Starting phenix.real_space_refine on Thu Jul 2 20:55:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_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_2026/7qcl_13896.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.cif" model { file = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qcl_13896/07_2026/7qcl_13896.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 2.17, per 1000 atoms: 0.22 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: 1.77 Conformation dependent library (CDL) restraints added in 311.3 milliseconds 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: 0.29 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: 1.39 Time building geometry restraints manager: 2.05 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 - 17.99: 4737 17.99 - 35.98: 404 35.98 - 53.97: 133 53.97 - 71.96: 38 71.96 - 89.94: 22 Dihedral angle restraints: 5334 sinusoidal: 2158 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 5331 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: 22.000 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: 0.220 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 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 : 15.237 86.466 3110 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 36.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (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 ARG 0.018 0.001 ARG B4804 TYR 0.016 0.001 TYR A4869 PHE 0.018 0.002 PHE A4928 TRP 0.024 0.003 TRP A4424 HIS 0.013 0.001 HIS A4425 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.70 (10108) covalent geometry : angle 1.77778 / 1.12 (13793) SS BOND : bond 0.04076 / 2.97 ( 60) SS BOND : angle 5.45110 / 4.15 ( 120) hydrogen bonds : bond 0.17228 / 11.18 ( 198) hydrogen bonds : angle 8.39968 / 5.73 ( 501) link_ALPHA1-3 : bond 0.00478 / 0.27 ( 11) link_ALPHA1-3 : angle 3.11335 / 2.02 ( 33) link_ALPHA1-6 : bond 0.00658 / 0.39 ( 10) link_ALPHA1-6 : angle 2.71753 / 1.56 ( 30) link_BETA1-2 : bond 0.00497 / 0.26 ( 19) link_BETA1-2 : angle 2.89439 / 1.87 ( 57) link_BETA1-4 : bond 0.00532 / 0.33 ( 55) link_BETA1-4 : angle 2.43408 / 1.75 ( 165) link_BETA1-6 : bond 0.00317 / 0.20 ( 12) link_BETA1-6 : angle 1.84587 / 1.27 ( 36) link_NAG-ASN : bond 0.02441 / 1.74 ( 16) link_NAG-ASN : angle 10.70748 / 7.30 ( 48) *********************** 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 : 0.363 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: 0.4553 (t) outliers start: 65 outliers final: 26 residues processed: 127 average time/residue: 0.0870 time to fit residues: 16.1742 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 : 0.350 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.104451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073034 restraints weight = 43644.201| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 5.80 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 10291 Z= 0.272 Angle : 1.307 27.724 14282 Z= 0.547 Chirality : 0.063 0.525 1897 Planarity : 0.006 0.064 1605 Dihedral : 9.697 85.293 1200 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.59 % Allowed : 11.27 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.25), residues: 1076 helix: 1.98 (0.67), residues: 74 sheet: 0.29 (0.36), residues: 204 loop : -1.97 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B4864 TYR 0.053 0.002 TYR A4891 PHE 0.020 0.002 PHE A4854 TRP 0.032 0.002 TRP A4376 HIS 0.006 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (10108) covalent geometry : angle 1.20673 / 0.52 (13793) SS BOND : bond 0.00469 / 0.30 ( 60) SS BOND : angle 2.27841 / 1.51 ( 120) hydrogen bonds : bond 0.04338 / 2.72 ( 198) hydrogen bonds : angle 7.34879 / 4.99 ( 501) link_ALPHA1-3 : bond 0.01306 / 0.82 ( 11) link_ALPHA1-3 : angle 3.19173 / 2.32 ( 33) link_ALPHA1-6 : bond 0.01022 / 0.69 ( 10) link_ALPHA1-6 : angle 2.02972 / 1.21 ( 30) link_BETA1-2 : bond 0.01007 / 0.63 ( 19) link_BETA1-2 : angle 1.76978 / 1.25 ( 57) link_BETA1-4 : bond 0.00972 / 0.58 ( 55) link_BETA1-4 : angle 2.67399 / 2.03 ( 165) link_BETA1-6 : bond 0.00788 / 0.53 ( 12) link_BETA1-6 : angle 1.70128 / 1.14 ( 36) link_NAG-ASN : bond 0.02273 / 1.53 ( 16) link_NAG-ASN : angle 6.09233 / 3.80 ( 48) *********************** 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 80 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 0.358 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 4376 TRP cc_start: 0.8818 (t60) cc_final: 0.8461 (t60) REVERT: A 4852 LEU cc_start: 0.8198 (mt) cc_final: 0.7960 (mt) REVERT: A 4924 CYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4460 (m) outliers start: 35 outliers final: 27 residues processed: 78 average time/residue: 0.0877 time to fit residues: 10.3715 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 : 0.358 ------------------------------------------------------------------------------- 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 4890 VAL 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 A residue 4924 CYS Chi-restraints excluded: chain A residue 4941 CYS 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 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Chi-restraints excluded: chain B residue 4940 LYS 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 99 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4193 r_free = 0.4193 target = 0.105023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.073658 restraints weight = 43129.433| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 5.95 r_work: 0.3009 rms_B_bonded: 5.85 restraints_weight: 2.0000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2484 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= 0.200 Angle : 1.110 29.436 14282 Z= 0.459 Chirality : 0.056 0.484 1897 Planarity : 0.005 0.051 1605 Dihedral : 8.572 88.834 1175 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.69 % Allowed : 13.11 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.26), residues: 1076 helix: 2.24 (0.67), residues: 71 sheet: 0.38 (0.35), residues: 208 loop : -1.83 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4804 TYR 0.041 0.002 TYR A4891 PHE 0.010 0.001 PHE A4854 TRP 0.025 0.002 TRP A4870 HIS 0.003 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (10108) covalent geometry : angle 1.03241 / 0.44 (13793) SS BOND : bond 0.00473 / 0.32 ( 60) SS BOND : angle 1.62098 / 1.08 ( 120) hydrogen bonds : bond 0.03448 / 2.16 ( 198) hydrogen bonds : angle 6.99891 / 4.76 ( 501) link_ALPHA1-3 : bond 0.01206 / 0.76 ( 11) link_ALPHA1-3 : angle 2.67458 / 1.95 ( 33) link_ALPHA1-6 : bond 0.00944 / 0.62 ( 10) link_ALPHA1-6 : angle 1.94352 / 1.13 ( 30) link_BETA1-2 : bond 0.00845 / 0.53 ( 19) link_BETA1-2 : angle 1.42663 / 1.00 ( 57) link_BETA1-4 : bond 0.00939 / 0.58 ( 55) link_BETA1-4 : angle 2.52403 / 1.90 ( 165) link_BETA1-6 : bond 0.00627 / 0.42 ( 12) link_BETA1-6 : angle 1.63517 / 1.09 ( 36) link_NAG-ASN : bond 0.01181 / 0.76 ( 16) link_NAG-ASN : angle 4.52212 / 3.07 ( 48) *********************** 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 : 0.353 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: A 4675 MET cc_start: 0.8891 (ptp) cc_final: 0.8648 (ptp) REVERT: B 4870 TRP cc_start: 0.8463 (p-90) cc_final: 0.8105 (p-90) outliers start: 36 outliers final: 25 residues processed: 80 average time/residue: 0.0707 time to fit residues: 9.0013 Evaluate side-chains 63 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 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 A residue 4941 CYS Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4352 CYS Chi-restraints excluded: chain B residue 4388 TYR 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 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 4940 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.0020 chunk 19 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 0.0670 overall best weight: 0.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4512 GLN B4552 ASN B4686 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.105981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.074481 restraints weight = 43631.710| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.88 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10291 Z= 0.171 Angle : 1.056 31.358 14282 Z= 0.429 Chirality : 0.055 0.455 1897 Planarity : 0.005 0.049 1605 Dihedral : 8.091 98.954 1173 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.92 % Favored : 90.99 % Rotamer: Outliers : 3.28 % Allowed : 14.34 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.26), residues: 1076 helix: 2.10 (0.66), residues: 71 sheet: 0.41 (0.35), residues: 205 loop : -1.80 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4804 TYR 0.035 0.001 TYR A4891 PHE 0.030 0.001 PHE A4854 TRP 0.016 0.002 TRP A4376 HIS 0.004 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10108) covalent geometry : angle 