Starting phenix.real_space_refine on Wed Feb 14 17:39:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_13896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_13896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_13896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_13896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qcl_13896/02_2024/7qcl_13896_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 140 5.16 5 C 6064 2.51 5 N 1437 2.21 5 O 2241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4819": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9884 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4177 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 501} Chain breaks: 3 Chain: "B" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4177 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 501} Chain breaks: 3 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 171 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 4, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {'BMA': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 146 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "Q" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.87, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 6.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 13 sheets defined 8.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 4580 through 4582 No H-bonds generated for 'chain 'A' and resid 4580 through 4582' Processing helix chain 'A' and resid 4595 through 4601 removed outlier: 3.539A pdb=" N ASP A4600 " --> pdb=" O GLU A4596 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A4601 " --> pdb=" O ALA A4597 " (cutoff:3.500A) Processing helix chain 'A' and resid 4642 through 4648 removed outlier: 4.519A pdb=" N ILE A4647 " --> pdb=" O LEU A4643 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS A4648 " --> pdb=" O CYS A4644 " (cutoff:3.500A) Processing helix chain 'A' and resid 4650 through 4656 removed outlier: 4.621A pdb=" N GLN A4654 " --> pdb=" O LEU A4651 " (cutoff:3.500A) Processing helix chain 'A' and resid 4662 through 4674 Processing helix chain 'A' and resid 4684 through 4695 Processing helix chain 'A' and resid 4908 through 4911 No H-bonds generated for 'chain 'A' and resid 4908 through 4911' Processing helix chain 'B' and resid 4595 through 4600 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) No H-bonds generated for 'chain 'B' and resid 4595 through 4600' Processing helix chain 'B' and resid 4642 through 4647 removed outlier: 3.545A pdb=" N LEU B4646 " --> pdb=" O PRO B4642 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE B4647 " --> pdb=" O LEU B4643 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4642 through 4647' Processing helix chain 'B' and resid 4662 through 4674 Processing helix chain 'B' and resid 4684 through 4694 Processing helix chain 'B' and resid 4702 through 4705 Processing helix chain 'B' and resid 4908 through 4911 No H-bonds generated for 'chain 'B' and resid 4908 through 4911' Processing sheet with id= A, first strand: chain 'A' and resid 4382 through 4385 Processing sheet with id= B, first strand: chain 'A' and resid 4414 through 4417 Processing sheet with id= C, first strand: chain 'A' and resid 4430 through 4435 removed outlier: 3.655A pdb=" N VAL A4547 " --> pdb=" O ILE A4542 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 4439 through 4441 Processing sheet with id= E, first strand: chain 'A' and resid 4509 through 4512 removed outlier: 3.845A pdb=" N VAL A4459 " --> pdb=" O VAL A4471 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A4473 " --> pdb=" O VAL A4457 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL A4457 " --> pdb=" O ILE A4473 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 4717 through 4720 Processing sheet with id= G, 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= H, first strand: chain 'B' and resid 4414 through 4417 Processing sheet with id= I, first strand: chain 'B' and resid 4447 through 4449 Processing sheet with id= J, first strand: chain 'B' and resid 4509 through 4512 removed outlier: 5.827A pdb=" N ILE B4473 " --> pdb=" O VAL B4457 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL B4457 " --> pdb=" O ILE B4473 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 4717 through 4720 Processing sheet with id= L, first strand: chain 'B' and resid 4780 through 4782 Processing sheet with id= M, first strand: chain 'B' and resid 4818 through 4822 171 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 6.92 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: 92.83 - 101.28: 41 101.28 - 109.72: 2246 109.72 - 118.17: 6533 118.17 - 126.61: 4823 126.61 - 135.06: 150 Bond angle restraints: 13793 Sorted by residual: angle pdb=" N GLY A4927 " pdb=" CA GLY A4927 " pdb=" C GLY A4927 " ideal model delta sigma weight residual 113.58 100.81 12.77 1.07e+00 8.73e-01 1.42e+02 angle pdb=" N VAL A4904 " pdb=" CA VAL