Starting phenix.real_space_refine on Thu Feb 5 00:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.map" model { file = "/net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kh7_62334/02_2026/9kh7_62334.cif" } resolution = 3.0 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= 0.004 sd= 0.086 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 42 5.16 5 C 8892 2.51 5 N 2364 2.21 5 O 2652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13962 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "E" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "F" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2282 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 15, 'TRANS': 277} Chain breaks: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13962 At special positions: 0 Unit cell: (118.69, 153.55, 72.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 12 15.00 O 2652 8.00 N 2364 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 561.7 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 52.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.773A pdb=" N GLU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.793A pdb=" N CYS A 41 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.610A pdb=" N ILE A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.716A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.698A pdb=" N LEU A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.172A pdb=" N ILE A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 289 through 308 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 16 through 33 removed outlier: 3.536A pdb=" N GLU B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.792A pdb=" N CYS B 41 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.610A pdb=" N ILE B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.715A pdb=" N LEU B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.698A pdb=" N LEU B 177 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.172A pdb=" N ILE B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 289 through 308 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'C' and resid 12 through 14 No H-bonds generated for 'chain 'C' and resid 12 through 14' Processing helix chain 'C' and resid 15 through 33 removed outlier: 3.933A pdb=" N THR C 19 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.792A pdb=" N CYS C 41 " --> pdb=" O ILE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 61 removed outlier: 3.504A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.610A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.716A pdb=" N LEU C 113 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.698A pdb=" N LEU C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 4.174A pdb=" N ILE C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 289 through 308 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'D' and resid 12 through 14 No H-bonds generated for 'chain 'D' and resid 12 through 14' Processing helix chain 'D' and resid 15 through 33 removed outlier: 4.174A pdb=" N THR D 19 " --> pdb=" O ARG D 15 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.792A pdb=" N CYS D 41 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 removed outlier: 3.648A pdb=" N ILE D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.610A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.715A pdb=" N LEU D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.698A pdb=" N LEU D 177 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 4.174A pdb=" N ILE D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 289 through 308 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.865A pdb=" N THR E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.793A pdb=" N CYS E 41 " --> pdb=" O ILE E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.606A pdb=" N ILE E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.609A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE E 71 " --> pdb=" O ILE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.716A pdb=" N LEU E 113 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.699A pdb=" N LEU E 177 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 4.173A pdb=" N ILE E 185 " --> pdb=" O ASP E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 289 through 308 Processing helix chain 'E' and resid 309 through 314 Processing helix chain 'F' and resid 12 through 14 No H-bonds generated for 'chain 'F' and resid 12 through 14' Processing helix chain 'F' and resid 15 through 33 removed outlier: 3.975A pdb=" N THR F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 removed