Starting phenix.real_space_refine on Wed Sep 17 06:02:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c5r_45221/09_2025/9c5r_45221.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c5r_45221/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c5r_45221/09_2025/9c5r_45221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c5r_45221/09_2025/9c5r_45221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c5r_45221/09_2025/9c5r_45221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c5r_45221/09_2025/9c5r_45221.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.28, per 1000 atoms: 0.22 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: 0.35 Conformation dependent library (CDL) restraints added in 148.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 0.66 Time building geometry restraints manager: 0.48 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- 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 : 7.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.27), 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 TYR 0.006 0.001 TYR I 39 PHE 0.013 0.004 PHE B 94 HIS 0.008 0.005 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00576 ( 5850) covalent geometry : angle 0.78927 ( 7890) hydrogen bonds : bond 0.21067 ( 116) hydrogen bonds : angle 9.04559 ( 348) *********************** 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 : 0.215 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: 0.7322 time to fit residues: 101.2153 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 : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 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 = 0.4407 r_free = 0.4407 target = 0.182318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137961 restraints weight = 5977.803| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.33 r_work: 0.3691 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5850 Z= 0.109 Angle : 0.551 6.057 7890 Z= 0.287 Chirality : 0.049 0.130 1020 Planarity : 0.003 0.026 1000 Dihedral : 4.459 15.081 820 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.54 % Allowed : 12.03 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR J 39 PHE 0.009 0.002 PHE C 94 HIS 0.005 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 5850) covalent geometry : angle 0.55053 ( 7890) hydrogen bonds : bond 0.04614 ( 116) hydrogen bonds : angle 5.70432 ( 348) *********************** 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: 15 poor density : 123 time to evaluate : 0.146 Fit side-chains REVERT: C 110 GLU cc_start: 0.7816 (mp0) cc_final: 0.7583 (mp0) REVERT: E 43 LYS cc_start: 0.8169 (ptpt) cc_final: 0.7940 (ptpp) REVERT: F 43 LYS cc_start: 0.8167 (ptpt) cc_final: 0.7850 (ptmt) REVERT: G 38 LEU cc_start: 0.5887 (tt) cc_final: 0.5379 (tt) REVERT: H 38 LEU cc_start: 0.6080 (tt) cc_final: 0.5762 (tt) REVERT: I 60 LYS cc_start: 0.8733 (mttm) cc_final: 0.8495 (mttm) outliers start: 15 outliers final: 7 residues processed: 129 average time/residue: 0.6892 time to fit residues: 92.0403 Evaluate side-chains 117 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 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 70 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN G 79 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 = 0.4358 r_free = 0.4358 target = 0.178078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130014 restraints weight = 5922.903| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.43 r_work: 0.3577 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 5850 Z= 0.333 Angle : 0.811 6.140 7890 Z= 0.447 Chirality : 0.056 0.162 1020 Planarity : 0.005 0.052 1000 Dihedral : 5.226 16.607 820 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 5.42 % Allowed : 13.90 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR H 39 PHE 0.023 0.006 PHE D 94 HIS 0.005 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00758 ( 5850) covalent geometry : angle 0.81090 ( 7890) hydrogen bonds : bond 0.06803 ( 116) hydrogen bonds : angle 6.29200 ( 348) *********************** 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 146 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.237 Fit side-chains REVERT: D 43 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7936 (ptpp) REVERT: E 43 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7955 (ptpp) REVERT: F 43 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7941 (ptmt) REVERT: G 38 LEU cc_start: 0.6217 (tt) cc_final: 0.5743 (tt) REVERT: H 38 LEU cc_start: 0.6068 (tt) cc_final: 0.5690 (tt) REVERT: I 46 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: I 62 GLN cc_start: 0.8551 (tt0) cc_final: 0.8321 (mt0) REVERT: J 43 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7988 (ptpp) REVERT: J 58 LYS cc_start: 0.8274 (mttt) cc_final: 0.8066 (mttp) outliers start: 32 outliers final: 21 residues processed: 128 average time/residue: 0.7242 time to fit residues: 95.7418 Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 65 ASN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 75 THR 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 