A4904 " pdb=" C VAL A4904 " ideal model delta sigma weight residual 110.74 120.37 -9.63 9.10e-01 1.21e+00 1.12e+02 angle pdb=" N ASN B4825 " pdb=" CA ASN B4825 " pdb=" C ASN B4825 " ideal model delta sigma weight residual 109.42 94.11 15.31 1.48e+00 4.57e-01 1.07e+02 angle pdb=" N VAL A4904 " pdb=" CA VAL A4904 " pdb=" CB VAL A4904 " ideal model delta sigma weight residual 110.64 98.46 12.18 1.20e+00 6.94e-01 1.03e+02 angle pdb=" N LYS B4844 " pdb=" CA LYS B4844 " pdb=" C LYS B4844 " ideal model delta sigma weight residual 111.36 122.14 -10.78 1.09e+00 8.42e-01 9.78e+01 ... (remaining 13788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6988 23.98 - 47.97: 446 47.97 - 71.95: 82 71.95 - 95.93: 90 95.93 - 119.92: 189 Dihedral angle restraints: 7795 sinusoidal: 4619 harmonic: 3176 Sorted by residual: dihedral pdb=" CB CYS A4682 " pdb=" SG CYS A4682 " pdb=" SG CYS A4709 " pdb=" CB CYS A4709 " ideal model delta sinusoidal sigma weight residual 93.00 -177.06 -89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS B4713 " pdb=" SG CYS B4713 " pdb=" SG CYS B4746 " pdb=" CB CYS B4746 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A4399 " pdb=" SG CYS A4399 " pdb=" SG CYS A4423 " pdb=" CB CYS A4423 " ideal model delta sinusoidal sigma weight residual -86.00 -172.39 86.39 1 1.00e+01 1.00e-02 9.00e+01 ... (remaining 7792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 1727 0.198 - 0.396: 146 0.396 - 0.594: 17 0.594 - 0.791: 3 0.791 - 0.989: 4 Chirality restraints: 1897 Sorted by residual: chirality pdb=" C1 NAG D 5 " pdb=" O2 MAN D 4 " pdb=" C2 NAG D 5 " pdb=" O5 NAG D 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.45e+03 chirality pdb=" C1 NAG L 5 " pdb=" O2 MAN L 4 " pdb=" C2 NAG L 5 " pdb=" O5 NAG L 5 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-02 2.50e+03 2.35e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.74e+03 ... (remaining 1894 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.355 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG I 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 5 " -0.355 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG Q 5 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG Q 5 " -0.142 2.00e-02 2.50e+03 pdb=" N2 NAG Q 5 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG Q 5 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG I 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.127 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 47 2.43 - 3.05: 7493 3.05 - 3.67: 15070 3.67 - 4.28: 22373 4.28 - 4.90: 33449 Nonbonded interactions: 78432 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 78427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 12.250 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: 40.450 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 31.650 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.070 10108 Z= 0.660 Angle : 1.778 16.850 13793 Z= 1.124 Chirality : 0.123 0.989 1897 Planarity : 0.038 0.305 1605 Dihedral : 25.313 119.917 5571 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 36.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.94 % Favored : 89.96 % Rotamer: Outliers : 6.66 % Allowed : 6.66 % Favored : 86.68 % Cbeta Deviations : 2.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 1076 helix: 1.36 (0.65), residues: 74 sheet: -0.01 (0.37), residues: 204 loop : -2.01 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A4424 HIS 0.013 0.001 HIS A4425 PHE 0.018 0.002 PHE A4928 TYR 0.016 0.001 TYR A4869 ARG 0.018 0.001 ARG B4804 *********************** 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 fitting. rotamer outliers: 65 poor density : 67 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4703 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6707 (t0) REVERT: A 4892 SER cc_start: 0.4851 (OUTLIER) cc_final: 0.4564 (t) outliers start: 65 outliers final: 26 residues processed: 127 average time/residue: 0.2033 time to fit residues: 36.9447 Evaluate side-chains 70 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 42 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4595 CYS Chi-restraints excluded: chain A residue 4703 ASN Chi-restraints excluded: chain A residue 4734 SER Chi-restraints excluded: chain A residue 4813 CYS Chi-restraints excluded: chain A residue 4846 LYS Chi-restraints excluded: chain A residue 4866 CYS Chi-restraints excluded: chain A residue 4877 CYS Chi-restraints excluded: chain A residue 4892 SER Chi-restraints excluded: chain A residue 4908 THR Chi-restraints excluded: chain A residue 4912 VAL Chi-restraints excluded: chain A residue 4913 ILE Chi-restraints excluded: chain A residue 4916 THR Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4352 CYS Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4478 CYS Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4815 GLU Chi-restraints excluded: chain B residue 4837 LYS Chi-restraints excluded: chain B residue 4840 THR