Starting phenix.real_space_refine on Sun Apr 27 13:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.map" model { file = "/net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5r_45221/04_2025/9c5r_45221.cif" } resolution = 2.61 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= 0.003 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: 3 Type Number sf(0) Gaussians C 3640 2.51 5 N 990 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5840 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "C" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "D" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "E" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "F" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "G" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "H" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "I" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Chain: "J" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 584 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 2 Time building chain proxies: 3.83, per 1000 atoms: 0.66 Number of scatterers: 5840 At special positions: 0 Unit cell: (113.295, 124.085, 45.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1210 8.00 N 990 7.00 C 3640 6.00 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: 1.25 Conformation dependent library (CDL) restraints added in 682.3 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 49 removed outlier: 6.299A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR C 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLU C 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N SER E 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY C 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR E 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS C 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU E 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N SER G 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY E 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR G 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS E 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N GLU G 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N SER I 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY G 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N THR I 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS G 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU I 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 65 removed outlier: 6.945A pdb=" N ALA C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU C 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA E 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR C 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA C 56 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU E 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA G 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR E 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL G 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA E 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU G 57 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA I 53 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR G 54 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL I 55 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA G 56 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU I 57 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 81 removed outlier: 9.127A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLY C 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N GLN C 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N GLY E 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR C 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR E 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL E 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N GLY G 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR E 72 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N THR G 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL E 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL G 77 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA E 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N GLN G 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ALA E 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N THR G 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N LYS E 80 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL G 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N GLY I 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR G 72 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR I 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL G 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL I 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA G 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N GLN I 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N THR I 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS G 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 92 removed outlier: 6.908A pdb=" N SER A 87 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE C 88 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA A 89 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY C 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA E 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE C 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA E 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ALA C 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER E 87 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE G 88 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA E 89 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY G 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ALA I 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE G 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ALA I 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ALA G 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 20 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 49 removed outlier: 6.362A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR D 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS B 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N GLU D 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL D 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N SER F 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR F 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS D 43 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLU F 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N SER H 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY F 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N THR H 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS F 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLU H 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N SER J 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR J 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS H 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N GLU J 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 52 through 65 removed outlier: 7.008A pdb=" N ALA D 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR B 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL D 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA B 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU D 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR D 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL F 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA D 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU F 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA H 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR F 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL H 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA F 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU H 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA J 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR H 54 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL J 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA H 56 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU J 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 81 removed outlier: 9.120A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N GLY D 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR B 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THR D 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL B 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N GLN D 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N GLY F 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR D 72 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N THR F 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLN F 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL F 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLY H 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR F 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR H 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL F 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL H 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ALA F 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLN H 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 9.137A pdb=" N VAL H 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N GLY J 73 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR H 72 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N THR J 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL H 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL J 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA H 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N GLN J 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 92 removed outlier: 6.965A pdb=" N SER B 87 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE D 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 89 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER D 87 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE F 88 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA D 89 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY F 86 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALA H 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE F 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ALA H 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ALA F 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY H 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA J 89 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE H 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA J 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ALA H 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 95 through 96 116 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 1090 1.27 - 1.34: 880 1.34 - 1.41: 160 1.41 - 1.48: 980 1.48 - 1.55: 2740 Bond restraints: 5850 Sorted by residual: bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.99e+00 bond pdb=" CB ASN I 65 " pdb=" CG ASN I 65 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.99e+00 bond pdb=" CB ASN J 65 " pdb=" CG ASN J 65 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" CB ASN G 65 " pdb=" CG ASN G 65 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 1.516 1.467 0.049 2.50e-02 1.60e+03 3.90e+00 ... (remaining 5845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7464 1.51 - 3.03: 324 3.03 - 4.54: 92 4.54 - 6.05: 0 6.05 - 7.56: 10 Bond angle restraints: 7890 Sorted by residual: angle pdb=" C HIS D 50 " pdb=" CA HIS D 50 " pdb=" CB HIS D 50 " ideal model delta sigma weight residual 114.16 106.60 7.56 2.31e+00 1.87e-01 1.07e+01 angle pdb=" C HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 114.16 106.62 7.54 2.31e+00 1.87e-01 1.07e+01 angle pdb=" C HIS C 50 " pdb=" CA HIS C 50 " pdb=" CB HIS C 50 " ideal model delta sigma weight residual 114.16 106.62 7.54 2.31e+00 1.87e-01 1.07e+01 angle pdb=" C HIS J 50 " pdb=" CA HIS J 50 " pdb=" CB HIS J 50 " ideal model delta sigma weight residual 114.16 106.63 7.53 2.31e+00 1.87e-01 1.06e+01 angle pdb=" C HIS G 50 " pdb=" CA HIS G 50 " pdb=" CB HIS G 50 " ideal model delta sigma weight residual 114.16 106.65 7.51 2.31e+00 1.87e-01 1.06e+01 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3240 17.56 - 35.13: 170 35.13 - 52.69: 30 52.69 - 70.25: 0 70.25 - 87.81: 20 Dihedral angle restraints: 3460 sinusoidal: 1200 harmonic: 2260 Sorted by residual: dihedral pdb=" CB GLU E 57 " pdb=" CG GLU E 57 " pdb=" CD GLU E 57 " pdb=" OE1 GLU E 57 " ideal model delta sinusoidal sigma weight residual 0.00 -87.81 87.81 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 57 " pdb=" CG GLU C 57 " pdb=" CD GLU C 57 " pdb=" OE1 GLU C 57 " ideal model delta sinusoidal sigma weight residual 0.00 -87.79 87.79 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU G 57 " pdb=" CG GLU G 57 " pdb=" CD GLU G 57 " pdb=" OE1 GLU G 57 " ideal