Starting phenix.real_space_refine on Mon Jul 28 11:22:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_12265.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_12265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_12265.map" model { file = "/net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_12265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ncg_12265/07_2025/7ncg_12265.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.43, per 1000 atoms: 0.52 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: 2.81 Conformation dependent library (CDL) restraints added in 821.0 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: 1.16 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: 3.72 Time building geometry restraints manager: 3.39 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: 0.01 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.040 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (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 HIS 0.012 0.004 HIS A 50 PHE 0.064 0.018 PHE C 94 TYR 0.051 0.014 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.12883 ( 93) hydrogen bonds : angle 7.48645 ( 279) covalent geometry : bond 0.01246 ( 5076) covalent geometry : angle 2.19590 ( 6864) *********************** 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 : 0.872 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: 0.8264 (mttt) cc_final: 0.7524 (mmmt) REVERT: E 46 GLU cc_start: 0.7961 (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: 0.6701 (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: 0.5596 time to fit residues: 70.5716 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 : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 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 = 35)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.145173 restraints weight = 18390.042| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.88 r_work: 0.4223 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.001 HIS L 50 PHE 0.021 0.004 PHE A 94 TYR 0.006 0.001 TYR G 39 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 93) hydrogen bonds : angle 5.86938 ( 279) covalent geometry : bond 0.00336 ( 5076) covalent geometry : angle 0.58577 ( 6864) *********************** 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 : 0.782 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: 0.8172 (mttt) cc_final: 0.7794 (mtpp) REVERT: A 60 LYS cc_start: 0.7377 (mttt) cc_final: 0.7023 (mtpt) REVERT: B 43 LYS cc_start: 0.8307 (mttt) cc_final: 0.7999 (mtpp) REVERT: B 80 LYS cc_start: 0.8789 (tttt) cc_final: 0.8468 (tttm) REVERT: C 43 LYS cc_start: 0.8092 (mttt) cc_final: 0.7076 (mmmt) REVERT: C 46 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6858 (mm-30) REVERT: D 43 LYS cc_start: 0.8579 (mttt) cc_final: 0.8194 (mtpp) REVERT: E 43 LYS cc_start: 0.8418 (mttt) cc_final: 0.7374 (mmmt) REVERT: G 45 LYS cc_start: 0.8315 (mttt) cc_final: 0.8066 (mtpp) REVERT: G 60 LYS cc_start: 0.7430 (mttt) cc_final: 0.7147 (mtpt) REVERT: G 80 LYS cc_start: 0.8857 (tttt) cc_final: 0.8639 (tttm) REVERT: H 43 LYS cc_start: 0.8401 (mttt) cc_final: 0.8129 (mtpt) REVERT: J 43 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8321 (mttm) REVERT: J 60 LYS cc_start: 0.7547 (mttt) cc_final: 0.7329 (mttp) REVERT: K 43 LYS cc_start: 0.8377 (mttt) cc_final: 0.7917 (mtpp) outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.6703 time to fit residues: 71.8452 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 : 0.847 ------------------------------------------------------------------------------- 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 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4619 r_free = 0.4619 target = 0.176080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.144414 restraints weight = 18532.322| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 3.93 r_work: 0.4197 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5076 Z= 0.127 Angle : 0.530 4.668 6864 Z= 0.307 Chirality : 0.053 0.135 912 Planarity : 0.002 0.007 840 Dihedral : 5.345 14.232 732 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.97 % Allowed : 8.33 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.015 0.003 PHE A 94 TYR 0.005 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 93) hydrogen bonds : angle 5.50249 ( 279) covalent geometry : bond 0.00254 ( 5076) covalent geometry : angle 0.52994 ( 6864) *********************** 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 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.855 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: A 60 LYS cc_start: 0.7328 (mttt) cc_final: 0.7080 (mtpt) REVERT: B 43 LYS cc_start: 0.8357 (mttt) cc_final: 0.8019 (mtpt) REVERT: B 80 LYS cc_start: 0.8610 (tttt) cc_final: 0.8303 (tttm) REVERT: C 43 LYS cc_start: 0.8072 (mttt) cc_final: 0.7025 (mmmt) REVERT: D 43 LYS cc_start: 0.8493 (mttt) cc_final: 0.8129 (mtpp) REVERT: E 43 LYS cc_start: 0.8374 (mttt) cc_final: 0.7360 (mmmt) REVERT: F 43 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8425 (mtpp) REVERT: G 60 LYS cc_start: 