Starting phenix.real_space_refine on Sat Aug 23 06:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nca_12264/08_2025/7nca_12264.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3180 2.51 5 N 876 2.21 5 O 996 1.98 5 H 5376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10428 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10428 At special positions: 0 Unit cell: (80.94, 112.86, 52.44, 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: 1.00 Conformation dependent library (CDL) restraints added in 259.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 18 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 44 removed outlier: 6.651A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY E 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS E 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 43 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL K 40 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER K 42 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS F 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR K 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU J 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLY K 41 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL J 40 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS K 43 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER J 42 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR J 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N SER L 42 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY J 41 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N THR L 44 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS J 43 " --> pdb=" O THR L 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.046A pdb=" N VAL A 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N HIS A 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA F 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N GLY K 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N HIS F 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL J 49 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL K 52 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY J 51 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL J 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLY L 51 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N HIS J 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.624A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA K 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL F 55 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL J 55 " --> pdb=" O ALA L 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 66 removed outlier: 7.126A pdb=" N GLU A 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR F 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL F 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU F 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR K 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL F 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL K 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN J 62 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL K 63 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR J 64 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN K 65 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL J 66 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU J 61 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR L 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL J 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL L 66 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN J 65 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.692A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR K 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL J 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.764A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN F 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 78 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN K 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR J 75 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ALA K 78 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL J 77 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 79 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 82 through 83 removed outlier: 7.168A pdb=" N VAL A 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL F 82 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL J 82 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.933A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 89 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 89 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA J 89 " --> pdb=" O ILE L 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.973A pdb=" N GLY A 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS E 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY F 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL F 95 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 96 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY K 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE F 94 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL K 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N THR J 92 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL K 95 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N PHE J 94 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR J 92 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL L 95 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE J 94 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 44 removed outlier: 3.588A pdb=" N SER B 42 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR D 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.957A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LYS G 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL H 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS H 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL H 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR G 44 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLY I 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU G 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VAL I 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY I 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N HIS G 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.468A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.731A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU B 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU D 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR H 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL H 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN D 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU G 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR I 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL I 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.638A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR H 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.708A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN H 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.503A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU G 83 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL G 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.793A pdb=" N ALA B 89 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 89 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 89 " --> pdb=" O ILE I 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 96 removed outlier: 7.057A pdb=" N GLY B 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N LYS C 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY D 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 95 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 93 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE H 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL D 95 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LYS H 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N LYS H 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY I 93 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE G 94 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL I 95 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 96 " --> pdb=" O VAL I 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 36 hydrogen bonds defined for protein. 108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.04: 1200 1.04 - 1.16: 4176 1.16 - 1.29: 866 1.29 - 1.42: 1090 1.42 - 1.55: 3120 Bond restraints: 10452 Sorted by residual: bond pdb=" N THR F 72 " pdb=" H THR F 72 " 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 K 75 " pdb=" H THR K 75 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY F 41 " pdb=" H GLY F 41 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 TYR J 39 " pdb=" HE1 TYR J 39 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLY L 67 " pdb=" H GLY L 67 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 10447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12946 1.75 - 3.50: 4374 3.50 - 5.24: 1035 5.24 - 6.99: 611 6.99 - 8.74: 66 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N ALA C 90 " pdb=" CA ALA C 90 " pdb=" C ALA C 90 " ideal model delta sigma weight residual 110.06 116.62 -6.56 1.43e+00 4.89e-01 2.10e+01 angle pdb=" CB HIS G 50 " pdb=" CG HIS G 50 " pdb=" CD2 HIS G 50 " ideal model delta sigma weight residual 131.20 125.30 5.90 1.30e+00 5.92e-01 2.06e+01 angle pdb=" OE1 GLN A 79 " pdb=" CD GLN A 79 " pdb=" NE2 GLN A 79 " ideal model delta sigma weight residual 122.60 118.08 4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" OE1 GLN D 62 " pdb=" CD GLN D 62 " pdb=" NE2 GLN D 62 " ideal model delta sigma weight residual 122.60 118.19 4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " pdb=" CD2 HIS C 50 " ideal model delta sigma weight residual 131.20 125.52 5.68 1.30e+00 5.92e-01 1.91e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4166 16.11 - 32.23: 172 32.23 - 48.34: 146 48.34 - 64.46: 270 64.46 - 80.57: 34 Dihedral angle restraints: 4788 sinusoidal: 2664 harmonic: 2124 Sorted by residual: dihedral pdb=" CA ALA F 89 " pdb=" C ALA F 89 " pdb=" N ALA F 90 " pdb=" CA ALA F 90 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 354 0.045 - 0.089: 294 0.089 - 0.134: 179 0.134 - 0.179: 74 0.179 - 0.223: 11 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA VAL B 82 " pdb=" N VAL B 82 " pdb=" C VAL B 82 " pdb=" CB VAL B 82 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU G 57 " pdb=" N GLU G 57 " pdb=" C GLU G 57 " pdb=" CB GLU G 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU F 57 " pdb=" N GLU F 57 " pdb=" C GLU F 57 " pdb=" CB GLU F 57 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 909 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " -0.081 2.00e-02 2.50e+03 3.56e-02 3.81e+01 pdb=" CG TYR E 39 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR E 39 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR E 39 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR E 39 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 39 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 89 " -0.031 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" N ALA G 90 " 0.100 2.00e-02 2.50e+03 pdb=" CA ALA G 90 " -0.028 2.00e-02 2.50e+03 pdb=" H ALA G 90 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 89 " 0.031 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" N ALA A 90 " -0.098 2.00e-02 2.50e+03 pdb=" CA ALA A 90 " 0.028 2.00e-02 2.50e+03 pdb=" H ALA A 90 " 0.039 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.34: 1284 2.34 - 2.88: 20496 2.88 - 3.42: 21178 3.42 - 3.96: 25276 3.96 - 4.50: 38471 Nonbonded interactions: 106705 Sorted by model distance: nonbonded pdb=" O LYS H 43 " pdb=" HG1 THR H 44 " model vdw 1.803 2.450 nonbonded pdb=" O ALA K 53 " pdb=" HG1 THR K 54 " model vdw 1.811 2.450 nonbonded pdb=" O LYS G 43 " pdb=" HG1 THR G 44 " model vdw 1.819 2.450 nonbonded pdb=" O ALA J 53 " pdb=" HG1 THR J 54 " model vdw 1.822 2.450 nonbonded pdb=" OE2 GLU A 57 " pdb=" HZ2 LYS A 58 " model vdw 1.826 2.450 ... (remaining 106700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 0.037 5076 Z= 0.802 Angle : 2.035 7.221 6864 Z= 1.305 Chirality : 0.080 0.223 912 Planarity : 0.007 0.040 840 Dihedral : 10.639 80.570 1716 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.069 0.018 TYR E 39 PHE 0.035 0.008 PHE E 94 HIS 0.007 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01169 ( 5076) covalent geometry : angle 2.03524 ( 6864) hydrogen bonds : bond 0.43685 ( 36) hydrogen bonds : angle 5.90975 ( 108) *********************** 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 126 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7867 (tm-30) REVERT: D 57 GLU cc_start: 0.7625 (tp30) cc_final: 0.7382 (tp30) REVERT: D 80 LYS cc_start: 0.8342 (tttt) cc_final: 0.8101 (tttm) REVERT: L 44 THR cc_start: 0.8765 (m) cc_final: 