Chi-restraints excluded: chain B residue 4859 LYS Chi-restraints excluded: chain B residue 4860 MET Chi-restraints excluded: chain B residue 4865 CYS Chi-restraints excluded: chain B residue 4866 CYS Chi-restraints excluded: chain B residue 4900 CYS Chi-restraints excluded: chain B residue 4921 ASN Chi-restraints excluded: chain B residue 4924 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0050 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4788 ASN A4801 GLN B4645 GLN ** B4739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 10108 Z= 0.291 Angle : 1.190 30.775 13793 Z= 0.500 Chirality : 0.065 0.508 1897 Planarity : 0.006 0.066 1605 Dihedral : 23.415 119.200 3661 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.89 % Allowed : 9.63 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 1076 helix: 1.44 (0.66), residues: 74 sheet: 0.63 (0.38), residues: 188 loop : -1.84 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A4376 HIS 0.005 0.001 HIS B4704 PHE 0.019 0.002 PHE B4854 TYR 0.056 0.002 TYR A4891 ARG 0.002 0.000 ARG B4864 *********************** 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 87 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 49 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 82 average time/residue: 0.2139 time to fit residues: 27.1833 Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 43 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4578 ASN Chi-restraints excluded: chain A residue 4579 THR Chi-restraints excluded: chain A residue 4850 CYS Chi-restraints excluded: chain A residue 4869 TYR 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 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 4941 CYS Chi-restraints excluded: chain B residue 4351 GLU Chi-restraints excluded: chain B residue 4392 VAL Chi-restraints excluded: chain B residue 4461 GLU Chi-restraints excluded: chain B residue 4522 LEU 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 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 4941 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.0270 chunk 78 optimal weight: 5.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B4739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10108 Z= 0.268 Angle : 1.018 29.632 13793 Z= 0.427 Chirality : 0.057 0.422 1897 Planarity : 0.005 0.053 1605 Dihedral : 20.138 117.231 3634 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 3.59 % Allowed : 13.32 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1076 helix: 1.71 (0.67), residues: 72 sheet: 0.73 (0.37), residues: 188 loop : -1.65 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A4376 HIS 0.003 0.001 HIS B4704 PHE 0.011 0.001 PHE B4854 TYR 0.044 0.002 TYR A4891 ARG 0.003 0.000 ARG A4804 *********************** 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 81 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 46 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4931 MET cc_start: 0.5175 (mtm) cc_final: 0.4809 (ttm) outliers start: 35 outliers final: 21 residues processed: 77 average time/residue: 0.2038 time to fit residues: 24.5422 Evaluate side-chains 62 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR 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 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 4461 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4584 CYS Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4869 TYR Chi-restraints excluded: chain B residue 4900 CYS Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4917 HIS B4739 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10108 Z= 0.270 Angle : 0.958 25.587 13793 Z= 0.403 Chirality : 0.056 0.428 1897 Planarity : 0.004 0.046 1605 Dihedral : 18.426 110.029 3625 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.38 % Allowed : 14.14 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1076 helix: 1.65 (0.67), residues: 72 sheet: 1.18 (0.38), residues: 170 loop : -1.75 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B4870 HIS 0.004 0.001 HIS B4704 PHE 0.016 0.001 PHE B4928 TYR 0.032 0.002 TYR A4891 ARG 0.005 0.000 ARG A4804 *********************** 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 fitting. rotamer outliers: 33 poor density : 42 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 71 average time/residue: 0.1778 time to fit residues: 19.6430 Evaluate side-chains 64 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 38 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4395 VAL Chi-restraints excluded: chain A residue 4406 THR 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 4732 SER Chi-restraints excluded: chain A residue 4811 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 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 4404 MET Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4461 GLU 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 4814 VAL Chi-restraints excluded: chain B residue 4840 