Starting phenix.real_space_refine on Sun Apr 5 11:54:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ncg_12265/04_2026/7ncg_12265.map" } resolution = 3.43 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3180 2.51 5 N 876 2.21 5 O 996 1.98 5 H 5376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10428 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 1.99, per 1000 atoms: 0.19 Number of scatterers: 10428 At special positions: 0 Unit cell: (131.1, 78.66, 46.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 996 8.00 N 876 7.00 C 3180 6.00 H 5376 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 210.6 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 57.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 52 removed outlier: 8.929A pdb=" N TYR A 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N SER E 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLY A 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N THR E 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LYS A 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N GLU E 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LYS A 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL E 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N HIS E 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N LEU A 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLY F 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL A 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N LYS F 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N SER A 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N LYS F 45 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY F 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU A 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N VAL F 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLY F 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N HIS A 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU F 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLY K 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL F 40 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N LYS K 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N SER F 42 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 10.479A pdb=" N LYS K 45 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR F 44 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLY K 47 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU F 46 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N VAL K 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY K 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N HIS F 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR J 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL K 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY J 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER K 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS J 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR K 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS J 45 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 52 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR L 39 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL J 40 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY L 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER J 42 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS L 43 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR J 44 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS L 45 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL J 52 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.712A pdb=" N ALA A 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA J 56 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 66 removed outlier: 6.797A pdb=" N GLU E 61 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU A 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR F 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL F 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU F 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR K 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL K 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN F 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU K 61 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU J 61 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N THR L 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL J 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL L 66 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN J 65 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 70 through 82 removed outlier: 6.639A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLY E 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR E 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLN E 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ALA A 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N THR E 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N LYS A 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA F 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA F 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN A 