 " - pdb=" SG CYS A4830 " distance=2.06 Simple disulfide: pdb=" SG CYS A4789 " - pdb=" SG CYS A4800 " distance=2.03 Simple disulfide: pdb=" SG CYS A4805 " - pdb=" SG CYS A4831 " distance=2.02 Simple disulfide: pdb=" SG CYS A4813 " - pdb=" SG CYS A4836 " distance=2.03 Simple disulfide: pdb=" SG CYS A4838 " - pdb=" SG CYS A4865 " distance=2.02 Simple disulfide: pdb=" SG CYS A4843 " - pdb=" SG CYS A4866 " distance=2.03 Simple disulfide: pdb=" SG CYS A4850 " - pdb=" SG CYS A4871 " distance=2.03 Simple disulfide: pdb=" SG CYS A4877 " - pdb=" SG CYS A4900 " distance=2.03 Simple disulfide: pdb=" SG CYS A4895 " - pdb=" SG CYS A4937 " distance=2.03 Simple disulfide: pdb=" SG CYS A4898 " - pdb=" SG CYS A4915 " distance=2.04 Simple disulfide: pdb=" SG CYS A4920 " - pdb=" SG CYS A4938 " distance=2.09 Simple disulfide: pdb=" SG CYS A4924 " - pdb=" SG CYS A4941 " distance=2.05 Simple disulfide: pdb=" SG CYS B4352 " - pdb=" SG CYS B4386 " distance=2.02 Simple disulfide: pdb=" SG CYS B4381 " - pdb=" SG CYS B4422 " distance=2.06 Simple disulfide: pdb=" SG CYS B4399 " - pdb=" SG CYS B4423 " distance=2.06 Simple disulfide: pdb=" SG CYS B4407 " - pdb=" SG CYS B4428 " distance=2.03 Simple disulfide: pdb=" SG CYS B4430 " - pdb=" SG CYS B4576 " distance=2.03 Simple disulfide: pdb=" SG CYS B4432 " - pdb=" SG CYS B4573 " distance=2.03 Simple disulfide: pdb=" SG CYS B4454 " - pdb=" SG CYS B4612 " distance=2.03 Simple disulfide: pdb=" SG CYS B4478 " - pdb=" SG CYS B4486 " distance=2.03 Simple disulfide: pdb=" SG CYS B4584 " - pdb=" SG CYS B4595 " distance=2.02 Simple disulfide: pdb=" SG CYS B4638 " - pdb=" SG CYS B4673 " distance=2.03 Simple disulfide: pdb=" SG CYS B4644 " - pdb=" SG CYS B4668 " distance=2.03 Simple disulfide: pdb=" SG CYS B4655 " - pdb=" SG CYS B4692 " distance=2.03 Simple disulfide: pdb=" SG CYS B4682 " - pdb=" SG CYS B4709 " distance=2.04 Simple disulfide: pdb=" SG CYS B4698 " - pdb=" SG CYS B4722 " distance=2.03 Simple disulfide: pdb=" SG CYS B4713 " - pdb=" SG CYS B4746 " distance=2.04 Simple disulfide: pdb=" SG CYS B4730 " - pdb=" SG CYS B4766 " distance=2.02 Simple disulfide: pdb=" SG CYS B4748 " - pdb=" SG CYS B4762 " distance=2.03 Simple disulfide: pdb=" SG CYS B4768 " - pdb=" SG CYS B4791 " distance=2.03 Simple disulfide: pdb=" SG CYS B4786 " - pdb=" SG CYS B4830 " distance=2.03 Simple disulfide: pdb=" SG CYS B4789 " - pdb=" SG CYS B4800 " distance=2.03 Simple disulfide: pdb=" SG CYS B4805 " - pdb=" SG CYS B4831 " distance=2.04 Simple disulfide: pdb=" SG CYS B4813 " - pdb=" SG CYS B4836 " distance=2.04 Simple disulfide: pdb=" SG CYS B4838 " - pdb=" SG CYS B4865 " distance=2.02 Simple disulfide: pdb=" SG CYS B4843 " - pdb=" SG CYS B4866 " distance=2.03 Simple disulfide: pdb=" SG CYS B4850 " - pdb=" SG CYS B4871 " distance=2.03 Simple disulfide: pdb=" SG CYS B4877 " - pdb=" SG CYS B4900 " distance=2.03 Simple disulfide: pdb=" SG CYS B4898 " - pdb=" SG CYS B4915 " distance=2.02 Simple disulfide: pdb=" SG CYS B4920 " - pdb=" SG CYS B4938 " distance=2.00 Simple disulfide: pdb=" SG CYS B4924 " - pdb=" SG CYS B4941 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " NAG I 2 " - " MAN I 3 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA C 3 " - " MAN C 7 " " BMA D 3 " - " MAN D 9 " " BMA F 3 " - " MAN F 7 " " BMA G 3 " - " MAN G 7 " " BMA H 3 " - " MAN H 7 " " BMA J 3 " - " MAN J 7 " " BMA K 3 " - " MAN K 7 " " BMA L 3 " - " MAN L 7 " " BMA O 3 " - " MAN O 9 " " BMA Q 3 " - " MAN Q 7 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN C 7 " - " NAG C 8 " " MAN D 4 " - " NAG D 5 " " MAN D 9 " - " NAG D 10 " " MAN F 4 " - " NAG F 5 " " MAN F 7 " - " NAG F 8 " " MAN G 4 " - " NAG G 5 " " MAN G 7 " - " NAG G 8 " " MAN H 4 " - " NAG H 5 " " MAN H 7 " - " NAG H 8 " " MAN J 4 " - " NAG J 5 " " MAN J 7 " - " NAG J 8 " " MAN K 4 " - " NAG K 5 " " MAN K 7 " - " NAG K 8 " " MAN L 4 " - " NAG L 5 " " MAN L 7 " - " NAG L 8 " " MAN O 4 " - " NAG O 5 " " MAN Q 4 " - " NAG Q 5 " " MAN Q 7 " - " NAG Q 8 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG C 5 " - " GAL C 6 " " NAG C 8 " - " GAL C 9 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " MAN D 4 " - " NAG D 7 " " NAG D 5 " - " GAL D 6 " " NAG D 7 " - " GAL D 8 " " MAN D 9 " - " NAG D 12 " " NAG D 10 " - " GAL D 11 " " NAG D 12 " - " GAL D 13 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG F 8 " - " GAL F 9 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG G 5 " - " GAL G 6 " " NAG G 8 " - " GAL G 9 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG H 5 " - " GAL H 6 " " NAG H 8 " - " GAL H 9 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 4 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " " NAG J 8 " - " GAL J 9 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG K 5 " - " GAL K 6 " " NAG K 8 " - " GAL K 9 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG L 5 " - " GAL L 6 " " NAG L 8 " - " GAL L 9 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " MAN O 4 " - " NAG O 7 " " NAG O 5 " - " GAL O 6 " " NAG O 7 " - " GAL O 8 " " MAN O 9 " - " NAG O 10 " " NAG O 10 " - " GAL O 11 