THR Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4881 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 10108 Z= 0.330 Angle : 0.947 24.127 13793 Z= 0.405 Chirality : 0.055 0.410 1897 Planarity : 0.005 0.045 1605 Dihedral : 17.584 112.828 3623 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.38 % Allowed : 14.96 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1076 helix: 1.48 (0.66), residues: 77 sheet: 1.27 (0.38), residues: 171 loop : -1.85 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B4376 HIS 0.004 0.001 HIS B4704 PHE 0.030 0.002 PHE A4854 TYR 0.016 0.001 TYR B4388 ARG 0.004 0.000 ARG A4702 *********************** 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 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 39 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 66 average time/residue: 0.1658 time to fit residues: 17.5442 Evaluate side-chains 61 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 39 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR 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 4811 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 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 4404 MET Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4461 GLU 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 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10108 Z= 0.257 Angle : 0.911 19.763 13793 Z= 0.387 Chirality : 0.054 0.398 1897 Planarity : 0.004 0.044 1605 Dihedral : 16.867 112.420 3623 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.28 % Allowed : 15.47 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1076 helix: 1.16 (0.64), residues: 80 sheet: 1.30 (0.38), residues: 170 loop : -1.79 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B4870 HIS 0.004 0.001 HIS B4704 PHE 0.014 0.001 PHE B4854 TYR 0.017 0.001 TYR B4891 ARG 0.003 0.000 ARG A4702 *********************** 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 74 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 42 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4792 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8856 (pp) outliers start: 32 outliers final: 24 residues processed: 70 average time/residue: 0.1853 time to fit residues: 19.9556 Evaluate side-chains 61 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 36 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR 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 4732 SER Chi-restraints excluded: chain A residue 4792 LEU Chi-restraints excluded: chain A residue 4811 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 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 4404 MET Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4461 GLU 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 4814 VAL Chi-restraints excluded: chain B residue 4904 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10108 Z= 0.314 Angle : 0.919 21.822 13793 Z= 0.394 Chirality : 0.054 0.401 1897 Planarity : 0.004 0.042 1605 Dihedral : 16.250 113.743 3623 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.07 % Allowed : 16.70 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1076 helix: 1.53 (0.68), residues: 73 sheet: 1.36 (0.39), residues: 171 loop : -1.72 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A4376 HIS 0.004 0.001 HIS B4704 PHE 0.011 0.001 PHE A4854 TYR 0.015 0.001 TYR A4884 ARG 0.005 0.000 ARG B4864 *********************** 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 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 36 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4792 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8850 (pp) outliers start: 30 outliers final: 23 residues processed: 63 average time/residue: 0.1647 time to fit residues: 16.7244 Evaluate side-chains 55 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR 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 4792 LEU Chi-restraints excluded: chain A residue 4811 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 4912 VAL 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 4404 MET Chi-restraints excluded: chain B residue 4406 THR Chi-restraints excluded: chain B residue 4457 VAL Chi-restraints excluded: chain B residue 4461 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 VAL Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4921 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4911 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5564 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10108 Z= 0.246 Angle : 0.890 20.737 13793 Z= 0.378 Chirality : 0.053 0.405 1897 Planarity : 0.004 0.044 1605 Dihedral : 15.793 113.682 3623 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.56 % Allowed : 17.83 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1076 helix: 1.51 (0.68), residues: 72 sheet: 1.27 (0.39), residues: 181 loop : -1.66 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A4870 HIS 0.004 0.001 HIS B4704 