model delta sinusoidal sigma weight residual 0.00 -87.77 87.77 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 553 0.032 - 0.063: 257 0.063 - 0.094: 50 0.094 - 0.126: 143 0.126 - 0.157: 17 Chirality restraints: 1020 Sorted by residual: chirality pdb=" CB VAL A 16 " pdb=" CA VAL A 16 " pdb=" CG1 VAL A 16 " pdb=" CG2 VAL A 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB VAL I 16 " pdb=" CA VAL I 16 " pdb=" CG1 VAL I 16 " pdb=" CG2 VAL I 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CB VAL D 16 " pdb=" CA VAL D 16 " pdb=" CG1 VAL D 16 " pdb=" CG2 VAL D 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1017 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 107 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO F 108 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 108 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 108 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 107 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO E 108 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 107 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO I 108 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO I 108 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO I 108 " -0.024 5.00e-02 4.00e+02 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1856 2.86 - 3.37: 4908 3.37 - 3.88: 9230 3.88 - 4.39: 10266 4.39 - 4.90: 21136 Nonbonded interactions: 47396 Sorted by model distance: nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU J 46 " pdb=" NZ LYS J 80 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU H 46 " pdb=" NZ LYS H 80 " model vdw 2.346 3.120 ... (remaining 47391 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.700 Find NCS groups from input model: 0.120 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.006 0.050 5850 Z= 0.260 Angle : 0.789 7.563 7890 Z= 0.436 Chirality : 0.054 0.157 1020 Planarity : 0.005 0.043 1000 Dihedral : 13.540 87.812 2020 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.98 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS I 50 PHE 0.013 0.004 PHE B 94 TYR 0.006 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.21067 ( 116) hydrogen bonds : angle 9.04559 ( 348) covalent geometry : bond 0.00576 ( 5850) covalent geometry : angle 0.78927 ( 7890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.589 Fit side-chains REVERT: B 46 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 43 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7868 (ptpp) REVERT: F 43 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7608 (ptmt) REVERT: F 45 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7960 (mtpt) REVERT: F 46 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7941 (mt-10) REVERT: H 38 LEU cc_start: 0.6297 (tt) cc_final: 0.6021 (tt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 1.8496 time to fit residues: 255.2794 Evaluate side-chains 104 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 79 GLN D 99 GLN F 99 GLN G 79 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.181982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134997 restraints weight = 5913.335| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.37 r_work: 0.3623 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5850 Z= 0.200 Angle : 0.675 5.770 7890 Z= 0.362 Chirality : 0.051 0.135 1020 Planarity : 0.004 0.033 1000 Dihedral : 4.888 16.096 820 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.39 % Allowed : 11.86 % Favored : 84.75 % 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: -2.96 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 PHE 0.015 0.004 PHE G 94 TYR 0.006 0.001 TYR J 39 Details of bonding type rmsd hydrogen bonds : bond 0.05870 ( 116) hydrogen bonds : angle 5.99348 ( 348) covalent geometry : bond 0.00443 ( 5850) covalent geometry : angle 0.67464 ( 7890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.583 Fit side-chains REVERT: E 43 LYS cc_start: 0.8208 (ptpt) cc_final: 0.7912 (ptpp) REVERT: F 43 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7864 (ptmt) REVERT: G 38 LEU cc_start: 0.5995 (tt) cc_final: 0.5507 (tt) REVERT: G 109 GLN cc_start: 0.7415 (mp10) cc_final: 0.7132 (mp10) REVERT: H 38 LEU cc_start: 0.5964 (tt) cc_final: 0.5617 (tt) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.6306 time to fit residues: 209.1340 Evaluate side-chains 119 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN E 99 GLN F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.179489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132829 restraints weight = 5945.683| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.39 r_work: 0.3595 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 5850 Z= 0.317 Angle : 0.806 6.669 7890 Z= 0.442 Chirality : 0.055 0.155 1020 Planarity : 0.005 0.054 1000 Dihedral : 5.285 16.400 820 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.08 % Allowed : 15.93 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.15 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 50 PHE 0.021 0.005 PHE D 94 TYR 0.008 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.06635 ( 116) hydrogen bonds : angle 6.34384 ( 348) covalent geometry : bond 0.00719 ( 5850) covalent geometry : angle 0.80650 ( 7890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.682 Fit side-chains REVERT: A 46 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: B 79 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: E 43 LYS cc_start: 0.8227 (ptpt) cc_final: 0.8018 (ptpp) REVERT: F 43 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7933 (ptmt) REVERT: G 38 LEU cc_start: 0.6201 (tt) cc_final: 0.5721 (tt) REVERT: H 38 LEU cc_start: 0.6093 (tt) cc_final: 0.5741 (tt) REVERT: I 46 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: I 62 GLN cc_start: 0.8519 (tt0) cc_final: 0.8283 (mt0) REVERT: J 43 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7976 (ptpp) outliers start: 30 outliers final: 22 residues processed: 132 average time/residue: 2.0136 time to fit residues: 274.2047 Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.178247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131163 restraints weight = 6018.289| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.33 r_work: 0.3605 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5850 Z= 0.229 Angle : 0.688 6.232 7890 Z= 0.374 Chirality : 0.051 0.139 1020 Planarity : 0.004 0.056 1000 Dihedral : 5.122 15.989 820 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 5.93 % Allowed : 18.81 