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG Q 5 " - " GAL Q 6 " " NAG Q 8 " - " GAL Q 9 " BETA1-6 " NAG C 1 " - " FUC C 10 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 14 " " NAG E 1 " - " FUC E 4 " " NAG F 1 " - " FUC F 10 " " NAG G 1 " - " FUC G 10 " " NAG I 1 " - " FUC I 5 " " NAG J 1 " - " FUC J 10 " " NAG L 1 " - " FUC L 10 " " NAG M 1 " - " FUC M 4 " " NAG N 1 " - " FUC N 4 " " NAG O 1 " - " FUC O 12 " " NAG Q 1 " - " FUC Q 10 " NAG-ASN " NAG A5002 " - " ASN A4389 " " NAG B5002 " - " ASN B4389 " " NAG C 1 " - " ASN A4832 " " NAG D 1 " - " ASN A4567 " " NAG E 1 " - " ASN B4906 " " NAG F 1 " - " ASN B4839 " " NAG G 1 " - " ASN A4703 " " NAG H 1 " - " ASN B4578 " " NAG I 1 " - " ASN A4738 " " NAG J 1 " - " ASN A4839 " " NAG K 1 " - " ASN A4578 " " NAG L 1 " - " ASN B4703 " " NAG M 1 " - " ASN A4906 " " NAG N 1 " - " ASN B4738 " " NAG O 1 " - " ASN B4567 " " NAG Q 1 " - " ASN B4832 " Time building additional restraints: 4.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 11.3% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 4579 through 4583 removed outlier: 3.707A pdb=" N ASP A4582 " --> pdb=" O THR A4579 " (cutoff:3.500A) Processing helix chain 'A' and resid 4594 through 4600 removed outlier: 3.558A pdb=" N ALA A4598 " --> pdb=" O ASN A4594 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A4600 " --> pdb=" O GLU A4596 " (cutoff:3.500A) Processing helix chain 'A' and resid 4641 through 4646 Processing helix chain 'A' and resid 4647 through 4651 removed outlier: 6.053A pdb=" N SER A4650 " --> pdb=" O ILE A4647 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A4651 " --> pdb=" O LYS A4648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4647 through 4651' Processing helix chain 'A' and resid 4652 through 4657 removed outlier: 4.140A pdb=" N ALA A4657 " --> pdb=" O ALA A4653 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4675 removed outlier: 3.732A pdb=" N MET A4675 " --> pdb=" O ASP A4671 " (cutoff:3.500A) Processing helix chain 'A' and resid 4683 through 4695 Processing helix chain 'A' and resid 4907 through 4912 Processing helix chain 'B' and resid 4594 through 4601 removed outlier: 3.748A pdb=" N ALA B4598 " --> pdb=" O ASN B4594 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B4599 " --> pdb=" O CYS B4595 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B4600 " --> pdb=" O GLU B4596 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B4601 " --> pdb=" O ALA B4597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4594 through 4601' Processing helix chain 'B' and resid 4641 through 4646 removed outlier: 3.789A pdb=" N GLN B4645 " --> pdb=" O SER B4641 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B4646 " --> pdb=" O PRO B4642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4641 through 4646' Processing helix chain 'B' and resid 4647 through 4648 No H-bonds generated for 'chain 'B' and resid 4647 through 4648' Processing helix chain 'B' and resid 4649 through 4653 removed outlier: 3.563A pdb=" N PHE B4652 " --> pdb=" O ASP B4649 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4675 removed outlier: 3.721A pdb=" N MET B4675 " --> pdb=" O ASP B4671 " (cutoff:3.500A) Processing helix chain 'B' and resid 4683 through 4695 Processing helix chain 'B' and resid 4702 through 4706 removed outlier: 3.535A pdb=" N HIS B4706 " --> pdb=" O ASN B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4912 Processing sheet with id=AA1, first strand: chain 'A' and resid 4382 through 4386 Processing sheet with id=AA2, first strand: chain 'A' and resid 4414 through 4417 Processing sheet with id=AA3, first strand: chain 'A' and resid 4430 through 4435 Processing sheet with id=AA4, first strand: chain 'A' and resid 4439 through 4441 Processing sheet with id=AA5, first strand: chain 'A' and resid 4509 through 4512 removed outlier: 8.992A pdb=" N PHE A4469 " --> pdb=" O GLU A4460 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU A4460 " --> pdb=" O PHE A4469 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A4471 " --> pdb=" O LEU A4458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 4718 through 4723 removed outlier: 4.363A pdb=" N CYS A4722 " --> pdb=" O VAL A4743 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A4743 " --> pdb=" O CYS A4722 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4753 through 4754 Processing sheet with id=AA8, first strand: chain 'A' and resid 4780 through 4782 removed outlier: 3.695A pdb=" N GLU A4780 " --> pdb=" O CYS A4791 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A4789 " --> pdb=" O PHE A4782 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 4823 through 4824 Processing sheet with id=AB1, first strand: chain 'B' and resid 4414 through 4417 Processing sheet with id=AB2, first strand: chain 'B' and resid 4447 through 4449 Processing sheet with id=AB3, first strand: chain 'B' and resid 4509 through 4512 removed outlier: 6.662A pdb=" N VAL B4471 " --> pdb=" O LEU B4458 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B4570 " --> pdb=" O GLU B4460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 4718 through 4723 removed outlier: 4.534A pdb=" N CYS B4722 " --> pdb=" O VAL B4743 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B4743 " --> pdb=" O CYS B4722 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4753 through 4754 Processing sheet with id=AB6, first strand: chain 'B' and resid 4768 through 4769 Processing sheet with id=AB7, first strand: chain 'B' and resid 4780 through 4782 Processing sheet with id=AB8, first strand: chain 'B' and resid 4818 through 4822 198 hydrogen bonds defined for protein. 