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 29 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN D 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 = 0.4431 r_free = 0.4431 target = 0.184378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.137689 restraints weight = 6021.295| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.40 r_work: 0.3693 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5850 Z= 0.104 Angle : 0.523 6.208 7890 Z= 0.278 Chirality : 0.048 0.125 1020 Planarity : 0.003 0.045 1000 Dihedral : 4.554 14.898 820 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.73 % Allowed : 17.46 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.27), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR I 39 PHE 0.009 0.002 PHE C 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 5850) covalent geometry : angle 0.52324 ( 7890) hydrogen bonds : bond 0.03989 ( 116) hydrogen bonds : angle 5.48659 ( 348) *********************** 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 140 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.217 Fit side-chains REVERT: E 43 LYS cc_start: 0.8258 (ptpt) cc_final: 0.8023 (ptpp) REVERT: F 43 LYS cc_start: 0.8290 (ptpt) cc_final: 0.7907 (ptmt) REVERT: G 38 LEU cc_start: 0.6006 (tt) cc_final: 0.5552 (tt) REVERT: H 38 LEU cc_start: 0.6066 (tt) cc_final: 0.5705 (tt) REVERT: I 62 GLN cc_start: 0.8438 (tt0) cc_final: 0.8191 (mt0) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.7280 time to fit residues: 94.8423 Evaluate side-chains 125 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 75 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 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 56 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN D 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 = 0.4376 r_free = 0.4376 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131261 restraints weight = 6063.609| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.42 r_work: 0.3575 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 5850 Z= 0.292 Angle : 0.745 6.936 7890 Z= 0.409 Chirality : 0.053 0.144 1020 Planarity : 0.004 0.054 1000 Dihedral : 5.200 16.447 820 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.75 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR I 39 PHE 0.022 0.006 PHE H 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 5850) covalent geometry : angle 0.74491 ( 7890) hydrogen bonds : bond 0.06197 ( 116) hydrogen bonds : angle 6.26474 ( 348) *********************** 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 141 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.146 Fit side-chains REVERT: B 79 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: D 43 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7955 (ptpp) REVERT: E 43 LYS cc_start: 0.8224 (ptpt) cc_final: 0.7974 (ptpp) REVERT: F 43 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7970 (ptmt) REVERT: G 38 LEU cc_start: 0.6237 (tt) cc_final: 0.5779 (tt) REVERT: H 38 LEU cc_start: 0.6110 (tt) cc_final: 0.5753 (tt) REVERT: I 46 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: I 62 GLN cc_start: 0.8589 (tt0) cc_final: 0.8330 (mt0) REVERT: J 43 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7972 (ptpp) REVERT: J 58 LYS cc_start: 0.8242 (mttt) cc_final: 0.8040 (mttp) outliers start: 28 outliers final: 23 residues processed: 131 average time/residue: 0.7420 time to fit residues: 100.4040 Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 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 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 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 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 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN E 65 ASN 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 = 0.4382 r_free = 0.4382 target = 0.178003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130944 restraints weight = 5959.269| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.24 r_work: 0.3619 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5850 Z= 0.207 Angle : 0.650 7.407 7890 Z= 0.352 Chirality : 0.050 0.138 1020 Planarity : 0.004 0.055 1000 Dihedral : 5.042 16.811 820 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 5.76 % Allowed : 19.49 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.018 0.004 PHE D 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 5850) covalent geometry : angle 0.65003 ( 7890) hydrogen bonds : bond 0.05297 ( 116) hydrogen bonds : angle 6.07524 ( 348) *********************** 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 143 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.165 Fit side-chains REVERT: B 79 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: D 43 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7761 (ptpp) REVERT: E 43 LYS cc_start: 0.8211 (ptpt) cc_final: 0.7970 (ptpp) REVERT: F 43 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7951 (ptmt) REVERT: G 38 LEU cc_start: 0.6255 (tt) cc_final: 0.5810 (tt) REVERT: H 38 LEU cc_start: 0.6115 (tt) cc_final: 0.5770 (tt) REVERT: I 46 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: I 57 GLU cc_start: 0.7551 (tt0) cc_final: 0.7172 (tt0) REVERT: I 62 GLN cc_start: 0.8519 (tt0) cc_final: 0.8246 (mt0) REVERT: J 43 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (ptpt) REVERT: J 50 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.3778 (p90) outliers start: 34 outliers final: 22 residues processed: 131 average time/residue: 0.7062 time to fit residues: 95.6173 Evaluate side-chains 133 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 79 GLN D 99 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 = 0.4395 r_free = 0.4395 target = 0.179628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.131624 restraints weight = 5947.384| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.37 r_work: 0.3610 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5850 Z= 0.163 Angle : 0.594 7.764 7890 Z= 0.318 Chirality : 0.049 0.133 1020 Planarity : 0.003 0.052 1000 Dihedral : 4.864 17.377 820 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 6.44 % Allowed : 18.81 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.26), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR G 39 PHE 0.015 0.004 PHE D 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5850) covalent geometry : angle 0.59421 ( 7890) hydrogen bonds : bond 0.04769 ( 116) hydrogen bonds : angle 5.87264 ( 348) *********************** 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 146 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.271 Fit side-chains REVERT: B 79 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: E 43 LYS cc_start: 0.8261 (ptpt) cc_final: 0.8047 (ptpp) REVERT: F 43 LYS cc_start: 0.8359 (ptpt) cc_final: 0.8005 (ptmt) REVERT: G 38 LEU cc_start: 0.6293 (tt) cc_final: 0.5848 (tt) REVERT: H 38 LEU cc_start: 0.6176 (tt) cc_final: 0.5833 (tt) REVERT: I 57 GLU cc_start: 0.7663 (tt0) cc_final: 0.7309 (tt0) REVERT: I 62 GLN cc_start: 0.8504 (tt0) cc_final: 0.8234 (mt0) REVERT: J 43 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8475 (ptpt) REVERT: J 50 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.3882 (p90) outliers start: 38 outliers final: 25 residues processed: 134 average time/residue: 0.6879 time to fit residues: 95.4044 Evaluate side-chains 135 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 50 HIS 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 16 VAL 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 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 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 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 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN D 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 = 0.4404 r_free = 0.4404 target = 0.180219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.132643 restraints weight = 5910.834| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.36 r_work: 0.3632 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2273 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= 0.150 Angle : 0.578 8.863 7890 Z= 0.308 Chirality : 0.048 0.132 1020 Planarity : 0.003 0.050 1000 Dihedral : 4.807 17.904 820 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 5.93 % Allowed : 19.15 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (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 TYR 0.005 0.001 TYR I 39 PHE 0.014 0.003 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5850) covalent geometry : angle 0.57784 ( 7890) hydrogen bonds : bond 0.04483 ( 116) hydrogen bonds : angle 5.76731 ( 348) *********************** 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 144 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.245 Fit side-chains REVERT: B 79 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8543 (tt0) REVERT: D 43 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7827 (ptpp) REVERT: E 43 LYS cc_start: 0.8252 (ptpt) cc_final: 0.8050 (ptpp) REVERT: F 43 LYS cc_start: 0.8321 (ptpt) cc_final: 0.7969 (ptmt) REVERT: G 38 LEU cc_start: 0.6271 (tt) cc_final: 0.5827 (tt) REVERT: H 38 LEU cc_start: 0.6175 (tt) cc_final: 0.5828 (tt) REVERT: I 62 GLN cc_start: 0.8441 (tt0) cc_final: 0.8171 (mt0) REVERT: J 43 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8486 (ptpt) REVERT: J 50 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.3699 (p90) outliers start: 35 outliers final: 25 residues processed: 135 average time/residue: 0.6712 time to fit residues: 93.8554 Evaluate side-chains 137 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 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 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 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 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 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 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN F 79 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 = 0.4385 r_free = 0.4385 target = 0.179526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130904 