0.7499 (mttt) cc_final: 0.7197 (mttp) REVERT: G 80 LYS cc_start: 0.8788 (tttt) cc_final: 0.8537 (tttm) REVERT: H 43 LYS cc_start: 0.8360 (mttt) cc_final: 0.8072 (mtpt) REVERT: J 60 LYS cc_start: 0.7464 (mttt) cc_final: 0.7131 (mttp) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.7668 time to fit residues: 74.3071 Evaluate side-chains 79 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 63 VAL 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 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4533 r_free = 0.4533 target = 0.169074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.137841 restraints weight = 19255.633| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.95 r_work: 0.4109 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5076 Z= 0.247 Angle : 0.626 4.748 6864 Z= 0.364 Chirality : 0.053 0.137 912 Planarity : 0.003 0.010 840 Dihedral : 5.886 15.358 732 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.97 % Allowed : 11.43 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS L 50 PHE 0.019 0.004 PHE A 94 TYR 0.011 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 93) hydrogen bonds : angle 5.88825 ( 279) covalent geometry : bond 0.00525 ( 5076) covalent geometry : angle 0.62553 ( 6864) *********************** 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 88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.830 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: B 43 LYS cc_start: 0.8460 (mttt) cc_final: 0.8083 (mtpt) REVERT: C 43 LYS cc_start: 0.8283 (mttt) cc_final: 0.7909 (mtpp) REVERT: D 43 LYS cc_start: 0.8708 (mttt) cc_final: 0.8390 (mtpp) REVERT: D 60 LYS cc_start: 0.7257 (mttt) cc_final: 0.6877 (mttm) REVERT: E 43 LYS cc_start: 0.8328 (mttt) cc_final: 0.7431 (mmmt) REVERT: E 83 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6764 (mp0) REVERT: F 43 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8498 (mtpp) REVERT: I 60 LYS cc_start: 0.7904 (mttt) cc_final: 0.7629 (mttp) REVERT: I 83 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6244 (mp0) REVERT: J 60 LYS cc_start: 0.7469 (mttt) cc_final: 0.7184 (mttp) REVERT: J 83 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6022 (mp0) REVERT: K 45 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7652 (mmtt) REVERT: L 58 LYS cc_start: 0.8526 (mttt) cc_final: 0.8300 (mttm) REVERT: L 61 GLU cc_start: 0.7711 (mp0) cc_final: 0.5744 (tp30) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.6570 time to fit residues: 63.3397 Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4537 r_free = 0.4537 target = 0.169908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.138622 restraints weight = 19262.358| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 3.98 r_work: 0.4112 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4356 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= 0.175 Angle : 0.556 4.654 6864 Z= 0.323 Chirality : 0.053 0.137 912 Planarity : 0.002 0.007 840 Dihedral : 5.527 13.655 732 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 1.16 % Allowed : 12.40 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.24), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 50 PHE 0.016 0.003 PHE A 94 TYR 0.007 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 93) hydrogen bonds : angle 5.73294 ( 279) covalent geometry : bond 0.00352 ( 5076) covalent geometry : angle 0.55551 ( 6864) *********************** 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 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.769 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: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.8485 (mttt) cc_final: 0.8137 (mtpt) REVERT: C 43 LYS cc_start: 0.8257 (mttt) cc_final: 0.7898 (mtpp) REVERT: D 43 LYS cc_start: 0.8687 (mttt) cc_final: 0.8366 (mtpp) REVERT: D 60 LYS cc_start: 0.7293 (mttt) cc_final: 0.6904 (mttp) REVERT: E 43 LYS cc_start: 0.8347 (mttt) cc_final: 0.7218 (mmmt) REVERT: F 43 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8570 (mtpp) REVERT: F 60 LYS cc_start: 0.7409 (mttt) cc_final: 0.6998 (mttm) REVERT: I 60 LYS cc_start: 0.8081 (mttt) cc_final: 0.7779 (mttp) REVERT: I 83 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6202 (mp0) REVERT: J 60 LYS cc_start: 0.7471 (mttt) cc_final: 0.7165 (mttp) REVERT: L 61 GLU cc_start: 0.7776 (mp0) cc_final: 0.5791 (tp30) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.6899 time to fit residues: 70.7450 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 : 0.853 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 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 = 0.4524 r_free = 0.4524 target = 0.168512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.137634 restraints weight = 19435.056| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 3.93 r_work: 0.4106 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4629 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= 0.202 Angle : 0.579 4.707 6864 Z= 0.339 Chirality : 0.054 0.142 912 Planarity : 0.002 0.007 840 Dihedral : 5.654 13.788 732 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 