501 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: 2.92 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1503 1.31 - 1.44: 2942 1.44 - 1.56: 5501 1.56 - 1.69: 4 1.69 - 1.82: 158 Bond restraints: 10108 Sorted by residual: bond pdb=" CA VAL B4861 " pdb=" C VAL B4861 " ideal model delta sigma weight residual 1.524 1.595 -0.070 1.05e-02 9.07e+03 4.47e+01 bond pdb=" N CYS A4399 " pdb=" CA CYS A4399 " ideal model delta sigma weight residual 1.458 1.511 -0.054 1.18e-02 7.18e+03 2.09e+01 bond pdb=" CA VAL A4814 " pdb=" C VAL A4814 " ideal model delta sigma weight residual 1.519 1.569 -0.050 1.14e-02 7.69e+03 1.94e+01 bond pdb=" CA SER B4873 " pdb=" CB SER B4873 " ideal model delta sigma weight residual 1.528 1.464 0.064 1.48e-02 4.57e+03 1.87e+01 bond pdb=" C MET B4383 " pdb=" O MET B4383 " ideal model delta sigma weight residual 1.234 1.177 0.057 1.38e-02 5.25e+03 1.72e+01 ... (remaining 10103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 12852 3.37 - 6.74: 820 6.74 - 10.11: 100 10.11 - 13.48: 17 13.48 - 16.85: 4 Bond angle restraints: 13793 Sorted by residual: angle pdb=" N GLY A4927 " pdb=" CA GLY A4927 " pdb=" C GLY A4927 " ideal model delta sigma weight residual 113.58 100.81 12.77 1.07e+00 8.73e-01 1.42e+02 angle pdb=" N VAL A4904 " pdb=" CA VAL A4904 " pdb=" C VAL A4904 " ideal model delta sigma weight residual 110.74 120.37 -9.63 9.10e-01 1.21e+00 1.12e+02 angle pdb=" N ASN B4825 " pdb=" CA ASN B4825 " pdb=" C ASN B4825 " ideal model delta sigma weight residual 109.42 94.11 15.31 1.48e+00 4.57e-01 1.07e+02 angle pdb=" N VAL A4904 " pdb=" CA VAL A4904 " pdb=" CB VAL A4904 " ideal model delta sigma weight residual 110.64 98.46 12.18 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N LYS B4844 " pdb=" CA LYS B4844 " pdb=" C LYS B4844 " ideal model delta sigma weight residual 111.36 122.14 -10.78 1.09e+00 8.42e-01 9.78e+01 ... (remaining 13788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6988 23.98 - 47.97: 446 47.97 - 71.95: 82 71.95 - 95.93: 90 95.93 - 119.92: 189 Dihedral angle restraints: 7795 sinusoidal: 4619 harmonic: 3176 Sorted by residual: dihedral pdb=" CB CYS A4682 " pdb=" SG CYS A4682 " pdb=" SG CYS A4709 " pdb=" CB CYS A4709 " ideal model delta sinusoidal sigma weight residual 93.00 -177.06 -89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS B4713 " pdb=" SG CYS B4713 " pdb=" SG CYS B4746 " pdb=" CB CYS B4746 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A4399 " pdb=" SG CYS A4399 " pdb=" SG CYS A4423 " pdb=" CB CYS A4423 " ideal model delta sinusoidal sigma weight residual -86.00 -172.39 86.39 1 1.00e+01 1.00e-02 9.00e+01 ... (remaining 7792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 1727 0.198 - 0.396: 146 0.396 - 0.594: 17 0.594 - 0.791: 3 0.791 - 0.989: 4 Chirality restraints: 1897 Sorted by residual: chirality pdb=" C1 NAG D 5 " pdb=" O2 MAN D 4 " pdb=" C2 NAG D 5 " pdb=" O5 NAG D 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.45e+03 chirality pdb=" C1 NAG L 5 " pdb=" O2 MAN L 4 " pdb=" C2 NAG L 5 " pdb=" O5 NAG L 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-02 2.50e+03 2.35e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.74e+03 ... (remaining 1894 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.355 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG I 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 5 " -0.355 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG Q 5 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG Q 5 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG Q 5 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG Q 5 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG I 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.127 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 45 2.43 - 3.05: 7471 3.05 - 3.67: 15040 3.67 - 4.28: 22328 4.28 - 4.90: 33440 Nonbonded interactions: 78324 Sorted by model distance: nonbonded pdb=" OE2 GLU A4398 " pdb=" O CYS A4399 " model vdw 1.816 3.040 nonbonded pdb=" OG1 THR A4577 " pdb="CA CA A5003 " model vdw 1.864 2.510 nonbonded pdb=" CE3 TRP A4376 " pdb=" O TRP A4377 " model vdw 1.871 3.340 nonbonded pdb=" ND1 HIS A4505 " pdb=" CE MET A4506 " model vdw 2.001 3.540 nonbonded pdb=" OD1 ASP A4583 " pdb="CA CA A5003 " model vdw 2.040 2.510 ... (remaining 78319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 2) selection = (chain 'F' and resid 2) selection = (chain 'G' and resid 2) selection = (chain 'H' and resid 1) selection = (chain 'J' and resid 2) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 2) selection = (chain 'Q' and resid 2) } ncs_group { reference = (chain 'D' and (resid 7 through 8 or resid 12 through 14)) selection = (chain 'O' and (resid 5 through 6 or resid 10 through 12)) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'N' } 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: 210.810 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 31.880 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.256 10291 Z= 0.714 Angle : 1.958 48.427 14282 Z= 1.156 Chirality : 0.123 0.989 1897 Planarity : 0.038 0.305 1605 Dihedral : 25.313 119.917 5571 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 36.