outlier: 3.793A pdb=" N CYS F 41 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 61 removed outlier: 3.607A pdb=" N ALA F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 74 removed outlier: 3.610A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE F 71 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 Processing helix chain 'F' and resid 94 through 105 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.716A pdb=" N LEU F 113 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.698A pdb=" N LEU F 177 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 193 removed outlier: 4.173A pdb=" N ILE F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 289 through 308 Processing helix chain 'F' and resid 309 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 133 removed outlier: 3.609A pdb=" N ILE A 122 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 133 removed outlier: 6.550A pdb=" N ILE A 45 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A 47 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ILE A 122 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N SER A 49 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 48 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 11 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N TYR A 268 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 203 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 128 through 133 removed outlier: 3.610A pdb=" N ILE B 122 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 133 removed outlier: 6.551A pdb=" N ILE B 45 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY B 47 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N ILE B 122 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N SER B 49 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 48 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 11 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR B 268 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 203 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 133 removed outlier: 3.610A pdb=" N ILE C 122 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 133 removed outlier: 6.551A pdb=" N ILE C 45 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY C 47 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE C 122 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR C 268 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 203 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 128 through 133 removed outlier: 3.610A pdb=" N ILE D 122 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 128 through 133 removed outlier: 6.551A pdb=" N ILE D 45 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY D 47 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N ILE D 122 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR D 268 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 203 " --> pdb=" O TYR D 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 128 through 133 removed outlier: 3.609A pdb=" N ILE E 122 " --> pdb=" O VAL E 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 133 removed outlier: 6.550A pdb=" N ILE E 45 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY E 47 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ILE E 122 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR E 268 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 203 " --> pdb=" O TYR E 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 128 through 133 removed outlier: 3.609A pdb=" N ILE F 122 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 128 through 133 removed outlier: 6.550A pdb=" N ILE F 45 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY F 47 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ILE F 122 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR F 268 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE F 203 " --> pdb=" O TYR F 268 " (cutoff:3.500A) 676 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2362 1.31 - 1.44: 3643 1.44 - 1.56: 8185 1.56 - 1.69: 24 1.69 - 1.81: 72 Bond restraints: 14286 Sorted by residual: bond pdb=" CBC 4BW C 500 " pdb=" OAC 4BW C 500 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CBC 4BW F 500 " pdb=" OAC 4BW F 500 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" CBC 4BW D 500 " pdb=" OAC 4BW D 500 " ideal model delta sigma weight residual 1.230 1.391 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" CBC 4BW E 500 " pdb=" OAC 4BW E 500 " ideal model delta sigma weight residual 1.230 1.390 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" CBC 4BW A 500 " pdb=" OAC 4BW A 