1.74 % Allowed : 12.21 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (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 HIS 0.005 0.002 HIS L 50 PHE 0.017 0.003 PHE A 94 TYR 0.009 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 93) hydrogen bonds : angle 5.83278 ( 279) covalent geometry : bond 0.00417 ( 5076) covalent geometry : angle 0.57933 ( 6864) *********************** 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: 9 poor density : 85 time to evaluate : 0.778 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: B 43 LYS cc_start: 0.8514 (mttt) cc_final: 0.8138 (mtpt) REVERT: C 43 LYS cc_start: 0.8291 (mttt) cc_final: 0.7924 (mtpp) REVERT: C 83 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6760 (mp0) REVERT: D 43 LYS cc_start: 0.8690 (mttt) cc_final: 0.8372 (mtpp) REVERT: D 60 LYS cc_start: 0.7366 (mttt) cc_final: 0.6993 (mttm) REVERT: E 43 LYS cc_start: 0.8401 (mttt) cc_final: 0.7236 (mmmt) REVERT: F 43 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8561 (mtpp) REVERT: F 60 LYS cc_start: 0.7392 (mttt) cc_final: 0.6973 (mttp) REVERT: I 60 LYS cc_start: 0.8145 (mttt) cc_final: 0.7823 (mttp) REVERT: I 83 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6309 (mp0) REVERT: J 60 LYS cc_start: 0.7452 (mttt) cc_final: 0.7139 (mttp) REVERT: J 83 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6012 (mp0) REVERT: K 43 LYS cc_start: 0.8295 (mttt) cc_final: 0.7943 (mtpp) outliers start: 9 outliers final: 9 residues processed: 87 average time/residue: 0.6506 time to fit residues: 66.1309 Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.170631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.139328 restraints weight = 19304.907| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.96 r_work: 0.4127 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5076 Z= 0.126 Angle : 0.517 4.627 6864 Z= 0.301 Chirality : 0.054 0.147 912 Planarity : 0.001 0.006 840 Dihedral : 5.280 12.274 732 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.94 % Allowed : 12.60 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 50 PHE 0.012 0.003 PHE A 94 TYR 0.005 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02702 ( 93) hydrogen bonds : angle 5.63595 ( 279) covalent geometry : bond 0.00249 ( 5076) covalent geometry : angle 0.51722 ( 6864) *********************** 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 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.804 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: symmetry clash REVERT: B 43 LYS cc_start: 0.8490 (mttt) cc_final: 0.8114 (mtpt) REVERT: C 43 LYS cc_start: 0.8267 (mttt) cc_final: 0.7907 (mtpp) REVERT: D 43 LYS cc_start: 0.8666 (mttt) cc_final: 0.8341 (mtpp) REVERT: D 60 LYS cc_start: 0.7353 (mttt) cc_final: 0.6956 (mttm) REVERT: E 43 LYS cc_start: 0.8407 (mttt) cc_final: 0.7261 (mmmt) REVERT: F 43 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8603 (mtpp) REVERT: F 60 LYS cc_start: 0.7282 (mttt) cc_final: 0.6913 (mttm) REVERT: I 60 LYS cc_start: 0.8090 (mttt) cc_final: 0.7774 (mttp) REVERT: I 83 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6182 (mp0) REVERT: J 83 GLU cc_start: 0.6700 (mt-10) cc_final: 0.5974 (mp0) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.6462 time to fit residues: 64.8906 Evaluate side-chains 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 L residue 58 LYS Chi-restraints excluded: chain L residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.172658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.141178 restraints weight = 19026.921| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 3.90 r_work: 0.4155 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 5076 Z= 0.100 Angle : 0.490 4.606 6864 Z= 0.285 Chirality : 0.053 0.135 912 Planarity : 0.001 0.005 840 Dihedral : 5.010 12.335 732 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.26), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.010 0.002 PHE A 94 TYR 0.004 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02735 ( 93) hydrogen bonds : angle 5.45911 ( 279) covalent geometry : bond 0.00198 ( 5076) covalent geometry : angle 0.48986 ( 6864) *********************** 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 95 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.139 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: 0.8519 (mttt) cc_final: 0.8175 (mtpp) REVERT: C 43 LYS cc_start: 0.8260 (mttt) cc_final: 0.7890 (mtpp) REVERT: D 60 LYS cc_start: 0.7282 (mttt) cc_final: 0.6867 (mttm) REVERT: E 43 LYS cc_start: 0.8406 (mttt) cc_final: 0.7264 (mmmt) REVERT: E 83 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6746 (mp0) REVERT: F 43 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8642 (mtpp) REVERT: H 43 LYS cc_start: 0.8546 (mttt) cc_final: 0.8246 (mtpt) REVERT: I 60 LYS cc_start: 0.8050 (mttt) cc_final: 0.7738 (mttp) REVERT: I 83 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6145 (mp0) REVERT: J 83 GLU cc_start: 0.6646 (mt-10) cc_final: 0.5993 (mp0) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.8251 time to fit residues: 87.1108 