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.017 0.004 PHE D 94 TYR 0.006 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 116) hydrogen bonds : angle 6.13966 ( 348) covalent geometry : bond 0.00516 ( 5850) covalent geometry : angle 0.68801 ( 7890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.645 Fit side-chains REVERT: A 46 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: B 79 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: E 43 LYS cc_start: 0.8227 (ptpt) cc_final: 0.7934 (ptpp) REVERT: F 43 LYS cc_start: 0.8317 (ptpt) cc_final: 0.7953 (ptmt) REVERT: F 79 GLN cc_start: 0.8816 (tt0) cc_final: 0.8607 (tt0) REVERT: G 38 LEU cc_start: 0.6215 (tt) cc_final: 0.5713 (tt) REVERT: H 38 LEU cc_start: 0.6166 (tt) cc_final: 0.5811 (tt) REVERT: I 46 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: I 62 GLN cc_start: 0.8544 (tt0) cc_final: 0.8268 (mt0) REVERT: J 43 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8410 (ptpt) outliers start: 35 outliers final: 29 residues processed: 130 average time/residue: 1.9044 time to fit residues: 256.7973 Evaluate side-chains 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 20.0000 chunk 69 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN D 65 ASN F 79 GLN F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.182847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.135573 restraints weight = 5960.073| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.31 r_work: 0.3651 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5850 Z= 0.133 Angle : 0.562 6.809 7890 Z= 0.298 Chirality : 0.048 0.128 1020 Planarity : 0.003 0.043 1000 Dihedral : 4.769 15.546 820 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.25 % Allowed : 19.32 % Favored : 75.42 % 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: -3.02 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.013 0.003 PHE D 94 TYR 0.003 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 116) hydrogen bonds : angle 5.74095 ( 348) covalent geometry : bond 0.00290 ( 5850) covalent geometry : angle 0.56204 ( 7890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.600 Fit side-chains REVERT: A 46 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: A 99 GLN cc_start: 0.7868 (tt0) cc_final: 0.7603 (mt0) REVERT: D 43 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7827 (ptpp) REVERT: E 43 LYS cc_start: 0.8265 (ptpt) cc_final: 0.8029 (ptpp) REVERT: F 43 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7979 (ptmt) REVERT: F 79 GLN cc_start: 0.8817 (tt0) cc_final: 0.8590 (tt0) REVERT: G 38 LEU cc_start: 0.6282 (tt) cc_final: 0.5837 (tt) REVERT: H 38 LEU cc_start: 0.6159 (tt) cc_final: 0.5788 (tt) REVERT: I 62 GLN cc_start: 0.8480 (tt0) cc_final: 0.8238 (mt0) REVERT: J 43 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8457 (ptpt) outliers start: 31 outliers final: 21 residues processed: 132 average time/residue: 1.4907 time to fit residues: 204.0779 Evaluate side-chains 134 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 0.0010 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.180554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132854 restraints weight = 5890.826| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.35 r_work: 0.3632 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5850 Z= 0.144 Angle : 0.565 7.934 7890 Z= 0.302 Chirality : 0.048 0.130 1020 Planarity : 0.003 0.039 1000 Dihedral : 4.768 15.456 820 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.61 % Allowed : 19.15 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.013 0.003 PHE H 94 TYR 0.004 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 116) hydrogen bonds : angle 5.73583 ( 348) covalent geometry : bond 0.00319 ( 5850) covalent geometry : angle 0.56478 ( 7890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.583 Fit side-chains REVERT: A 99 GLN cc_start: 0.7829 (tt0) cc_final: 0.7566 (mt0) REVERT: D 43 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7873 (ptpp) REVERT: E 43 LYS cc_start: 0.8275 (ptpt) cc_final: 0.8059 (ptpp) REVERT: F 43 LYS cc_start: 0.8338 (ptpt) cc_final: 0.7975 (ptmt) REVERT: G 38 LEU cc_start: 0.6334 (tt) cc_final: 0.5892 (tt) REVERT: H 38 LEU cc_start: 0.6142 (tt) cc_final: 0.5786 (tt) REVERT: I 62 GLN cc_start: 0.8518 (tt0) cc_final: 0.8249 (mt0) REVERT: J 43 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8469 (ptpt) REVERT: J 50 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.3667 (p90) outliers start: 39 outliers final: 26 residues processed: 134 average time/residue: 1.3648 time to fit residues: 189.9057 Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.176598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129592 restraints weight = 5906.858| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.21 r_work: 0.3586 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 5850 Z= 0.338 Angle : 0.792 7.449 7890 Z= 0.435 Chirality : 0.055 0.147 1020 Planarity : 0.004 0.048 1000 Dihedral : 5.346 16.386 820 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 8.47 % Allowed : 17.63 % Favored : 73.90 % 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: -3.25 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 50 PHE 0.023 0.006 PHE D 94 TYR 0.007 0.002 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.06254 ( 116) hydrogen bonds : angle 6.29502 ( 348) covalent geometry : bond 0.00772 ( 5850) covalent geometry : angle 0.79163 ( 7890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.637 Fit side-chains REVERT: D 115 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5474 (t0) REVERT: E 43 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8140 (ptpp) REVERT: F 43 LYS cc_start: 0.8308 (ptpt) cc_final: 0.7947 (ptmt) REVERT: G 38 LEU cc_start: 0.6475 (tt) cc_final: 0.5976 (tt) REVERT: H 38 LEU cc_start: 0.6290 (tt) cc_final: 0.5939 (tt) REVERT: I 46 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (mt-10) REVERT: I 62 GLN cc_start: 0.8590 (tt0) cc_final: 0.8324 (mt0) REVERT: J 43 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7977 (ptpp) REVERT: J 50 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.3883 (p90) outliers start: 50 outliers final: 34 residues processed: 148 average time/residue: 1.3413 time to fit residues: 206.2814 Evaluate side-chains 146 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN F 99 GLN G 99 GLN J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.180065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.132353 restraints weight = 5838.636| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.32 