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS F 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL F 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 74 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR F 75 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA K 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL F 77 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA K 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN F 79 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS K 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR F 81 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL K 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL J 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLY K 73 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR J 72 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR K 75 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL J 74 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N VAL K 77 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ALA J 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N GLN K 79 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N ALA J 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N THR K 81 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS J 80 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL L 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR J 75 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA L 76 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL J 77 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA L 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN J 79 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS L 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR J 81 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL L 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.778A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL J 95 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 50 removed outlier: 8.924A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU D 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N LEU D 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N GLY H 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL D 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N LYS H 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N SER D 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 10.550A pdb=" N LYS H 45 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY H 47 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU D 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL H 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY H 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N HIS D 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N HIS H 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL G 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL H 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLY G 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR I 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL G 40 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY I 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER G 42 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS I 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR G 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS I 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.655A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA G 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 66 removed outlier: 6.791A pdb=" N GLU C 61 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU B 61 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU D 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR H 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL H 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN D 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU H 61 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU G 61 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 70 through 82 removed outlier: 6.515A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLY C 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 10.642A pdb=" N THR C 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N LYS B 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B 75 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA D 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS D 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 75 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA H 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA H 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN D 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS H 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR D 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL H 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLY H 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR G 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR H 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLN H 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ALA G 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 