0.8450 (t) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.2830 time to fit residues: 41.6724 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 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 = 0.3828 r_free = 0.3828 target = 0.112657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090957 restraints weight = 24207.196| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.51 r_work: 0.3426 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5076 Z= 0.163 Angle : 0.564 4.176 6864 Z= 0.326 Chirality : 0.053 0.140 912 Planarity : 0.002 0.008 840 Dihedral : 5.797 52.689 735 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.78 % Allowed : 8.33 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.68 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR C 39 PHE 0.013 0.003 PHE L 94 HIS 0.003 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5076) covalent geometry : angle 0.56444 ( 6864) hydrogen bonds : bond 0.05704 ( 36) hydrogen bonds : angle 5.29352 ( 108) *********************** 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 103 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.295 Fit side-chains REVERT: D 57 GLU cc_start: 0.8361 (tp30) cc_final: 0.8065 (tp30) REVERT: J 80 LYS cc_start: 0.8516 (tttt) cc_final: 0.8278 (tttm) REVERT: L 44 THR cc_start: 0.8492 (m) cc_final: 0.8275 (t) outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.2213 time to fit residues: 27.2290 Evaluate side-chains 88 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.115443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092846 restraints weight = 24049.502| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.56 r_work: 0.3454 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.106 Angle : 0.467 4.351 6864 Z= 0.263 Chirality : 0.053 0.142 912 Planarity : 0.001 0.005 840 Dihedral : 4.536 17.040 732 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.16 % Allowed : 9.30 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.15), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.010 0.002 PHE I 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 5076) covalent geometry : angle 0.46688 ( 6864) hydrogen bonds : bond 0.05159 ( 36) hydrogen bonds : angle 4.92228 ( 108) *********************** 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 104 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.292 Fit side-chains REVERT: D 57 GLU cc_start: 0.8485 (tp30) cc_final: 0.8063 (tp30) REVERT: I 38 LEU cc_start: 0.9139 (tt) cc_final: 0.8859 (tp) REVERT: J 80 LYS cc_start: 0.8486 (tttt) cc_final: 0.8262 (tttm) outliers start: 6 outliers final: 6 residues processed: 98 average time/residue: 0.2015 time to fit residues: 24.7391 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 : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain J residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.115634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093105 restraints weight = 23990.708| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.54 r_work: 0.3444 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5076 Z= 0.128 Angle : 0.477 3.651 6864 Z= 0.270 Chirality : 0.053 0.145 912 Planarity : 0.001 0.006 840 Dihedral : 4.518 17.394 732 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.55 % Allowed : 9.50 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR H 39 PHE 0.013 0.003 PHE I 94 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5076) covalent geometry : angle 0.47672 ( 6864) hydrogen bonds : bond 0.05813 ( 36) hydrogen bonds : angle 5.14291 ( 108) *********************** 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 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.298 Fit side-chains REVERT: D 57 GLU cc_start: 0.8534 (tp30) cc_final: 0.8147 (tp30) REVERT: G 62 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: H 57 GLU cc_start: 0.8322 (tp30) cc_final: 0.7994 (tp30) REVERT: J 80 LYS cc_start: 0.8500 (tttt) cc_final: 0.8260 (tttm) REVERT: K 97 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7310 (mmtt) outliers start: 8 outliers final: 4 residues processed: 88 average time/residue: 0.1961 time to fit residues: 21.7585 Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain K residue 97 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.114983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092581 restraints weight = 24078.481| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.54 r_work: 0.3432 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4291 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= 0.147 Angle : 0.490 3.999 6864 Z= 0.281 Chirality : 0.053 0.149 912 Planarity : 0.002 0.005 840 Dihedral : 4.601 17.700 732 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.33 % Allowed : 9.11 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 39 PHE 0.011 0.003 PHE L 94 HIS 0.002 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5076) covalent geometry : angle 0.48999 ( 6864) hydrogen bonds : bond 0.06500 ( 36) hydrogen bonds : angle 5.34437 ( 108) *********************** 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 95 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: H 57 GLU cc_start: 0.8352 (tp30) cc_final: 0.8027 (tp30) REVERT: J 80 LYS cc_start: 0.8577 (tttt) cc_final: 0.8312 (tttm) REVERT: K 97 LYS cc_start: 0.7966 (mptt) cc_final: 0.7743 (mmtt) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.2058 time to fit residues: 22.6504 Evaluate side-chains 90 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain K residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 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 = 0.3850 r_free = 0.3850 target = 0.115817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.094728 restraints weight = 23345.116| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.32 r_work: 0.3468 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5076 Z= 0.103 Angle : 0.443 3.729 6864 Z= 0.250 Chirality : 0.053 0.146 912 Planarity : 0.001 0.004 840 Dihedral : 4.408 17.070 732 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.55 % Allowed : 10.47 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.21), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.008 0.002 PHE B 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5076) covalent geometry : angle 0.44299 ( 6864) hydrogen bonds : bond 0.04719 ( 36) hydrogen bonds : angle 5.01041 ( 108) *********************** 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 85 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.318 