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 H residue 59 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain L residue 58 LYS 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 29 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.170478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138888 restraints weight = 19331.076| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 3.97 r_work: 0.4120 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5076 Z= 0.161 Angle : 0.536 4.774 6864 Z= 0.311 Chirality : 0.053 0.135 912 Planarity : 0.002 0.018 840 Dihedral : 5.197 12.186 732 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.26), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.012 0.003 PHE G 94 TYR 0.007 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 93) hydrogen bonds : angle 5.63413 ( 279) covalent geometry : bond 0.00330 ( 5076) covalent geometry : angle 0.53567 ( 6864) *********************** 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 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.787 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: C 43 LYS cc_start: 0.8290 (mttt) cc_final: 0.7955 (mtpp) REVERT: D 43 LYS cc_start: 0.8711 (mttt) cc_final: 0.8257 (mtpp) REVERT: D 60 LYS cc_start: 0.7379 (mttt) cc_final: 0.6964 (mttm) REVERT: E 43 LYS cc_start: 0.8408 (mttt) cc_final: 0.7251 (mmmt) REVERT: F 43 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8596 (mtpp) REVERT: F 60 LYS cc_start: 0.7317 (mttt) cc_final: 0.6946 (mttm) REVERT: G 83 GLU cc_start: 0.6688 (mt-10) cc_final: 0.5964 (mp0) REVERT: H 43 LYS cc_start: 0.8545 (mttt) cc_final: 0.8241 (mtpt) REVERT: I 60 LYS cc_start: 0.8084 (mttt) cc_final: 0.7763 (mttp) REVERT: I 83 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6175 (mp0) REVERT: J 83 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6014 (mp0) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.6333 time to fit residues: 63.5741 Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 58 LYS 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 26 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4574 r_free = 0.4574 target = 0.172224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.140651 restraints weight = 19110.706| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 3.91 r_work: 0.4145 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5076 Z= 0.119 Angle : 0.502 4.659 6864 Z= 0.292 Chirality : 0.054 0.135 912 Planarity : 0.002 0.019 840 Dihedral : 5.012 12.281 732 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.26), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.009 0.002 PHE G 94 TYR 0.005 0.001 TYR J 39 Details of bonding type rmsd hydrogen bonds : bond 0.02684 ( 93) hydrogen bonds : angle 5.53056 ( 279) covalent geometry : bond 0.00239 ( 5076) covalent geometry : angle 0.50248 ( 6864) ********************** 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 92 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.884 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: 0.8533 (mttt) cc_final: 0.8061 (mtpp) REVERT: C 43 LYS cc_start: 0.8326 (mttt) cc_final: 0.7927 (mtpp) REVERT: D 43 LYS cc_start: 0.8721 (mttt) cc_final: 0.8254 (mtpp) REVERT: D 60 LYS cc_start: 0.7352 (mttt) cc_final: 0.6932 (mttm) REVERT: E 43 LYS cc_start: 0.8445 (mttt) cc_final: 0.7314 (mmmt) REVERT: E 60 LYS cc_start: 0.7634 (mttt) cc_final: 0.7348 (mtpt) REVERT: F 43 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8698 (mtpp) REVERT: G 83 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6015 (mp0) REVERT: H 43 LYS cc_start: 0.8565 (mttt) cc_final: 0.8227 (mtpt) REVERT: I 60 LYS cc_start: 0.8063 (mttt) cc_final: 0.7746 (mttp) REVERT: I 83 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6177 (mp0) REVERT: J 83 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6022 (mp0) REVERT: L 83 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6513 (mp0) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.8256 time to fit residues: 81.0779 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 J residue 59 THR Chi-restraints excluded: chain L residue 58 LYS 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 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.169888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.138550 restraints weight = 19376.228| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 3.95 r_work: 0.4120 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5076 Z= 0.169 Angle : 0.542 4.784 6864 Z= 0.316 Chirality : 0.053 0.134 912 Planarity : 0.002 0.016 840 Dihedral : 5.248 12.281 732 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 1.74 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.25), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 50 PHE 0.013 0.003 PHE G 94 TYR 0.007 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 93) hydrogen bonds : angle 5.68770 ( 279) covalent geometry : bond 0.00344 ( 5076) covalent geometry : angle 0.54248 ( 6864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5707.20 seconds wall clock time: 101 minutes 42.91 seconds (6102.91 seconds total)