10.757A pdb=" N THR H 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N LYS G 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL I 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR G 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA I 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL G 77 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN G 79 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS I 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR G 81 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL I 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 95 through 96 removed outlier: 6.796A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 279 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: 2.06 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.96: 110 0.96 - 1.11: 5266 1.11 - 1.26: 864 1.26 - 1.41: 1016 1.41 - 1.56: 3196 Bond restraints: 10452 Sorted by residual: bond pdb=" N ALA H 56 " pdb=" H ALA H 56 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 PHE C 94 " pdb=" HE2 PHE C 94 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N PHE G 94 " pdb=" H PHE G 94 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N THR D 75 " pdb=" H THR D 75 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS H 50 " pdb=" HE1 HIS H 50 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 10447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12241 1.74 - 3.48: 4761 3.48 - 5.22: 1284 5.22 - 6.96: 679 6.96 - 8.70: 67 Bond angle restraints: 19032 Sorted by residual: angle pdb=" CA PHE A 94 " pdb=" CB PHE A 94 " pdb=" CG PHE A 94 " ideal model delta sigma weight residual 113.80 120.82 -7.02 1.00e+00 1.00e+00 4.93e+01 angle pdb=" CA PHE C 94 " pdb=" CB PHE C 94 " pdb=" CG PHE C 94 " ideal model delta sigma weight residual 113.80 120.77 -6.97 1.00e+00 1.00e+00 4.86e+01 angle pdb=" CA PHE E 94 " pdb=" CB PHE E 94 " pdb=" CG PHE E 94 " ideal model delta sigma weight residual 113.80 120.15 -6.35 1.00e+00 1.00e+00 4.03e+01 angle pdb=" N THR F 59 " pdb=" CA THR F 59 " pdb=" C THR F 59 " ideal model delta sigma weight residual 110.41 117.37 -6.96 1.23e+00 6.61e-01 3.21e+01 angle pdb=" CA PHE F 94 " pdb=" CB PHE F 94 " pdb=" CG PHE F 94 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4179 15.81 - 31.62: 199 31.62 - 47.42: 91 47.42 - 63.23: 258 63.23 - 79.04: 61 Dihedral angle restraints: 4788 sinusoidal: 2664 harmonic: 2124 Sorted by residual: dihedral pdb=" CA VAL G 74 " pdb=" C VAL G 74 " pdb=" N THR G 75 " pdb=" CA THR G 75 " ideal model delta harmonic sigma weight residual 180.00 155.12 24.88 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA VAL H 74 " pdb=" C VAL H 74 " pdb=" N THR H 75 " pdb=" CA THR H 75 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA VAL L 74 " pdb=" C VAL L 74 " pdb=" N THR L 75 " pdb=" CA THR L 75 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 402 0.053 - 0.105: 305 0.105 - 0.158: 164 0.158 - 0.211: 36 0.211 - 0.263: 5 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA LYS K 45 " pdb=" N LYS K 45 " pdb=" C LYS K 45 " pdb=" CB LYS K 45 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 45 " pdb=" N LYS B 45 " pdb=" C LYS B 45 " pdb=" CB LYS B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS C 58 " pdb=" N LYS C 58 " pdb=" C LYS C 58 " pdb=" CB LYS C 58 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 909 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 94 " -0.053 2.00e-02 2.50e+03 3.97e-02 4.73e+01 pdb=" CG PHE L 94 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE L 94 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE L 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 94 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE L 94 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE L 94 " -0.021 2.00e-02 2.50e+03 pdb=" HD1 PHE L 94 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE L 94 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE L 94 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE L 94 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE L 94 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 65 " 0.035 2.00e-02 2.50e+03 4.85e-02 3.52e+01 pdb=" CG ASN H 65 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 65 " -0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN H 65 " 0.046 2.00e-02 2.50e+03 pdb="HD21 ASN H 65 " -0.077 2.00e-02 2.50e+03 pdb="HD22 ASN H 65 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.086 2.00e-02 2.50e+03 3.42e-02 3.51e+01 pdb=" CG PHE C 94 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE C 94 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE C 94 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE C 94 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE C 94 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE C 94 " 0.034 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.28: 1355 2.28 - 2.84: 20520 2.84 - 3.39: 24437 3.39 - 3.95: 32774 3.95 - 4.50: 46164 Nonbonded interactions: 125250 Sorted by model distance: nonbonded pdb=" OE1 GLU B 61 " pdb=" HZ1 LYS D 96 " model vdw 1.729 2.450 nonbonded pdb=" HZ3 LYS G 96 " pdb=" OE1 GLU H 61 " model vdw 1.753 2.450 