PHE 0.009 0.001 PHE A4854 TYR 0.018 0.001 TYR A4869 ARG 0.003 0.000 ARG A4702 *********************** 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 59 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 34 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4931 MET cc_start: 0.3861 (mmp) cc_final: 0.3458 (tmm) outliers start: 25 outliers final: 19 residues processed: 56 average time/residue: 0.2207 time to fit residues: 20.6644 Evaluate side-chains 51 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4741 VAL Chi-restraints excluded: chain A residue 4811 THR Chi-restraints excluded: chain A residue 4906 ASN 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 4461 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 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 4938 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10108 Z= 0.269 Angle : 0.881 18.353 13793 Z= 0.377 Chirality : 0.053 0.415 1897 Planarity : 0.004 0.042 1605 Dihedral : 15.305 114.131 3621 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 2.36 % Allowed : 18.24 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1076 helix: 1.64 (0.69), residues: 71 sheet: 1.30 (0.39), residues: 181 loop : -1.64 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B4870 HIS 0.004 0.001 HIS B4704 PHE 0.009 0.001 PHE A4854 TYR 0.017 0.001 TYR A4884 ARG 0.003 0.000 ARG A4702 *********************** 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 56 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 33 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4791 CYS cc_start: 0.6699 (OUTLIER) cc_final: 0.6333 (t) outliers start: 23 outliers final: 20 residues processed: 55 average time/residue: 0.1765 time to fit residues: 15.7965 Evaluate side-chains 54 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 33 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4406 THR Chi-restraints excluded: chain A residue 4457 VAL Chi-restraints excluded: chain A residue 4500 LEU Chi-restraints excluded: chain A residue 4741 VAL Chi-restraints excluded: chain A residue 4791 CYS Chi-restraints excluded: chain A residue 4811 THR Chi-restraints excluded: chain A residue 4906 ASN Chi-restraints excluded: chain A residue 4912 VAL 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 4461 GLU Chi-restraints excluded: chain B residue 4522 LEU Chi-restraints excluded: chain B residue 4730 CYS Chi-restraints excluded: chain B residue 4790 VAL Chi-restraints excluded: chain B residue 4814 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 102 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10108 Z= 0.197 Angle : 0.849 15.997 13793 Z= 0.361 Chirality : 0.052 0.424 1897 Planarity : 0.004 0.041 1605 Dihedral : 14.737 113.902 3621 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.84 % Allowed : 18.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1076 helix: 1.43 (0.68), residues: 72 sheet: 1.26 (0.38), residues: 187 loop : -1.66 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A4376 HIS 0.004 0.001 HIS B4704 PHE 0.012 0.001 PHE A4854 TYR 0.017 0.001 TYR A4884 ARG 0.002 0.000 ARG A4702 ********************** 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 55 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 37 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4791 CYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6240 (t) REVERT: A 4931 MET cc_start: 0.3775 (mmp) cc_final: 0.3360 (tmm) REVERT: B 4931 MET cc_start: 0.5042 (mtm) cc_final: 0.4675 (ttm) outliers start: 18 outliers final: 15 residues processed: 53 average time/residue: 0.2175 time to fit residues: 17.1042 Evaluate side-chains 50 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 34 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 4791 CYS Chi-restraints excluded: chain A residue 4811 THR Chi-restraints excluded: chain A residue 4906 ASN 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 4461 GLU 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 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 91 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.106268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074091 restraints weight = 43155.891| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.53 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10108 Z= 0.227 Angle : 0.846 14.907 13793 Z= 0.361 Chirality : 0.051 0.427 1897 Planarity : 0.005 0.087 1605 Dihedral : 14.345 113.688 3620 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.84 % Allowed : 18.55 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1076 helix: 1.70 (0.71), residues: 67 sheet: 1.31 (0.38), residues: 185 loop : -1.62 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A4376 HIS 0.004 0.001 HIS B4704 PHE 0.010 0.001 PHE A4854 TYR 0.017 0.001 TYR A4884 ARG 0.004 0.000 ARG A4804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.83 seconds wall clock time: 47 minutes 42.94 seconds (2862.94 seconds total)