Fit side-chains REVERT: H 57 GLU cc_start: 0.8368 (tp30) cc_final: 0.8028 (tp30) REVERT: H 83 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7632 (mt-10) REVERT: J 80 LYS cc_start: 0.8544 (tttt) cc_final: 0.8278 (tttm) REVERT: K 97 LYS cc_start: 0.7943 (mptt) cc_final: 0.7716 (mmtt) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.2036 time to fit residues: 20.7870 Evaluate side-chains 81 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain K residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.116555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095522 restraints weight = 23096.746| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.30 r_work: 0.3479 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4550 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= 0.088 Angle : 0.419 3.682 6864 Z= 0.234 Chirality : 0.053 0.143 912 Planarity : 0.001 0.003 840 Dihedral : 4.206 15.981 732 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.007 0.002 PHE C 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 5076) covalent geometry : angle 0.41935 ( 6864) hydrogen bonds : bond 0.03999 ( 36) hydrogen bonds : angle 4.78137 ( 108) *********************** 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 82 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.307 Fit side-chains REVERT: A 61 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7818 (mt-10) REVERT: H 83 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7570 (mt-10) REVERT: I 46 GLU cc_start: 0.8038 (tt0) cc_final: 0.7833 (tt0) REVERT: J 80 LYS cc_start: 0.8536 (tttt) cc_final: 0.8271 (tttm) REVERT: K 97 LYS cc_start: 0.7785 (mptt) cc_final: 0.7549 (mmtt) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1805 time to fit residues: 18.5015 Evaluate side-chains 80 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain K residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.116086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095167 restraints weight = 23091.816| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.31 r_work: 0.3474 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.099 Angle : 0.429 3.777 6864 Z= 0.241 Chirality : 0.053 0.144 912 Planarity : 0.001 0.004 840 Dihedral : 4.213 16.348 732 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.36 % Allowed : 12.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.009 0.002 PHE I 94 HIS 0.002 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5076) covalent geometry : angle 0.42919 ( 6864) hydrogen bonds : bond 0.04702 ( 36) hydrogen bonds : angle 4.88833 ( 108) *********************** 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 81 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.323 Fit side-chains REVERT: A 61 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 83 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7585 (mt-10) REVERT: I 46 GLU cc_start: 0.8096 (tt0) cc_final: 0.7869 (tt0) REVERT: J 80 LYS cc_start: 0.8537 (tttt) cc_final: 0.8265 (tttm) REVERT: K 97 LYS cc_start: 0.8004 (mptt) cc_final: 0.7759 (mmtt) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.1876 time to fit residues: 18.6053 Evaluate side-chains 80 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain J residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.116594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094616 restraints weight = 23529.330| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.47 r_work: 0.3474 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5076 Z= 0.086 Angle : 0.411 4.064 6864 Z= 0.229 Chirality : 0.053 0.143 912 Planarity : 0.001 0.003 840 Dihedral : 4.112 15.533 732 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 12.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 39 PHE 0.007 0.002 PHE E 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 5076) covalent geometry : angle 0.41130 ( 6864) hydrogen bonds : bond 0.03844 ( 36) hydrogen bonds : angle 4.70186 ( 108) *********************** 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 82 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.297 Fit side-chains REVERT: A 61 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7836 (mt-10) REVERT: J 80 LYS cc_start: 0.8566 (tttt) cc_final: 0.8295 (tttm) REVERT: K 97 LYS cc_start: 0.7995 (mptt) cc_final: 0.7763 (mmtt) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.1808 time to fit residues: 18.4305 Evaluate side-chains 80 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain K residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094747 restraints weight = 23100.023| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.30 r_work: 0.3470 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5076 Z= 0.112 Angle : 0.440 3.591 6864 Z= 0.248 Chirality : 0.053 0.144 912 Planarity : 0.001 0.004 840 Dihedral : 4.244 16.478 732 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.16 % Allowed : 12.02 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.009 0.002 PHE I 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5076) covalent geometry : angle 0.43956 ( 6864) hydrogen bonds : bond 0.05201 ( 36) hydrogen bonds : angle 4.94940 ( 108) ********************** 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 85 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.315 Fit side-chains REVERT: A 61 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7819 (mt-10) REVERT: J 80 LYS cc_start: 0.8538 (tttt) cc_final: 0.8259 (tttm) REVERT: K 97 LYS cc_start: 0.7951 (mptt) cc_final: 0.7725 (mmtt) outliers start: 6 outliers final: 6 residues processed: 82 average time/residue: 0.1732 time to fit residues: 18.4551 Evaluate side-chains 85 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain H residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093320 restraints weight = 23557.976| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 3.49 r_work: 0.3446 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 5076 Z= 0.165 Angle : 0.503 3.983 6864 Z= 0.288 Chirality : 0.054 0.150 912 Planarity : 0.002 0.006 840 Dihedral : 4.582 17.876 732 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.74 % Allowed : 11.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.013 0.003 PHE A 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5076) covalent geometry : angle 0.50272 ( 6864) hydrogen bonds : bond 0.06928 ( 36) hydrogen bonds : angle 5.34371 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.62 seconds wall clock time: 39 minutes 59.69 seconds (2399.69 seconds total)