nonbonded pdb=" OE1 GLU A 61 " pdb=" HZ1 LYS F 96 " model vdw 1.758 2.450 nonbonded pdb=" OE1 GLU F 61 " pdb=" HZ1 LYS K 96 " model vdw 1.762 2.450 nonbonded pdb=" O GLU C 83 " pdb=" HG SER C 87 " model vdw 1.767 2.450 ... (remaining 125245 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.020 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: 0.040 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.120 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.012 0.042 5076 Z= 0.834 Angle : 2.196 7.783 6864 Z= 1.439 Chirality : 0.084 0.263 912 Planarity : 0.009 0.039 840 Dihedral : 10.992 79.035 1716 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.51 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.051 0.014 TYR C 39 PHE 0.064 0.018 PHE C 94 HIS 0.012 0.004 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01246 ( 5076) covalent geometry : angle 2.19590 ( 6864) hydrogen bonds : bond 0.12883 ( 93) hydrogen bonds : angle 7.48645 ( 279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.266 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: A 43 LYS cc_start: 0.8262 (mttt) cc_final: 0.8005 (mttm) REVERT: A 83 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6690 (mt-10) REVERT: B 43 LYS cc_start: 0.8011 (mttt) cc_final: 0.7691 (mtpp) REVERT: B 80 LYS cc_start: 0.8635 (tttt) cc_final: 0.8385 (tttm) REVERT: B 83 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 43 LYS cc_start: 0.7733 (mttt) cc_final: 0.6933 (mmmt) REVERT: C 46 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6925 (mm-30) REVERT: D 43 LYS cc_start: 0.8564 (mttt) cc_final: 0.8213 (mtpp) REVERT: E 43 LYS cc_start: 0.8265 (mttt) cc_final: 0.7524 (mmmt) REVERT: E 46 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7713 (mt-10) REVERT: G 80 LYS cc_start: 0.8509 (tttt) cc_final: 0.8296 (tttm) REVERT: H 46 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 45 LYS cc_start: 0.8276 (mttt) cc_final: 0.8020 (mptt) REVERT: J 80 LYS cc_start: 0.8513 (tttt) cc_final: 0.8300 (tttm) REVERT: K 46 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7580 (mt-10) REVERT: K 60 LYS cc_start: 0.7097 (mttt) cc_final: 0.6702 (mtmt) REVERT: K 61 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6939 (mp0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2493 time to fit residues: 31.3340 Evaluate side-chains 75 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.145118 restraints weight = 18529.286| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.90 r_work: 0.4222 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5076 Z= 0.155 Angle : 0.586 4.913 6864 Z= 0.341 Chirality : 0.052 0.143 912 Planarity : 0.002 0.013 840 Dihedral : 6.050 16.097 732 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.78 % Allowed : 6.01 % Favored : 93.22 % 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: -2.26 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 39 PHE 0.021 0.004 PHE A 94 HIS 0.004 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5076) covalent geometry : angle 0.58577 ( 6864) hydrogen bonds : bond 0.02919 ( 93) hydrogen bonds : angle 5.86938 ( 279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.259 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: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8171 (mttt) cc_final: 0.7792 (mtpp) REVERT: A 60 LYS cc_start: 0.7375 (mttt) cc_final: 0.7022 (mtpt) REVERT: B 43 LYS cc_start: 0.8305 (mttt) cc_final: 0.7998 (mtpp) REVERT: B 80 LYS cc_start: 0.8787 (tttt) cc_final: 0.8465 (tttm) REVERT: C 43 LYS cc_start: 0.8091 (mttt) cc_final: 0.7075 (mmmt) REVERT: C 46 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6857 (mm-30) REVERT: D 43 LYS cc_start: 0.8577 (mttt) cc_final: 0.8193 (mtpp) REVERT: E 43 LYS cc_start: 0.8419 (mttt) cc_final: 0.7373 (mmmt) REVERT: G 45 LYS cc_start: 0.8317 (mttt) cc_final: 0.8068 (mtpp) REVERT: G 60 LYS cc_start: 0.7425 (mttt) cc_final: 0.7142 (mtpt) REVERT: G 80 LYS cc_start: 0.8856 (tttt) cc_final: 0.8637 (tttm) REVERT: H 43 LYS cc_start: 0.8400 (mttt) cc_final: 0.8128 (mtpt) REVERT: J 43 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8321 (mttm) REVERT: J 60 LYS cc_start: 0.7544 (mttt) cc_final: 0.7327 (mttp) REVERT: K 43 LYS cc_start: 0.8375 (mttt) cc_final: 0.7915 (mtpp) outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.3196 time to fit residues: 33.9413 Evaluate side-chains 81 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4587 r_free = 0.4587 target = 0.173483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.141690 restraints weight = 18919.483| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.98 r_work: 0.4167 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5076 Z= 0.166 Angle : 0.562 4.669 6864 Z= 0.327 Chirality : 0.053 0.135 912 Planarity : 0.002 0.007 840 Dihedral : 5.573 14.185 732 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.78 % Allowed : 8.72 % Favored : 90.50 % 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: -2.63 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.016 0.003 PHE A 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5076) covalent geometry : angle 0.56233 ( 6864) hydrogen bonds : bond 0.03160 ( 93) hydrogen bonds : angle 5.63826 ( 