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.94 % Favored : 89.96 % Rotamer: Outliers : 6.66 % Allowed : 6.66 % Favored : 86.68 % Cbeta Deviations : 2.64 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.25), residues: 1076 helix: 1.36 (0.65), residues: 74 sheet: -0.01 (0.37), residues: 204 loop : -2.01 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A4424 HIS 0.013 0.001 HIS A4425 PHE 0.018 0.002 PHE A4928 TYR 0.016 0.001 TYR A4869 ARG 0.018 0.001 ARG B4804 Details of bonding type rmsd link_NAG-ASN : bond 0.02441 ( 16) link_NAG-ASN : angle 10.70748 ( 48) link_ALPHA1-6 : bond 0.00658 ( 10) link_ALPHA1-6 : angle 2.71753 ( 30) link_BETA1-2 : bond 0.00497 ( 19) link_BETA1-2 : angle 2.89439 ( 57) link_BETA1-4 : bond 0.00532 ( 55) link_BETA1-4 : angle 2.43408 ( 165) link_ALPHA1-3 : bond 0.00478 ( 11) link_ALPHA1-3 : angle 3.11335 ( 33) hydrogen bonds : bond 0.17228 ( 198) hydrogen bonds : angle 8.39968 ( 501) link_BETA1-6 : bond 0.00317 ( 12) link_BETA1-6 : angle 1.84587 ( 36) SS BOND : bond 0.04076 ( 60) SS BOND : angle 5.45110 ( 120) covalent geometry : bond 0.01061 (10108) covalent geometry : angle 1.77778 (13793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 67 time to evaluate : 1.002 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4703 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6707 (t0) REVERT: A 4892 SER cc_start: 0.4851 (OUTLIER) cc_final: 0.4564 (t) outliers start: 65 outliers final: 26 residues processed: 127 average time/residue: 0.2102 time to fit residues: 38.1888 Evaluate side-chains 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4595 CYS Chi-restraints excluded: chain A residue 4703 ASN Chi-restraints excluded: chain A residue 4734 SER Chi-restraints excluded: chain A residue 4813 CYS Chi-restraints excluded: chain A residue 4846 LYS Chi-restraints excluded: chain A residue 4866 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4892 SER Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4912 VAL Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4352 CYS Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4815 GLU Chi-restraints excluded: chain B residue 4837 LYS Chi-restraints excluded: chain B residue 4840 THR Chi-restraints excluded: chain B residue 4859 LYS Chi-restraints excluded: chain B residue 4860 MET Chi-restraints excluded: chain B residue 4865 CYS Chi-restraints excluded: chain B residue 4866 CYS Chi-restraints excluded: chain B residue 4900 CYS Chi-restraints excluded: chain B residue 4921 ASN Chi-restraints excluded: chain B residue 4924 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4917 HIS ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4552 ASN B4645 GLN B4686 GLN ** B4739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.104723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073379 restraints weight = 42937.037| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 5.71 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 10291 Z= 0.253 Angle : 1.369 30.130 14282 Z= 0.560 Chirality : 0.067 0.543 1897 Planarity : 0.006 0.065 1605 Dihedral : 22.973 116.956 3661 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.46 % Favored : 91.45 % Rotamer: Outliers : 3.79 % Allowed : 10.96 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.67 (0.25), residues: 1076 helix: 2.16 (0.67), residues: 72 sheet: 0.15 (0.35), residues: 212 loop : -1.95 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A4376 HIS 0.005 0.001 HIS B4704 PHE 0.019 0.002 PHE B4854 TYR 0.056 0.002 TYR A4891 ARG 0.004 0.001 ARG B4864 Details of bonding type rmsd link_NAG-ASN : bond 0.01472 ( 16) link_NAG-ASN : angle 6.14474 ( 48) link_ALPHA1-6 : bond 0.01267 ( 10) link_ALPHA1-6 : angle 2.60655 ( 30) link_BETA1-2 : bond 0.01143 ( 19) link_BETA1-2 : angle 2.02628 ( 57) link_BETA1-4 : bond 0.01074 ( 55) link_BETA1-4 : angle 3.01022 ( 165) link_ALPHA1-3 : bond 0.01813 ( 11) link_ALPHA1-3 : angle 3.59041 ( 33) hydrogen bonds : bond 0.03867 ( 198) hydrogen bonds : angle 7.26584 ( 501) link_BETA1-6 : bond 0.00923 ( 12) link_BETA1-6 : angle 1.79823 ( 36) SS BOND : bond 0.00493 ( 60) SS BOND : angle 1.94192 ( 120) covalent geometry : bond 0.00557 (10108) covalent geometry : angle 1.26366 (13793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 49 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4376 TRP cc_start: 0.8786 (t60) cc_final: 0.8368 (t60) REVERT: A 4852 LEU cc_start: 0.8208 (mt) cc_final: 0.7936 (tp) REVERT: A 4916 