0.98528 / 0.41 (13793) SS BOND : bond 0.00424 / 0.28 ( 60) SS BOND : angle 1.24257 / 0.81 ( 120) hydrogen bonds : bond 0.02744 / 1.70 ( 198) hydrogen bonds : angle 6.64280 / 4.56 ( 501) link_ALPHA1-3 : bond 0.01221 / 0.77 ( 11) link_ALPHA1-3 : angle 2.41089 / 1.70 ( 33) link_ALPHA1-6 : bond 0.00943 / 0.62 ( 10) link_ALPHA1-6 : angle 1.85564 / 1.09 ( 30) link_BETA1-2 : bond 0.00801 / 0.50 ( 19) link_BETA1-2 : angle 1.42697 / 0.98 ( 57) link_BETA1-4 : bond 0.00912 / 0.57 ( 55) link_BETA1-4 : angle 2.43472 / 1.83 ( 165) link_BETA1-6 : bond 0.00597 / 0.39 ( 12) link_BETA1-6 : angle 1.51943 / 1.00 ( 36) link_NAG-ASN : bond 0.01138 / 0.71 ( 16) link_NAG-ASN : angle 4.30986 / 2.93 ( 48) *********************** 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 75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 43 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4675 MET cc_start: 0.8815 (ptp) cc_final: 0.8536 (ptp) outliers start: 32 outliers final: 23 residues processed: 70 average time/residue: 0.0838 time to fit residues: 8.8709 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 : 0.342 ------------------------------------------------------------------------------- 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 4906 ASN 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 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 4840 THR Chi-restraints excluded: chain B residue 4859 LYS Chi-restraints excluded: chain B residue 4869 TYR 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 Chi-restraints excluded: chain B residue 4940 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4917 HIS B4552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.105323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.073554 restraints weight = 42867.724| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 5.69 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10291 Z= 0.186 Angle : 1.002 24.325 14282 Z= 0.415 Chirality : 0.053 0.440 1897 Planarity : 0.005 0.050 1605 Dihedral : 6.997 63.385 1166 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.97 % Allowed : 14.75 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.26), residues: 1076 helix: 2.23 (0.67), residues: 71 sheet: 0.71 (0.36), residues: 191 loop : -1.79 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B4804 TYR 0.022 0.001 TYR A4891 PHE 0.032 0.001 PHE B4854 TRP 0.028 0.002 TRP A4376 HIS 0.005 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10108) covalent geometry : angle 0.93271 / 0.40 (13793) SS BOND : bond 0.00475 / 0.30 ( 60) SS BOND : angle 1.27120 / 0.83 ( 120) hydrogen bonds : bond 0.03243 / 2.00 ( 198) hydrogen bonds : angle 6.48673 / 4.45 ( 501) link_ALPHA1-3 : bond 0.01160 / 0.74 ( 11) link_ALPHA1-3 : angle 2.14766 / 1.36 ( 33) link_ALPHA1-6 : bond 0.00892 / 0.59 ( 10) link_ALPHA1-6 : angle 1.79304 / 1.06 ( 30) link_BETA1-2 : bond 0.00691 / 0.41 ( 19) link_BETA1-2 : angle 1.35224 / 0.91 ( 57) link_BETA1-4 : bond 0.00861 / 0.54 ( 55) link_BETA1-4 : angle 2.32397 / 1.74 ( 165) link_BETA1-6 : bond 0.00529 / 0.35 ( 12) link_BETA1-6 : angle 1.56728 / 1.04 ( 36) link_NAG-ASN : bond 0.00968 / 0.59 ( 16) link_NAG-ASN : angle 4.13634 / 2.75 ( 48) *********************** 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 71 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4929 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6476 (mm-30) outliers start: 29 outliers final: 21 residues processed: 67 average time/residue: 0.0839 time to fit residues: 8.6371 Evaluate side-chains 60 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 4814 VAL Chi-restraints excluded: chain B residue 4859 LYS Chi-restraints excluded: chain B residue 4869 TYR Chi-restraints excluded: chain B residue 4878 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Chi-restraints excluded: chain B residue 4940 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.104864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.072931 restraints weight = 43262.582| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 6.00 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3375 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= 0.189 Angle : 0.988 22.982 14282 Z= 0.412 Chirality : 0.052 0.436 1897 Planarity : 0.005 0.060 1605 Dihedral : 6.628 59.757 1164 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.18 % Allowed : 15.47 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.25), residues: 