279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.273 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: A 60 LYS cc_start: 0.7346 (mttt) cc_final: 0.7066 (mtpt) REVERT: B 43 LYS cc_start: 0.8373 (mttt) cc_final: 0.8071 (mttm) REVERT: B 80 LYS cc_start: 0.8611 (tttt) cc_final: 0.8285 (tttm) REVERT: C 43 LYS cc_start: 0.8121 (mttt) cc_final: 0.7051 (mmmt) REVERT: D 43 LYS cc_start: 0.8577 (mttt) cc_final: 0.8135 (mtpp) REVERT: E 43 LYS cc_start: 0.8341 (mttt) cc_final: 0.7302 (mmmt) REVERT: F 43 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8346 (mtpp) REVERT: F 61 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6978 (mp0) REVERT: H 43 LYS cc_start: 0.8345 (mttt) cc_final: 0.8095 (mtpt) REVERT: J 60 LYS cc_start: 0.7460 (mttt) cc_final: 0.7115 (mttp) REVERT: K 43 LYS cc_start: 0.8340 (mttt) cc_final: 0.8018 (mtpt) REVERT: K 61 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6645 (mp0) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 0.3429 time to fit residues: 32.3321 Evaluate side-chains 82 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.171733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.139908 restraints weight = 18986.053| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 3.97 r_work: 0.4135 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5076 Z= 0.169 Angle : 0.549 4.626 6864 Z= 0.318 Chirality : 0.053 0.135 912 Planarity : 0.002 0.007 840 Dihedral : 5.549 13.374 732 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.16 % Allowed : 10.08 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.24), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 39 PHE 0.016 0.003 PHE A 94 HIS 0.006 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5076) covalent geometry : angle 0.54932 ( 6864) hydrogen bonds : bond 0.02845 ( 93) hydrogen bonds : angle 5.68392 ( 279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.271 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: A 60 LYS cc_start: 0.7380 (mttt) cc_final: 0.7159 (mtpt) REVERT: B 43 LYS cc_start: 0.8412 (mttt) cc_final: 0.8067 (mtpt) REVERT: C 43 LYS cc_start: 0.8248 (mttt) cc_final: 0.7883 (mtpp) REVERT: C 83 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6690 (mp0) REVERT: D 43 LYS cc_start: 0.8690 (mttt) cc_final: 0.8374 (mtpp) REVERT: D 60 LYS cc_start: 0.7229 (mttt) cc_final: 0.6872 (mttm) REVERT: E 43 LYS cc_start: 0.8346 (mttt) cc_final: 0.7247 (mmmt) REVERT: F 43 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8531 (mtpp) REVERT: F 61 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7193 (mp0) REVERT: G 44 THR cc_start: 0.8380 (p) cc_final: 0.8156 (p) REVERT: H 58 LYS cc_start: 0.7890 (mttt) cc_final: 0.7689 (mttt) REVERT: I 60 LYS cc_start: 0.7900 (mttt) cc_final: 0.7616 (mttp) REVERT: I 83 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6148 (mp0) REVERT: J 60 LYS cc_start: 0.7447 (mttt) cc_final: 0.7102 (mttp) REVERT: J 83 GLU cc_start: 0.6674 (mt-10) cc_final: 0.5928 (mp0) REVERT: K 45 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7597 (mmtt) REVERT: K 61 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6731 (mp0) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.3214 time to fit residues: 30.0442 Evaluate side-chains 83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.169330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138128 restraints weight = 19463.221| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.99 r_work: 0.4103 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5076 Z= 0.207 Angle : 0.584 4.663 6864 Z= 0.340 Chirality : 0.053 0.141 912 Planarity : 0.002 0.008 840 Dihedral : 5.697 14.290 732 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.74 % Allowed : 11.43 % Favored : 86.82 % 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: -3.01 (0.24), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR D 39 PHE 0.017 0.003 PHE A 94 HIS 0.006 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5076) covalent geometry : angle 0.58378 ( 6864) hydrogen bonds : bond 0.03041 ( 93) hydrogen bonds : angle 5.80462 ( 279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.288 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8491 (mttt) cc_final: 0.8136 (mtpt) REVERT: C 43 LYS cc_start: 0.8289 (mttt) cc_final: 0.7919 (mtpp) REVERT: D 43 LYS cc_start: 0.8716 (mttt) cc_final: 0.8416 (mtpp) REVERT: D 60 LYS cc_start: 0.7328 (mttt) cc_final: 0.6957 (mttp) REVERT: E 43 LYS cc_start: 0.8396 (mttt) cc_final: 0.7215 (mmmt) REVERT: F 43 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8569 (mtpp) REVERT: F 60 LYS cc_start: 0.7271 (mttt) cc_final: 0.6864 (mttm) REVERT: I 60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7770 (mttp) REVERT: I 83 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6368 (mp0) REVERT: J 60 LYS cc_start: 0.7571 (mttt) cc_final: 0.7254 (mttp) outliers start: 9 outliers final: 9 residues processed: 89 average time/residue: 0.2999 time to fit residues: 31.1607 Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.171420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.140258 restraints weight = 19260.345| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.91 r_work: 0.4134 