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 4406 THR cc_start: 0.8839 (m) cc_final: 0.8620 (p) outliers start: 37 outliers final: 22 residues processed: 82 average time/residue: 0.2043 time to fit residues: 25.3158 Evaluate side-chains 67 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4912 VAL Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4352 CYS Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4840 THR Chi-restraints excluded: chain B residue 4859 LYS Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4900 CYS Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Chi-restraints excluded: chain B residue 4941 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4552 ASN B4686 GLN ** B4739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.073350 restraints weight = 43452.364| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 5.81 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10291 Z= 0.218 Angle : 1.154 29.235 14282 Z= 0.474 Chirality : 0.059 0.509 1897 Planarity : 0.005 0.051 1605 Dihedral : 20.033 115.944 3636 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.69 % Allowed : 12.81 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.53 (0.26), residues: 1076 helix: 1.98 (0.65), residues: 77 sheet: 0.42 (0.35), residues: 206 loop : -1.89 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A4870 HIS 0.003 0.001 HIS B4704 PHE 0.019 0.001 PHE B4854 TYR 0.037 0.002 TYR A4891 ARG 0.008 0.001 ARG B4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 16) link_NAG-ASN : angle 4.78129 ( 48) link_ALPHA1-6 : bond 0.01203 ( 10) link_ALPHA1-6 : angle 2.56074 ( 30) link_BETA1-2 : bond 0.00943 ( 19) link_BETA1-2 : angle 1.69642 ( 57) link_BETA1-4 : bond 0.00959 ( 55) link_BETA1-4 : angle 2.72416 ( 165) link_ALPHA1-3 : bond 0.01481 ( 11) link_ALPHA1-3 : angle 2.96527 ( 33) hydrogen bonds : bond 0.03650 ( 198) hydrogen bonds : angle 6.86163 ( 501) link_BETA1-6 : bond 0.00740 ( 12) link_BETA1-6 : angle 1.76376 ( 36) SS BOND : bond 0.00578 ( 60) SS BOND : angle 1.76260 ( 120) covalent geometry : bond 0.00475 (10108) covalent geometry : angle 1.06265 (13793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4675 MET cc_start: 0.8859 (ptp) cc_final: 0.8626 (ptp) REVERT: A 4852 LEU cc_start: 0.8174 (mt) cc_final: 0.7736 (tp) outliers start: 36 outliers final: 26 residues processed: 78 average time/residue: 0.1759 time to fit residues: 21.5609 Evaluate side-chains 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4890 VAL Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4352 CYS Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4869 TYR Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4900 CYS Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0060 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4552 ASN B4686 GLN B4739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.105810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.074218 restraints weight = 43302.261| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 5.90 r_work: 0.3032 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10291 Z= 0.176 Angle : 1.065 26.777 14282 Z= 0.432 Chirality : 0.056 0.454 1897 Planarity : 0.005 0.047 1605 Dihedral : 18.256 111.707 3630 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.87 % Allowed : 14.55 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.47 (0.26), residues: 1076 helix: 2.19 (0.67), residues: 71 sheet: 0.44 (0.35), residues: 205 loop : -1.82 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B4870 HIS 0.005 0.001 HIS B4704 PHE 0.016 0.001 PHE B4854 TYR 0.031 0.001 TYR A4891 ARG 0.004 0.000 ARG B4804 Details of bonding type rmsd link_NAG-ASN : bond 0.01141 ( 16) link_NAG-ASN : angle 4.43895 ( 48) link_ALPHA1-6 : bond 0.01251 ( 10) link_ALPHA1-6 : angle 2.43501 ( 30) link_BETA1-2 : bond 0.00974 ( 19) link_BETA1-2 : angle 1.78619 ( 57) link_BETA1-4 : bond 0.00921 ( 55) link_BETA1-4 : angle 2.73881 ( 165) link_ALPHA1-3 : bond 0.01424 ( 11) link_ALPHA1-3 : angle 2.76167 ( 33) hydrogen bonds : bond 0.02917 ( 198) hydrogen bonds : angle 6.57799 ( 501) link_BETA1-6 : bond 0.00734 ( 12) link_BETA1-6 : angle 1.61787 ( 36) SS BOND : bond 0.00421 ( 60) SS BOND : angle 1.36843 ( 120) covalent geometry : bond 0.00373 (10108) covalent geometry : angle 0.97438 (13793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4852 LEU cc_start: 0.8267 (mt) cc_final: 0.7755 (tp) REVERT: A 4929 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6236 (mm-30) REVERT: B 4870 TRP cc_start: 0.8159 (p-90) cc_final: 0.7864 (p-90) outliers start: 28 outliers final: 18 residues processed: 69 average time/residue: 0.2060 time to fit residues: 21.5300 Evaluate side-chains 57 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4395 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4840 THR Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B4552 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.104926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.072146 restraints weight = 42845.215| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 4.81 