1076 helix: 1.89 (0.65), residues: 77 sheet: 0.94 (0.37), residues: 183 loop : -1.85 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A4804 TYR 0.014 0.001 TYR A4884 PHE 0.020 0.001 PHE B4854 TRP 0.030 0.002 TRP B4377 HIS 0.004 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (10108) covalent geometry : angle 0.92134 / 0.39 (13793) SS BOND : bond 0.00398 / 0.28 ( 60) SS BOND : angle 1.27690 / 0.84 ( 120) hydrogen bonds : bond 0.03277 / 2.00 ( 198) hydrogen bonds : angle 6.40839 / 4.42 ( 501) link_ALPHA1-3 : bond 0.01063 / 0.66 ( 11) link_ALPHA1-3 : angle 2.13275 / 1.38 ( 33) link_ALPHA1-6 : bond 0.00875 / 0.57 ( 10) link_ALPHA1-6 : angle 1.78954 / 1.06 ( 30) link_BETA1-2 : bond 0.00698 / 0.42 ( 19) link_BETA1-2 : angle 1.34449 / 0.91 ( 57) link_BETA1-4 : bond 0.00840 / 0.53 ( 55) link_BETA1-4 : angle 2.25235 / 1.70 ( 165) link_BETA1-6 : bond 0.00517 / 0.34 ( 12) link_BETA1-6 : angle 1.53234 / 1.01 ( 36) link_NAG-ASN : bond 0.00947 / 0.58 ( 16) link_NAG-ASN : angle 3.98598 / 2.62 ( 48) *********************** 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 70 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7861 (t0) REVERT: A 4860 MET cc_start: 0.6789 (mmp) cc_final: 0.6470 (mmm) outliers start: 31 outliers final: 23 residues processed: 67 average time/residue: 0.0741 time to fit residues: 7.8439 Evaluate side-chains 62 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 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 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4866 CYS Chi-restraints excluded: chain B residue 4869 TYR 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 Chi-restraints excluded: chain B residue 4940 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.099847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066389 restraints weight = 43865.553| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.96 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10291 Z= 0.187 Angle : 0.957 21.211 14282 Z= 0.401 Chirality : 0.051 0.433 1897 Planarity : 0.005 0.043 1605 Dihedral : 6.575 57.869 1160 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.28 % Allowed : 16.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.25), residues: 1076 helix: 2.14 (0.68), residues: 71 sheet: 0.92 (0.36), residues: 193 loop : -1.77 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A4804 TYR 0.016 0.001 TYR A4884 PHE 0.015 0.001 PHE B4854 TRP 0.041 0.002 TRP A4376 HIS 0.005 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (10108) covalent geometry : angle 0.89306 / 0.39 (13793) SS BOND : bond 0.00384 / 0.27 ( 60) SS BOND : angle 1.19592 / 0.79 ( 120) hydrogen bonds : bond 0.03278 / 2.01 ( 198) hydrogen bonds : angle 6.31051 / 4.35 ( 501) link_ALPHA1-3 : bond 0.01013 / 0.63 ( 11) link_ALPHA1-3 : angle 2.04639 / 1.32 ( 33) link_ALPHA1-6 : bond 0.00853 / 0.55 ( 10) link_ALPHA1-6 : angle 1.74169 / 1.04 ( 30) link_BETA1-2 : bond 0.00686 / 0.42 ( 19) link_BETA1-2 : angle 1.29339 / 0.87 ( 57) link_BETA1-4 : bond 0.00820 / 0.52 ( 55) link_BETA1-4 : angle 2.17483 / 1.64 ( 165) link_BETA1-6 : bond 0.00490 / 0.32 ( 12) link_BETA1-6 : angle 1.52674 / 1.01 ( 36) link_NAG-ASN : bond 0.00895 / 0.54 ( 16) link_NAG-ASN : angle 3.86875 / 2.50 ( 48) *********************** 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 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 41 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7736 (t0) REVERT: A 4792 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8550 (pp) REVERT: A 4860 MET cc_start: 0.6150 (mmp) cc_final: 0.5947 (mmm) REVERT: B 4816 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8643 (p0) outliers start: 32 outliers final: 21 residues processed: 71 average time/residue: 0.0809 time to fit residues: 9.0009 Evaluate side-chains 57 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 4457 VAL Chi-restraints excluded: chain B residue 4522 LEU 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 4866 CYS 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 Chi-restraints excluded: chain B residue 4940 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.099590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.066909 restraints weight = 43539.588| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.73 r_work: 0.2997 rms_B_bonded: 5.70 restraints_weight: 2.0000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3819 