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5076 Z= 0.123 Angle : 0.514 4.612 6864 Z= 0.297 Chirality : 0.053 0.133 912 Planarity : 0.001 0.012 840 Dihedral : 5.280 12.745 732 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.36 % Allowed : 12.40 % Favored : 86.24 % 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: -2.77 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 39 PHE 0.013 0.002 PHE A 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5076) covalent geometry : angle 0.51383 ( 6864) hydrogen bonds : bond 0.02699 ( 93) hydrogen bonds : angle 5.54310 ( 279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.261 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8483 (mttt) cc_final: 0.8128 (mtpt) REVERT: C 43 LYS cc_start: 0.8257 (mttt) cc_final: 0.7908 (mtpp) REVERT: D 43 LYS cc_start: 0.8728 (mttt) cc_final: 0.8414 (mtpp) REVERT: D 60 LYS cc_start: 0.7302 (mttt) cc_final: 0.6913 (mttp) REVERT: E 43 LYS cc_start: 0.8386 (mttt) cc_final: 0.7222 (mmmt) REVERT: E 58 LYS cc_start: 0.8193 (mttm) cc_final: 0.7986 (mttm) REVERT: F 43 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8592 (mtpp) REVERT: F 60 LYS cc_start: 0.7181 (mttt) cc_final: 0.6835 (mttm) REVERT: I 60 LYS cc_start: 0.8078 (mttt) cc_final: 0.7773 (mttp) REVERT: I 83 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6196 (mp0) REVERT: J 83 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6004 (mp0) REVERT: K 45 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7348 (mmtt) outliers start: 7 outliers final: 6 residues processed: 87 average time/residue: 0.3039 time to fit residues: 30.6546 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4526 r_free = 0.4526 target = 0.168919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.137966 restraints weight = 19714.264| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 3.95 r_work: 0.4106 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5076 Z= 0.199 Angle : 0.570 4.670 6864 Z= 0.333 Chirality : 0.054 0.140 912 Planarity : 0.002 0.015 840 Dihedral : 5.552 13.733 732 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 1.94 % Allowed : 12.40 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.00 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.016 0.003 PHE A 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5076) covalent geometry : angle 0.56963 ( 6864) hydrogen bonds : bond 0.03092 ( 93) hydrogen bonds : angle 5.79877 ( 279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.436 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8524 (mttt) cc_final: 0.8139 (mtpt) REVERT: C 43 LYS cc_start: 0.8304 (mttt) cc_final: 0.7958 (mtpp) REVERT: C 83 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6777 (mp0) REVERT: D 43 LYS cc_start: 0.8733 (mttt) cc_final: 0.8416 (mtpp) REVERT: D 60 LYS cc_start: 0.7455 (mttt) cc_final: 0.7063 (mttm) REVERT: E 43 LYS cc_start: 0.8415 (mttt) cc_final: 0.7248 (mmmt) REVERT: F 43 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8598 (mtpp) REVERT: F 60 LYS cc_start: 0.7231 (mttt) cc_final: 0.6878 (mttm) REVERT: H 45 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7288 (mmtt) REVERT: I 60 LYS cc_start: 0.8141 (mttt) cc_final: 0.7817 (mttp) REVERT: I 83 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6498 (mp0) REVERT: J 83 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6109 (mp0) REVERT: K 45 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7457 (mmtt) REVERT: L 61 GLU cc_start: 0.7631 (mp0) cc_final: 0.5781 (tp30) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.2916 time to fit residues: 30.1049 Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.169830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.138800 restraints weight = 19266.490| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 3.94 r_work: 0.4121 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5076 Z= 0.152 Angle : 0.529 4.667 6864 Z= 0.308 Chirality : 0.054 0.134 912 Planarity : 0.002 0.009 840 Dihedral : 5.312 12.563 732 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.74 % Allowed : 12.98 % Favored : 85.27 % 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: -2.90 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.013 0.003 PHE A 94 HIS 0.003 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 5076) covalent geometry : angle 0.52889 ( 6864) hydrogen bonds : bond 0.02807 ( 93) hydrogen bonds : angle 5.67487 ( 279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8541 (mttt) cc_final: 0.8188 (mtpp) REVERT: C 43 LYS cc_start: 0.8305 (mttt) cc_final: 0.7274 (mmmt) REVERT: D 60 LYS cc_start: 0.7451 (mttt) cc_final: 0.7053 (mttm) REVERT: E 43 LYS cc_start: 0.8430 (mttt) cc_final: 0.7270 (mmmt) REVERT: F 43 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8636 (mtpp) REVERT: F 60 LYS cc_start: 0.7197 (mttt) cc_final: 0.6897 (mttm) REVERT: F 61 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7159 (mp0) REVERT: G 83 GLU cc_start: 0.6651 (mt-10) cc_final: 0.5969 (mp0) REVERT: H 43 LYS cc_start: 0.8538 (mttt) cc_final: 0.8241 (mtpt) REVERT: H 45 LYS cc_start: 0.7625 (mtpt) cc_final: 0.7263 (mmtt) REVERT: I 60 LYS cc_start: 0.8138 (mttt) cc_final: 0.7822 (mttp) REVERT: I 83 