r_work: 0.3631 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5850 Z= 0.145 Angle : 0.578 7.925 7890 Z= 0.309 Chirality : 0.049 0.130 1020 Planarity : 0.003 0.042 1000 Dihedral : 4.858 15.417 820 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 7.46 % Allowed : 18.47 % Favored : 74.07 % 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: -3.10 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.014 0.003 PHE D 94 TYR 0.004 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 116) hydrogen bonds : angle 5.91584 ( 348) covalent geometry : bond 0.00319 ( 5850) covalent geometry : angle 0.57800 ( 7890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.662 Fit side-chains REVERT: A 99 GLN cc_start: 0.8013 (tt0) cc_final: 0.7697 (mt0) REVERT: B 79 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: D 43 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7845 (ptpp) REVERT: D 115 ASP cc_start: 0.5640 (OUTLIER) cc_final: 0.5377 (t0) REVERT: E 43 LYS cc_start: 0.8237 (ptpt) cc_final: 0.8029 (ptpp) REVERT: F 43 LYS cc_start: 0.8354 (ptpt) cc_final: 0.7986 (ptmt) REVERT: G 38 LEU cc_start: 0.6369 (tt) cc_final: 0.5898 (tt) REVERT: H 38 LEU cc_start: 0.6245 (tt) cc_final: 0.5878 (tt) REVERT: I 50 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.3434 (p-80) REVERT: I 62 GLN cc_start: 0.8530 (tt0) cc_final: 0.8256 (mt0) REVERT: J 43 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8376 (ptpt) REVERT: J 50 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.3669 (p90) outliers start: 44 outliers final: 34 residues processed: 141 average time/residue: 1.4263 time to fit residues: 209.0663 Evaluate side-chains 148 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 115 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN G 99 GLN J 65 ASN J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.177916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130689 restraints weight = 5951.141| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.31 r_work: 0.3604 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5850 Z= 0.221 Angle : 0.660 9.005 7890 Z= 0.357 Chirality : 0.051 0.138 1020 Planarity : 0.003 0.043 1000 Dihedral : 5.047 16.497 820 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 7.46 % Allowed : 18.98 % Favored : 73.56 % 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: -3.16 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.018 0.005 PHE D 94 TYR 0.006 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 116) hydrogen bonds : angle 6.07204 ( 348) covalent geometry : bond 0.00502 ( 5850) covalent geometry : angle 0.65976 ( 7890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.650 Fit side-chains REVERT: B 79 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 43 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8123 (ptpp) REVERT: D 115 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5396 (t0) REVERT: F 43 LYS cc_start: 0.8312 (ptpt) cc_final: 0.7946 (ptmt) REVERT: G 38 LEU cc_start: 0.6382 (tt) cc_final: 0.5905 (tt) REVERT: H 38 LEU cc_start: 0.6238 (tt) cc_final: 0.5882 (tt) REVERT: I 50 HIS cc_start: 0.6107 (OUTLIER) cc_final: 0.3287 (p-80) REVERT: I 57 GLU cc_start: 0.7727 (tt0) cc_final: 0.7368 (tt0) REVERT: I 62 GLN cc_start: 0.8562 (tt0) cc_final: 0.8281 (mt0) REVERT: J 43 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (ptpt) REVERT: J 50 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.3804 (p90) outliers start: 44 outliers final: 36 residues processed: 140 average time/residue: 1.4473 time to fit residues: 210.1984 Evaluate side-chains 150 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 65 ASN F 99 GLN G 99 GLN J 65 ASN J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.178667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130482 restraints weight = 5931.301| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.35 r_work: 0.3598 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5850 Z= 0.209 Angle : 0.649 7.788 7890 Z= 0.351 Chirality : 0.050 0.137 1020 Planarity : 0.003 0.042 1000 Dihedral : 5.042 16.883 820 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 7.29 % Allowed : 19.49 % Favored : 73.22 % 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: -3.16 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.017 0.004 PHE G 94 TYR 0.005 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 116) hydrogen bonds : angle 6.01862 ( 348) covalent geometry : bond 0.00472 ( 5850) covalent geometry : angle 0.64864 ( 7890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.074 Fit side-chains REVERT: B 79 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 43 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8093 (ptpp) REVERT: D 115 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5384 (t0) REVERT: F 43 LYS cc_start: 0.8317 (ptpt) cc_final: 0.7949 (ptmt) REVERT: G 38 LEU cc_start: 0.6423 (tt) cc_final: 0.5921 (tt) REVERT: H 38 LEU cc_start: 0.6274 (tt) cc_final: 0.5912 (tt) REVERT: I 50 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.3308 (p-80) REVERT: I 57 GLU cc_start: 0.7728 (tt0) cc_final: 0.7362 (tt0) REVERT: I 62 GLN cc_start: 0.8562 (tt0) cc_final: 0.8276 (mt0) REVERT: J 43 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8371 (ptpt) REVERT: J 50 HIS cc_start: 0.6625 (OUTLIER) cc_final: 0.3758 (p90) outliers start: 43 outliers final: 35 residues processed: 139 average time/residue: 1.4256 time to fit residues: 205.8532 Evaluate side-chains 148 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 115 ASP Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN G 99 GLN J 65 ASN J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131299 restraints weight = 6005.909| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.29 r_work: 0.3612 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5850 Z= 0.181 Angle : 0.618 7.875 7890 Z= 0.333 Chirality : 0.049 0.134 1020 Planarity : 0.003 0.042 1000 Dihedral : 4.987 17.484 820 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 7.46 % Allowed : 19.32 % Favored : 73.22 % 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: -3.14 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.016 0.004 PHE D 94 TYR 0.005 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 116) hydrogen bonds : angle 5.99688 ( 348) covalent geometry : bond 0.00407 ( 5850) covalent geometry : angle 0.61792 ( 7890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6169.19 seconds wall clock time: 107 minutes 48.86 seconds (6468.86 seconds total)