500 " ideal model delta sigma weight residual 1.230 1.386 -0.156 2.00e-02 2.50e+03 6.09e+01 ... (remaining 14281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 18942 3.62 - 7.24: 313 7.24 - 10.87: 69 10.87 - 14.49: 24 14.49 - 18.11: 26 Bond angle restraints: 19374 Sorted by residual: angle pdb=" N ARG A 15 " pdb=" CA ARG A 15 " pdb=" C ARG A 15 " ideal model delta sigma weight residual 110.70 101.33 9.37 1.55e+00 4.16e-01 3.65e+01 angle pdb=" OAD 4BW F 500 " pdb=" PBR 4BW F 500 " pdb=" OAH 4BW F 500 " ideal model delta sigma weight residual 122.13 104.02 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" OAD 4BW C 500 " pdb=" PBR 4BW C 500 " pdb=" OAH 4BW C 500 " ideal model delta sigma weight residual 122.13 104.08 18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" OAD 4BW D 500 " pdb=" PBR 4BW D 500 " pdb=" OAH 4BW D 500 " ideal model delta sigma weight residual 122.13 104.27 17.86 3.00e+00 1.11e-01 3.54e+01 angle pdb=" OAD 4BW E 500 " pdb=" PBR 4BW E 500 " pdb=" OAH 4BW E 500 " ideal model delta sigma weight residual 122.13 104.35 17.78 3.00e+00 1.11e-01 3.51e+01 ... (remaining 19369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 8409 33.54 - 67.08: 288 67.08 - 100.63: 31 100.63 - 134.17: 2 134.17 - 167.71: 24 Dihedral angle restraints: 8754 sinusoidal: 3732 harmonic: 5022 Sorted by residual: dihedral pdb=" CBG 4BW C 500 " pdb=" CBO 4BW C 500 " pdb=" NBQ 4BW C 500 " pdb=" OAX 4BW C 500 " ideal model delta sinusoidal sigma weight residual 140.95 -51.34 -167.71 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CBG 4BW F 500 " pdb=" CBO 4BW F 500 " pdb=" NBQ 4BW F 500 " pdb=" OAX 4BW F 500 " ideal model delta sinusoidal sigma weight residual 140.95 -51.55 -167.50 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CBG 4BW C 500 " pdb=" CBO 4BW C 500 " pdb=" NBQ 4BW C 500 " pdb=" CBI 4BW C 500 " ideal model delta sinusoidal sigma weight residual -98.89 68.41 -167.30 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 8751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1741 0.065 - 0.130: 327 0.130 - 0.194: 56 0.194 - 0.259: 12 0.259 - 0.324: 6 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA ARG A 15 " pdb=" N ARG A 15 " pdb=" C ARG A 15 " pdb=" CB ARG A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA ARG B 15 " pdb=" N ARG B 15 " pdb=" C ARG B 15 " pdb=" CB ARG B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' 4BW F 500 " pdb=" C1' 4BW F 500 " pdb=" C3' 4BW F 500 " pdb=" O2' 4BW F 500 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2139 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 15 " -0.561 9.50e-02 1.11e+02 2.51e-01 3.86e+01 pdb=" NE ARG D 15 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 15 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 15 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 15 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 15 " 0.508 9.50e-02 1.11e+02 2.28e-01 3.17e+01 pdb=" NE ARG E 15 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG E 15 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 15 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 15 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 190 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C ALA C 190 " -0.071 2.00e-02 2.50e+03 pdb=" O ALA C 190 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP C 191 " 0.024 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2436 2.76 - 3.30: 13045 3.30 - 3.83: 23620 3.83 - 4.37: 29751 4.37 - 4.90: 49749 Nonbonded interactions: 118601 Sorted by model distance: nonbonded pdb=" O GLU D 95 " pdb=" OG1 THR D 99 " model vdw 2.229 3.040 nonbonded pdb=" O GLU F 95 " pdb=" OG1 THR F 99 " model vdw 2.229 3.040 nonbonded pdb=" O GLU E 95 " pdb=" OG1 THR E 99 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP C 327 " pdb=" N GLY C 328 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP E 327 " pdb=" N GLY E 328 " model vdw 2.264 3.120 ... (remaining 118596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.011 0.163 14286 Z= 0.616 Angle : 1.422 18.108 19374 Z= 0.743 Chirality : 0.057 0.324 2142 Planarity : 0.011 0.251 2460 Dihedral : 19.094 167.708 5514 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.52 % Allowed : 6.01 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1710 helix: 0.37 (0.20), residues: 744 sheet: -1.10 (0.31), residues: 246 loop : -0.91 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 321 TYR 0.032 0.002 TYR B 192 PHE 0.017 0.002 PHE C 251 TRP 0.016 0.002 TRP B 104 HIS 0.003 0.001 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.01121 (14286) covalent geometry : angle 1.42247 (19374) hydrogen bonds : bond 0.19003 ( 640) hydrogen bonds : angle 7.55291 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8358 (mttt) cc_final: 0.8139 (mttm) REVERT: A 173 VAL cc_start: 0.8395 (m) cc_final: 0.8174 (m) REVERT: B 239 ASN cc_start: 0.7228 (m-40) cc_final: 0.7003 (t0) REVERT: B 243 LEU cc_start: 0.8675 (tt) cc_final: 0.8451 (tt) REVERT: C 94 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6704 (p0) REVERT: C 142 ARG cc_start: 0.7801 (mmt-90) cc_final: 0.6023 (ptt180) REVERT: D 28 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6250 (mt0) REVERT: D 31 LYS cc_start: 0.8071 (mttt) cc_final: 0.7740 (mtmt) REVERT: D 60 TYR cc_start: 0.9083 (t80) cc_final: 0.8645 (t80) REVERT: D 107 ASP cc_start: 0.6780 (m-30) cc_final: 0.5961 (t0) REVERT: D 147 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7708 (mmtt) REVERT: D 150 ASP cc_start: 0.7546 (m-30) cc_final: 0.7156 (t0) REVERT: D 248 GLN cc_start: 0.8702 (mm110) cc_final: 0.8499 (mm-40) REVERT: D 318 GLN cc_start: 0.7490 (mt0) cc_final: 0.7110 (mt0) REVERT: E 28 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6221 (mt0) REVERT: E 173 VAL cc_start: 0.7159 (m) cc_final: 0.6826 (t) REVERT: E 300 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7308 (mp) REVERT: E 310 ASP cc_start: 0.7402 (p0) cc_final: 0.6623 (t0) REVERT: E 318 GLN cc_start: 0.7514 (mt0) cc_final: 0.7135 (mt0) REVERT: F 60 TYR cc_start: 0.8595 (t80) cc_final: 0.8371 (t80) REVERT: F 121 THR cc_start: 0.8451 (t) cc_final: 0.8185 (m) REVERT: F 142 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.6079 (ptt180) outliers start: 67 outliers final: 9 residues processed: 368 average time/residue: 0.5858 time to fit residues: 235.5766 Evaluate side-chains 194 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 288 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 197 ASN B 74 HIS B 197 ASN C 33 ASN C 197 ASN D 250 GLN E 170 ASN F 33 ASN F 197 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108929 restraints weight = 16326.870| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.93 r_work: 0.3131 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14286 Z= 0.128 Angle : 0.573 10.542 19374 Z= 0.297 Chirality : 0.044 0.157 2142 Planarity : 0.005 0.043 2460 Dihedral : 18.080 156.240 2231 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.43 % Allowed : 12.69 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1710 helix: 0.98 (0.19), residues: 798 sheet: -0.67 (0.32), residues: 252 loop : -0.68 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 321 TYR 0.018 0.001 TYR B 14 PHE 0.023 0.001 PHE E 124 TRP 0.012 0.001 TRP E 104 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00294 (14286) covalent geometry : angle 0.57341 (19374) hydrogen bonds : bond 0.03950 ( 640) hydrogen bonds : angle 4.88450 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7903 (t80) cc_final: 0.7657 (t80) REVERT: A 49 SER cc_start: 0.8998 (m) cc_final: 0.8787 (t) REVERT: A 77 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7556 (ptpp) REVERT: A 198 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 14 TYR cc_start: 0.7862 (t80) cc_final: 0.7440 (t80) REVERT: B 27 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: B 239 ASN cc_start: 0.7275 (m-40) cc_final: 0.6850 (t0) REVERT: C 60 TYR cc_start: 0.8817 (t80) cc_final: 0.8596 (t80) REVERT: D 27 GLU cc_start: 0.7903 (tp30) cc_final: 0.7090 (tm-30) REVERT: D 28 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6214 (mt0) REVERT: D 107 ASP cc_start: 0.7412 (m-30) cc_final: 0.7161 (m-30) REVERT: D 124 PHE cc_start: 0.8630 (t80) cc_final: 0.8286 (t80) REVERT: D 150 ASP cc_start: 0.7723 (m-30) cc_final: 0.7142 (t0) REVERT: D 199 GLN cc_start: 0.8139 (pt0) cc_final: 0.7755 (pm20) REVERT: E 76 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5871 (p0) REVERT: E 107 ASP cc_start: 0.7166 (m-30) cc_final: 0.5991 (t0) REVERT: E 310 ASP cc_start: 0.7454 (p0) cc_final: 0.6553 (t0) REVERT: F 60 TYR cc_start: 0.8823 (t80) cc_final: 0.8482 (t80) REVERT: F 114 LYS cc_start: 0.8312 (mmtm) cc_final: 0.7403 (ptpt) REVERT: F 193 MET cc_start: 0.8606 (mmt) cc_final: 0.8392 (mmt) REVERT: F 252 MET cc_start: 0.8513 (mtm) cc_final: 0.8272 (mtp) outliers start: 36 outliers final: 10 residues processed: 232 average time/residue: 0.6242 time to fit residues: 157.7783 Evaluate side-chains 188 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 247 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 317 ASN E 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.159072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112592 