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6189 (mp0) REVERT: J 83 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6016 (mp0) REVERT: K 45 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7483 (mmtt) REVERT: L 61 GLU cc_start: 0.7581 (mp0) cc_final: 0.5728 (tp30) outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 0.2871 time to fit residues: 29.2491 Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.170906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.139587 restraints weight = 19105.705| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 3.94 r_work: 0.4131 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5076 Z= 0.133 Angle : 0.513 4.649 6864 Z= 0.299 Chirality : 0.054 0.134 912 Planarity : 0.002 0.009 840 Dihedral : 5.177 12.404 732 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.74 % Allowed : 13.57 % Favored : 84.69 % 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: -2.83 (0.26), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.012 0.003 PHE A 94 HIS 0.003 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5076) covalent geometry : angle 0.51317 ( 6864) hydrogen bonds : bond 0.02681 ( 93) hydrogen bonds : angle 5.58507 ( 279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.266 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8523 (mttt) cc_final: 0.8165 (mtpp) REVERT: C 43 LYS cc_start: 0.8286 (mttt) cc_final: 0.7911 (mtpp) REVERT: D 61 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7463 (mp0) REVERT: E 43 LYS cc_start: 0.8412 (mttt) cc_final: 0.7266 (mmmt) REVERT: F 43 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8613 (mtpp) REVERT: F 60 LYS cc_start: 0.7130 (mttt) cc_final: 0.6824 (mttm) REVERT: F 61 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7141 (mp0) REVERT: H 43 LYS cc_start: 0.8545 (mttt) cc_final: 0.8224 (mtpt) REVERT: H 45 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7364 (mmtt) REVERT: I 60 LYS cc_start: 0.8070 (mttt) cc_final: 0.7744 (mttp) REVERT: I 83 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6295 (mp0) REVERT: J 83 GLU cc_start: 0.6737 (mt-10) cc_final: 0.5997 (mp0) REVERT: K 45 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7414 (mmtt) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.3056 time to fit residues: 29.9049 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.169070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.137901 restraints weight = 19362.355| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.97 r_work: 0.4111 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5076 Z= 0.176 Angle : 0.552 4.796 6864 Z= 0.321 Chirality : 0.054 0.136 912 Planarity : 0.002 0.007 840 Dihedral : 5.363 12.369 732 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 1.55 % Allowed : 13.37 % Favored : 85.08 % 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: -2.99 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.015 0.003 PHE A 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5076) covalent geometry : angle 0.55204 ( 6864) hydrogen bonds : bond 0.02978 ( 93) hydrogen bonds : angle 5.71911 ( 279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.266 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8572 (mttt) cc_final: 0.8213 (mtpp) REVERT: C 43 LYS cc_start: 0.8453 (mttt) cc_final: 0.8071 (mtpp) REVERT: D 61 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7399 (mp0) REVERT: E 43 LYS cc_start: 0.8484 (mttt) cc_final: 0.7356 (mmmt) REVERT: F 43 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8515 (mtpp) REVERT: F 61 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7265 (mp0) REVERT: G 83 GLU cc_start: 0.6692 (mt-10) cc_final: 0.5985 (mp0) REVERT: H 43 LYS cc_start: 0.8551 (mttt) cc_final: 0.8273 (mtpt) REVERT: H 45 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7272 (mmtt) REVERT: I 60 LYS cc_start: 0.8153 (mttt) cc_final: 0.7831 (mttp) REVERT: I 83 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6272 (mp0) REVERT: J 83 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6027 (mp0) REVERT: K 43 LYS cc_start: 0.8486 (mttt) cc_final: 0.8089 (mtpp) REVERT: K 45 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7502 (mmtt) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.2972 time to fit residues: 29.0605 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.170064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.138860 restraints weight = 19552.239| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.97 r_work: 0.4121 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5076 Z= 0.150 Angle : 0.527 4.688 6864 Z= 0.307 Chirality : 0.054 0.135 912 Planarity : 0.002 0.007 840 Dihedral : 5.200 12.244 732 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 1.36 % Allowed : 14.53 % Favored : 84.11 % 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: -2.94 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.013 0.003 PHE A 94 HIS 0.004 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5076) covalent geometry : angle 0.52658 ( 6864) hydrogen bonds : bond 0.02743 ( 93) hydrogen bonds : angle 5.63126 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.79 seconds wall clock time: 44 minutes 21.33 seconds (2661.33 seconds total)