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10291 Z= 0.207 Angle : 1.063 30.243 14282 Z= 0.431 Chirality : 0.055 0.459 1897 Planarity : 0.005 0.056 1605 Dihedral : 17.247 112.797 3621 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.97 % Allowed : 15.27 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.25), residues: 1076 helix: 1.95 (0.66), residues: 77 sheet: 0.77 (0.36), residues: 191 loop : -1.88 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B4377 HIS 0.005 0.001 HIS B4704 PHE 0.010 0.001 PHE A4854 TYR 0.021 0.001 TYR A4891 ARG 0.010 0.001 ARG B4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 16) link_NAG-ASN : angle 4.29194 ( 48) link_ALPHA1-6 : bond 0.01244 ( 10) link_ALPHA1-6 : angle 2.32441 ( 30) link_BETA1-2 : bond 0.00896 ( 19) link_BETA1-2 : angle 1.71177 ( 57) link_BETA1-4 : bond 0.00853 ( 55) link_BETA1-4 : angle 2.71192 ( 165) link_ALPHA1-3 : bond 0.01300 ( 11) link_ALPHA1-3 : angle 2.64488 ( 33) hydrogen bonds : bond 0.03479 ( 198) hydrogen bonds : angle 6.52061 ( 501) link_BETA1-6 : bond 0.00677 ( 12) link_BETA1-6 : angle 1.69661 ( 36) SS BOND : bond 0.00433 ( 60) SS BOND : angle 1.28490 ( 120) covalent geometry : bond 0.00460 (10108) covalent geometry : angle 0.97696 (13793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4376 TRP cc_start: 0.8595 (t-100) cc_final: 0.8117 (t60) REVERT: A 4383 MET cc_start: 0.8953 (tpp) cc_final: 0.8665 (mpp) REVERT: A 4760 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7821 (t0) outliers start: 29 outliers final: 22 residues processed: 70 average time/residue: 0.1829 time to fit residues: 19.8316 Evaluate side-chains 62 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4459 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4753 MET Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain A residue 4941 CYS Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072946 restraints weight = 43172.461| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.95 r_work: 0.3006 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10291 Z= 0.176 Angle : 1.037 31.857 14282 Z= 0.418 Chirality : 0.055 0.432 1897 Planarity : 0.005 0.049 1605 Dihedral : 16.555 112.743 3621 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.89 % Rotamer: Outliers : 2.87 % Allowed : 16.09 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.25), residues: 1076 helix: 1.86 (0.65), residues: 77 sheet: 0.85 (0.36), residues: 193 loop : -1.85 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B4870 HIS 0.004 0.001 HIS B4704 PHE 0.008 0.001 PHE B4674 TYR 0.014 0.001 TYR B4891 ARG 0.012 0.001 ARG A4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00941 ( 16) link_NAG-ASN : angle 4.20370 ( 48) link_ALPHA1-6 : bond 0.01243 ( 10) link_ALPHA1-6 : angle 2.21853 ( 30) link_BETA1-2 : bond 0.00925 ( 19) link_BETA1-2 : angle 1.72765 ( 57) link_BETA1-4 : bond 0.00846 ( 55) link_BETA1-4 : angle 2.65747 ( 165) link_ALPHA1-3 : bond 0.01353 ( 11) link_ALPHA1-3 : angle 2.60929 ( 33) hydrogen bonds : bond 0.02952 ( 198) hydrogen bonds : angle 6.36723 ( 501) link_BETA1-6 : bond 0.00688 ( 12) link_BETA1-6 : angle 1.61279 ( 36) SS BOND : bond 0.00417 ( 60) SS BOND : angle 1.16831 ( 120) covalent geometry : bond 0.00380 (10108) covalent geometry : angle 0.95408 (13793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8279 (t0) REVERT: A 4792 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8605 (pp) REVERT: A 4931 MET cc_start: 0.6358 (mmp) cc_final: 0.4235 (tmm) REVERT: B 4376 TRP cc_start: 0.8511 (OUTLIER) cc_final: 0.8106 (p-90) REVERT: B 4404 MET cc_start: 0.8923 (tpp) cc_final: 0.8684 (tpp) REVERT: B 4870 TRP cc_start: 0.8273 (p-90) cc_final: 0.8014 (t60) outliers start: 28 outliers final: 17 residues processed: 67 average time/residue: 0.2404 time to fit residues: 24.8690 Evaluate side-chains 58 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4395 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4376 TRP Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.071490 restraints weight = 43256.082| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 5.83 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10291 Z= 0.211 Angle : 1.030 28.141 14282 Z= 0.421 Chirality : 0.054 0.423 1897 Planarity : 0.005 0.045 1605 Dihedral : 15.969 113.927 3621 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.92 % Favored : 90.99 % Rotamer: Outliers : 3.48 % Allowed : 16.29 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.26), residues: 1076 helix: 1.99 (0.68), residues: 73 sheet: 0.84 (0.36), residues: 194 loop : -1.76 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A4376 HIS 0.004 0.001 HIS B4704 PHE 0.012 0.001 PHE A4854 TYR 0.014 0.001 TYR A4388 ARG 0.007 0.001 ARG A4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 16) link_NAG-ASN : angle 4.03020 ( 48) link_ALPHA1-6 : bond 0.01186 ( 10) link_ALPHA1-6 : angle 2.20518 ( 30) link_BETA1-2 : bond 0.00854 ( 19) link_BETA1-2 : angle 1.70286 ( 57) link_BETA1-4 : bond 0.00797 ( 55) link_BETA1-4 : angle 2.59876 ( 165) link_ALPHA1-3 : bond 0.01299 ( 11) link_ALPHA1-3 : angle 2.61642 ( 33) hydrogen