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= 0.192 Angle : 0.954 21.875 14282 Z= 0.400 Chirality : 0.051 0.427 1897 Planarity : 0.005 0.043 1605 Dihedral : 6.825 74.280 1160 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.07 % Allowed : 16.19 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.26), residues: 1076 helix: 1.97 (0.67), residues: 73 sheet: 0.66 (0.36), residues: 205 loop : -1.73 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A4804 TYR 0.018 0.001 TYR A4884 PHE 0.023 0.001 PHE B4854 TRP 0.038 0.003 TRP A4870 HIS 0.004 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10108) covalent geometry : angle 0.89119 / 0.38 (13793) SS BOND : bond 0.00462 / 0.29 ( 60) SS BOND : angle 1.22297 / 0.81 ( 120) hydrogen bonds : bond 0.03301 / 2.02 ( 198) hydrogen bonds : angle 6.16705 / 4.25 ( 501) link_ALPHA1-3 : bond 0.00989 / 0.62 ( 11) link_ALPHA1-3 : angle 2.05614 / 1.34 ( 33) link_ALPHA1-6 : bond 0.00839 / 0.54 ( 10) link_ALPHA1-6 : angle 1.72780 / 1.04 ( 30) link_BETA1-2 : bond 0.00673 / 0.41 ( 19) link_BETA1-2 : angle 1.27935 / 0.86 ( 57) link_BETA1-4 : bond 0.00805 / 0.51 ( 55) link_BETA1-4 : angle 2.15072 / 1.62 ( 165) link_BETA1-6 : bond 0.00483 / 0.31 ( 12) link_BETA1-6 : angle 1.51158 / 1.00 ( 36) link_NAG-ASN : bond 0.00874 / 0.53 ( 16) link_NAG-ASN : angle 3.79252 / 2.45 ( 48) *********************** 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 66 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 36 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8215 (t0) REVERT: A 4792 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8652 (pp) REVERT: A 4931 MET cc_start: 0.6315 (mmp) cc_final: 0.4195 (tmm) REVERT: B 4816 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8576 (p0) outliers start: 30 outliers final: 22 residues processed: 64 average time/residue: 0.0729 time to fit residues: 7.6126 Evaluate side-chains 59 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 4877 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 4928 PHE 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 4840 THR Chi-restraints excluded: chain B residue 4866 CYS 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 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.105194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.072677 restraints weight = 42819.180| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 5.37 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10291 Z= 0.158 Angle : 0.944 22.514 14282 Z= 0.394 Chirality : 0.050 0.433 1897 Planarity : 0.004 0.043 1605 Dihedral : 6.612 74.662 1160 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.66 % Allowed : 16.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.25), residues: 1076 helix: 1.91 (0.66), residues: 73 sheet: 0.98 (0.37), residues: 188 loop : -1.77 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4804 TYR 0.018 0.001 TYR A4884 PHE 0.024 0.001 PHE B4854 TRP 0.030 0.002 TRP B4870 HIS 0.004 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10108) covalent geometry : angle 0.88255 / 0.38 (13793) SS BOND : bond 0.00424 / 0.31 ( 60) SS BOND : angle 1.20108 / 0.76 ( 120) hydrogen bonds : bond 0.02840 / 1.74 ( 198) hydrogen bonds : angle 6.01012 / 4.15 ( 501) link_ALPHA1-3 : bond 0.00990 / 0.62 ( 11) link_ALPHA1-3 : angle 1.97864 / 1.29 ( 33) link_ALPHA1-6 : bond 0.00853 / 0.55 ( 10) link_ALPHA1-6 : angle 1.68967 / 1.01 ( 30) link_BETA1-2 : bond 0.00689 / 0.43 ( 19) link_BETA1-2 : angle 1.26849 / 0.85 ( 57) link_BETA1-4 : bond 0.00819 / 0.52 ( 55) link_BETA1-4 : angle 2.13804 / 1.61 ( 165) link_BETA1-6 : bond 0.00492 / 0.32 ( 12) link_BETA1-6 : angle 1.43915 / 0.94 ( 36) link_NAG-ASN : bond 0.00854 / 0.52 ( 16) link_NAG-ASN : angle 3.74270 / 2.41 ( 48) *********************** 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: 26 poor density : 40 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 4792 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8518 (pp) REVERT: A 4931 MET cc_start: 0.6007 (mmp) cc_final: 0.3679 (tmm) REVERT: B 4816 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8679 (p0) REVERT: B 4870 TRP cc_start: 0.7821 (p-90) cc_final: 0.7574 (t60) outliers start: 26 outliers final: 21 residues processed: 63 average time/residue: 0.0699 time to fit residues: 7.2573 Evaluate side-chains 62 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 4877 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 