restraints weight = 5957.460| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.36 r_work: 0.3575 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5850 Z= 0.289 Angle : 0.740 7.464 7890 Z= 0.405 Chirality : 0.053 0.145 1020 Planarity : 0.004 0.057 1000 Dihedral : 5.239 18.642 820 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 6.44 % Allowed : 19.15 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR F 39 PHE 0.022 0.006 PHE G 94 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 5850) covalent geometry : angle 0.73969 ( 7890) hydrogen bonds : bond 0.05937 ( 116) hydrogen bonds : angle 6.20473 ( 348) *********************** 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 151 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.142 Fit side-chains REVERT: A 46 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: B 79 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: D 43 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7855 (ptpp) REVERT: F 43 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7963 (ptmt) REVERT: G 38 LEU cc_start: 0.6336 (tt) cc_final: 0.5841 (tt) REVERT: H 38 LEU cc_start: 0.6161 (tt) cc_final: 0.5809 (tt) REVERT: I 62 GLN cc_start: 0.8619 (tt0) cc_final: 0.8338 (mt0) REVERT: J 43 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8041 (ptpp) REVERT: J 50 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.3907 (p90) outliers start: 38 outliers final: 28 residues processed: 140 average time/residue: 0.7115 time to fit residues: 102.9546 Evaluate side-chains 143 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 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 45 LYS 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 65 ASN Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP 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 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.177978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.131473 restraints weight = 5991.356| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.22 r_work: 0.3613 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5850 Z= 0.195 Angle : 0.637 7.960 7890 Z= 0.343 Chirality : 0.050 0.137 1020 Planarity : 0.003 0.056 1000 Dihedral : 5.007 17.730 820 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 6.10 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.25), residues: 780 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 PHE 0.017 0.004 PHE D 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5850) covalent geometry : angle 0.63674 ( 7890) hydrogen bonds : bond 0.05052 ( 116) hydrogen bonds : angle 5.99070 ( 348) ********************** 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 147 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.218 Fit side-chains REVERT: A 46 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 79 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 43 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7837 (ptpp) REVERT: D 115 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.5376 (t0) REVERT: F 43 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7959 (ptmt) REVERT: G 38 LEU cc_start: 0.6351 (tt) cc_final: 0.5869 (tt) REVERT: H 38 LEU cc_start: 0.6187 (tt) cc_final: 0.5837 (tt) REVERT: I 57 GLU cc_start: 0.7667 (tt0) cc_final: 0.7343 (tt0) REVERT: I 62 GLN cc_start: 0.8535 (tt0) cc_final: 0.8254 (mt0) REVERT: J 43 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8373 (ptpt) REVERT: J 50 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.3783 (p90) outliers start: 36 outliers final: 27 residues processed: 137 average time/residue: 0.6835 time to fit residues: 97.0094 Evaluate side-chains 143 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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 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 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 65 ASN Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 115 ASP 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 75 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN E 65 ASN 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 = 0.4421 r_free = 0.4421 target = 0.181168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133899 restraints weight = 5909.461| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.32 r_work: 0.3655 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5850 Z= 0.120 Angle : 0.534 8.009 7890 Z= 0.283 Chirality : 0.048 0.128 1020 Planarity : 0.003 0.049 1000 Dihedral : 4.657 16.966 820 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.42 % Allowed : 20.85 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.26), 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 TYR 0.003 0.001 TYR I 39 PHE 0.012 0.003 PHE D 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5850) covalent geometry : angle 0.53350 ( 7890) hydrogen bonds : bond 0.03838 ( 116) hydrogen bonds : angle 5.65240 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.68 seconds wall clock time: 48 minutes 56.88 seconds (2936.88 seconds total)