bonds : bond 0.03604 ( 198) hydrogen bonds : angle 6.45121 ( 501) link_BETA1-6 : bond 0.00664 ( 12) link_BETA1-6 : angle 1.71775 ( 36) SS BOND : bond 0.00472 ( 60) SS BOND : angle 1.31238 ( 120) covalent geometry : bond 0.00472 (10108) covalent geometry : angle 0.94841 (13793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 38 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4383 MET cc_start: 0.8984 (tpp) cc_final: 0.8650 (mpp) REVERT: A 4760 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7859 (t0) REVERT: A 4792 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 4375 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 4816 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8691 (p0) outliers start: 34 outliers final: 22 residues processed: 68 average time/residue: 0.1694 time to fit residues: 18.8404 Evaluate side-chains 62 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4395 VAL Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4459 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4915 CYS Chi-restraints excluded: chain A residue 4920 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4375 THR Chi-restraints excluded: chain B residue 4376 TRP Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4774 VAL Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4816 ASP Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.104692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072235 restraints weight = 43655.691| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 5.34 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10291 Z= 0.177 Angle : 0.998 26.861 14282 Z= 0.406 Chirality : 0.053 0.415 1897 Planarity : 0.005 0.043 1605 Dihedral : 15.426 114.187 3620 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.97 % Allowed : 16.91 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.25), residues: 1076 helix: 1.94 (0.66), residues: 73 sheet: 0.84 (0.36), residues: 192 loop : -1.75 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B4376 HIS 0.004 0.001 HIS B4704 PHE 0.021 0.001 PHE A4854 TYR 0.013 0.001 TYR A4884 ARG 0.006 0.001 ARG A4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00906 ( 16) link_NAG-ASN : angle 3.99643 ( 48) link_ALPHA1-6 : bond 0.01194 ( 10) link_ALPHA1-6 : angle 2.12691 ( 30) link_BETA1-2 : bond 0.00876 ( 19) link_BETA1-2 : angle 1.68406 ( 57) link_BETA1-4 : bond 0.00807 ( 55) link_BETA1-4 : angle 2.54540 ( 165) link_ALPHA1-3 : bond 0.01301 ( 11) link_ALPHA1-3 : angle 2.51014 ( 33) hydrogen bonds : bond 0.02994 ( 198) hydrogen bonds : angle 6.28466 ( 501) link_BETA1-6 : bond 0.00685 ( 12) link_BETA1-6 : angle 1.63501 ( 36) SS BOND : bond 0.00409 ( 60) SS BOND : angle 1.25917 ( 120) covalent geometry : bond 0.00389 (10108) covalent geometry : angle 0.91709 (13793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (t0) REVERT: A 4792 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 4931 MET cc_start: 0.6139 (mmp) cc_final: 0.3788 (tmm) REVERT: B 4375 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8548 (p) REVERT: B 4816 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8683 (p0) REVERT: B 4870 TRP cc_start: 0.7971 (p-90) cc_final: 0.7723 (t60) outliers start: 29 outliers final: 19 residues processed: 64 average time/residue: 0.1647 time to fit residues: 16.9740 Evaluate side-chains 61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4459 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4920 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4375 THR Chi-restraints excluded: chain B residue 4376 TRP Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4774 VAL Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4816 ASP Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.104471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.071753 restraints weight = 43024.603| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.35 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10291 Z= 0.184 Angle : 0.990 22.805 14282 Z= 0.408 Chirality : 0.053 0.421 1897 Planarity : 0.004 0.043 1605 Dihedral : 15.111 114.315 3620 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.87 % Allowed : 17.11 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.26), residues: 1076 helix: 1.97 (0.67), residues: 73 sheet: 0.59 (0.36), residues: 205 loop : -1.74 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A4870 HIS 0.004 0.001 HIS B4704 PHE 0.012 0.001 PHE A4854 TYR 0.014 0.001 TYR B4388 ARG 0.005 0.000 ARG A4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00907 ( 16) link_NAG-ASN : angle 3.92946 ( 48) link_ALPHA1-6 : bond 0.01166 ( 10) link_ALPHA1-6 : angle 2.11701 ( 30) link_BETA1-2 : bond 0.00841 ( 19) link_BETA1-2 : angle 1.68132 ( 57) link_BETA1-4 : bond 0.00781 ( 55) link_BETA1-4 : angle 2.48677 ( 165) link_ALPHA1-3 : bond 0.01263 ( 11) link_ALPHA1-3 : angle 2.51581 ( 33) hydrogen bonds : bond 0.03177 ( 198) hydrogen bonds : angle 6.25159 ( 501) link_BETA1-6 : bond 0.00677 ( 12) link_BETA1-6 : angle 1.66851 ( 36) SS BOND : bond 0.00432 ( 60) SS BOND : angle 1.35634 ( 120) covalent geometry : bond 0.00411 (10108) covalent