4928 PHE 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 4675 MET 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 4866 CYS 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 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.104383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071518 restraints weight = 42805.247| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 5.39 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 10291 Z= 0.196 Angle : 0.954 18.155 14282 Z= 0.402 Chirality : 0.051 0.430 1897 Planarity : 0.004 0.042 1605 Dihedral : 6.756 77.428 1160 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.36 % Allowed : 17.42 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 1076 helix: 2.00 (0.67), residues: 73 sheet: 0.73 (0.37), residues: 200 loop : -1.78 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A4804 TYR 0.034 0.001 TYR A4869 PHE 0.025 0.001 PHE A4854 TRP 0.042 0.002 TRP B4376 HIS 0.004 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (10108) covalent geometry : angle 0.89195 / 0.39 (13793) SS BOND : bond 0.00535 / 0.39 ( 60) SS BOND : angle 1.45624 / 0.92 ( 120) hydrogen bonds : bond 0.03352 / 2.05 ( 198) hydrogen bonds : angle 6.08333 / 4.19 ( 501) link_ALPHA1-3 : bond 0.00944 / 0.59 ( 11) link_ALPHA1-3 : angle 2.00652 / 1.31 ( 33) link_ALPHA1-6 : bond 0.00807 / 0.52 ( 10) link_ALPHA1-6 : angle 1.68739 / 1.02 ( 30) link_BETA1-2 : bond 0.00644 / 0.39 ( 19) link_BETA1-2 : angle 1.23736 / 0.83 ( 57) link_BETA1-4 : bond 0.00784 / 0.50 ( 55) link_BETA1-4 : angle 2.09746 / 1.58 ( 165) link_BETA1-6 : bond 0.00458 / 0.30 ( 12) link_BETA1-6 : angle 1.50822 / 1.00 ( 36) link_NAG-ASN : bond 0.00857 / 0.52 ( 16) link_NAG-ASN : angle 3.66765 / 2.35 ( 48) ********************** 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 64 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4760 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7857 (t0) REVERT: A 4792 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8626 (pp) REVERT: A 4931 MET cc_start: 0.6202 (mmp) cc_final: 0.3800 (tmm) REVERT: B 4377 TRP cc_start: 0.7619 (t60) cc_final: 0.7298 (t60) REVERT: B 4816 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8758 (p0) REVERT: B 4870 TRP cc_start: 0.7870 (p-90) cc_final: 0.7608 (t60) outliers start: 23 outliers final: 19 residues processed: 62 average time/residue: 0.0828 time to fit residues: 7.8645 Evaluate side-chains 61 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 4877 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 4928 PHE 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 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 106 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 57 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.106530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.073932 restraints weight = 43997.406| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 5.53 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10291 Z= 0.160 Angle : 0.922 14.857 14282 Z= 0.386 Chirality : 0.050 0.436 1897 Planarity : 0.005 0.090 1605 Dihedral : 6.594 77.545 1160 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.46 % Allowed : 17.32 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 1076 helix: 1.90 (0.66), residues: 73 sheet: 0.70 (0.36), residues: 199 loop : -1.75 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B4804 TYR 0.030 0.001 TYR A4869 PHE 0.034 0.001 PHE A4854 TRP 0.031 0.002 TRP B4376 HIS 0.005 0.001 HIS B4704 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10108) covalent geometry : angle 0.86120 / 0.37 (13793) SS BOND : bond 0.00417 / 0.30 ( 60) SS BOND : angle 1.26817 / 0.79 ( 120) hydrogen bonds : bond 0.02799 / 1.71 ( 198) hydrogen bonds : angle 5.93080 / 4.10 ( 501) link_ALPHA1-3 : bond 0.00966 / 0.61 ( 11) link_ALPHA1-3 : angle 1.94182 / 1.27 ( 33) link_ALPHA1-6 : bond 0.00828 / 0.52 ( 10) link_ALPHA1-6 : angle 1.65022 / 0.99 ( 30) link_BETA1-2 : bond 0.00670 / 0.41 ( 19) link_BETA1-2 : angle 1.22263 / 0.82 ( 57) link_BETA1-4 : bond 0.00798 / 0.51 ( 55) link_BETA1-4 : angle 2.08194 / 1.56 ( 165) link_BETA1-6 : bond 0.00472 / 0.30 ( 12) link_BETA1-6 : angle 1.41527 / 0.92 ( 36) link_NAG-ASN : bond 0.00832 / 0.50 ( 16) link_NAG-ASN : angle 3.61614 / 2.30 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.98 seconds wall clock time: 50 minutes 13.98 seconds (3013.98 seconds total)