geometry : angle 0.90966 (13793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4675 MET cc_start: 0.8863 (ptp) cc_final: 0.8263 (mpp) REVERT: A 4760 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7893 (t0) REVERT: A 4792 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8600 (pp) REVERT: A 4931 MET cc_start: 0.6189 (mmp) cc_final: 0.3816 (tmm) REVERT: B 4375 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 4816 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8685 (p0) REVERT: B 4870 TRP cc_start: 0.8003 (p-90) cc_final: 0.7748 (t60) outliers start: 28 outliers final: 20 residues processed: 62 average time/residue: 0.1615 time to fit residues: 16.1293 Evaluate side-chains 61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4459 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4891 TYR Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4920 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4375 THR Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4774 VAL Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4816 ASP Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.105692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073248 restraints weight = 43320.539| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 5.43 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10291 Z= 0.171 Angle : 0.992 21.161 14282 Z= 0.409 Chirality : 0.053 0.430 1897 Planarity : 0.004 0.043 1605 Dihedral : 14.755 114.150 3620 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.36 % Allowed : 17.52 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.33 (0.26), residues: 1076 helix: 1.96 (0.67), residues: 73 sheet: 0.70 (0.36), residues: 199 loop : -1.73 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A4870 HIS 0.004 0.001 HIS B4704 PHE 0.014 0.001 PHE A4854 TYR 0.014 0.001 TYR A4884 ARG 0.005 0.001 ARG A4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 16) link_NAG-ASN : angle 3.94612 ( 48) link_ALPHA1-6 : bond 0.01155 ( 10) link_ALPHA1-6 : angle 2.06275 ( 30) link_BETA1-2 : bond 0.00844 ( 19) link_BETA1-2 : angle 1.67725 ( 57) link_BETA1-4 : bond 0.00783 ( 55) link_BETA1-4 : angle 2.44529 ( 165) link_ALPHA1-3 : bond 0.01289 ( 11) link_ALPHA1-3 : angle 2.48668 ( 33) hydrogen bonds : bond 0.02966 ( 198) hydrogen bonds : angle 6.03018 ( 501) link_BETA1-6 : bond 0.00709 ( 12) link_BETA1-6 : angle 1.63795 ( 36) SS BOND : bond 0.00464 ( 60) SS BOND : angle 1.59677 ( 120) covalent geometry : bond 0.00379 (10108) covalent geometry : angle 0.91002 (13793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4675 MET cc_start: 0.8831 (ptp) cc_final: 0.8264 (mpp) REVERT: A 4753 MET cc_start: 0.9063 (ttm) cc_final: 0.8843 (ptm) REVERT: A 4760 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 4792 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 4931 MET cc_start: 0.6147 (mmp) cc_final: 0.3697 (tmm) REVERT: B 4375 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 4870 TRP cc_start: 0.8067 (p-90) cc_final: 0.7806 (t60) outliers start: 23 outliers final: 19 residues processed: 59 average time/residue: 0.2229 time to fit residues: 20.4899 Evaluate side-chains 59 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4459 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4760 ASP Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4920 CYS Chi-restraints excluded: chain A residue 4928 PHE Chi-restraints excluded: chain B residue 4375 THR Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4774 VAL Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.106288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073747 restraints weight = 44030.548| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 5.47 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10291 Z= 0.167 Angle : 0.985 19.611 14282 Z= 0.404 Chirality : 0.052 0.441 1897 Planarity : 0.005 0.086 1605 Dihedral : 14.384 113.611 3620 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.46 % Allowed : 17.11 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.33 (0.26), residues: 1076 helix: 1.99 (0.67), residues: 73 sheet: 0.70 (0.36), residues: 199 loop : -1.73 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B4376 HIS 0.004 0.001 HIS B4704 PHE 0.014 0.001 PHE A4854 TYR 0.016 0.001 TYR A4884 ARG 0.015 0.001 ARG B4804 Details of bonding type rmsd link_NAG-ASN : bond 0.00910 ( 16) link_NAG-ASN : angle 3.89857 ( 48) link_ALPHA1-6 : bond 0.01146 ( 10) link_ALPHA1-6 : angle 2.04439 ( 30) link_BETA1-2 : bond 0.00833 ( 19) link_BETA1-2 : angle 1.66804 ( 57) link_BETA1-4 : bond 0.00782 ( 55) link_BETA1-4 : angle 2.41555 ( 165) link_ALPHA1-3 : bond 0.01229 ( 11) link_ALPHA1-3 : angle 2.44918 ( 33) hydrogen bonds : bond 0.02904 ( 198) hydrogen bonds : angle 6.01722 ( 501) link_BETA1-6 : bond 0.00748 ( 12) link_BETA1-6 : angle 1.64458 ( 36) SS BOND : bond 0.00436 ( 60) SS BOND : angle 1.45362 ( 120) covalent geometry : bond 0.00365 (10108) covalent geometry : angle 0.90583 (13793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.61 seconds wall clock time: 122 minutes 17.38 seconds (7337.38 seconds total)