restraints weight = 16624.077| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.91 r_work: 0.3092 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14286 Z= 0.226 Angle : 0.581 5.582 19374 Z= 0.301 Chirality : 0.045 0.153 2142 Planarity : 0.004 0.041 2460 Dihedral : 18.241 160.221 2210 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.64 % Allowed : 12.89 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1710 helix: 1.21 (0.18), residues: 798 sheet: -0.34 (0.32), residues: 252 loop : -0.65 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 126 TYR 0.015 0.002 TYR A 14 PHE 0.020 0.002 PHE D 251 TRP 0.008 0.001 TRP C 144 HIS 0.004 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00549 (14286) covalent geometry : angle 0.58073 (19374) hydrogen bonds : bond 0.04079 ( 640) hydrogen bonds : angle 4.54206 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 14 TYR cc_start: 0.8112 (t80) cc_final: 0.7789 (t80) REVERT: A 77 LYS cc_start: 0.7757 (ptpp) cc_final: 0.7427 (ptpp) REVERT: A 126 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.8058 (mtm110) REVERT: B 14 TYR cc_start: 0.8054 (t80) cc_final: 0.7518 (t80) REVERT: B 27 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: B 123 ASP cc_start: 0.8398 (t0) cc_final: 0.8181 (t0) REVERT: B 239 ASN cc_start: 0.7319 (m-40) cc_final: 0.6800 (t0) REVERT: C 114 LYS cc_start: 0.8231 (mttt) cc_final: 0.7799 (ptpt) REVERT: C 142 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.5914 (ptt180) REVERT: C 143 ASP cc_start: 0.7925 (m-30) cc_final: 0.7662 (m-30) REVERT: D 27 GLU cc_start: 0.8053 (tp30) cc_final: 0.7238 (tm-30) REVERT: D 28 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6309 (mt0) REVERT: D 107 ASP cc_start: 0.7436 (m-30) cc_final: 0.7112 (m-30) REVERT: D 150 ASP cc_start: 0.7871 (m-30) cc_final: 0.7279 (t0) REVERT: D 199 GLN cc_start: 0.8143 (pt0) cc_final: 0.7820 (pm20) REVERT: D 249 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6743 (tm-30) REVERT: E 76 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5887 (p0) REVERT: E 150 ASP cc_start: 0.7880 (m-30) cc_final: 0.7125 (t0) REVERT: E 193 MET cc_start: 0.9096 (mmt) cc_final: 0.8769 (mmt) REVERT: E 310 ASP cc_start: 0.7605 (p0) cc_final: 0.6775 (t0) REVERT: F 114 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7591 (ptpt) REVERT: F 143 ASP cc_start: 0.7956 (m-30) cc_final: 0.7716 (m-30) REVERT: F 193 MET cc_start: 0.8710 (mmt) cc_final: 0.8429 (mmt) outliers start: 54 outliers final: 15 residues processed: 217 average time/residue: 0.5236 time to fit residues: 124.4740 Evaluate side-chains 181 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS E 170 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113613 restraints weight = 16560.001| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.92 r_work: 0.3113 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14286 Z= 0.167 Angle : 0.533 5.371 19374 Z= 0.276 Chirality : 0.043 0.152 2142 Planarity : 0.004 0.039 2460 Dihedral : 18.011 158.506 2206 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.51 % Allowed : 13.97 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1710 helix: 1.47 (0.19), residues: 798 sheet: -0.57 (0.30), residues: 276 loop : -0.67 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 321 TYR 0.021 0.001 TYR A 14 PHE 0.020 0.001 PHE D 251 TRP 0.007 0.001 TRP E 104 HIS 0.003 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00403 (14286) covalent geometry : angle 0.53345 (19374) hydrogen bonds : bond 0.03587 ( 640) hydrogen bonds : angle 4.32248 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7456 (ptpp) REVERT: A 123 ASP cc_start: 0.8366 (t0) cc_final: 0.7919 (t0) REVERT: A 124 PHE cc_start: 0.8337 (t80) cc_final: 0.8038 (t80) REVERT: A 126 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8056 (mtm110) REVERT: A 141 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8694 (mtpp) REVERT: B 27 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 32 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 123 ASP cc_start: 0.8357 (t0) cc_final: 0.8110 (t0) REVERT: B 141 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8691 (mtpp) REVERT: B 239 ASN cc_start: 0.7312 (m-40) cc_final: 0.6846 (t0) REVERT: C 114 LYS cc_start: 0.8205 (mttt) cc_final: 0.7798 (ptpt) REVERT: C 142 ARG cc_start: 0.7999 (mmt-90) cc_final: 0.5982 (ptt180) REVERT: C 143 ASP cc_start: 0.7966 (m-30) cc_final: 0.7681 (m-30) REVERT: D 25 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6556 (tm-30) REVERT: D 28 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6351 (mt0) REVERT: D 107 ASP cc_start: 0.7334 (m-30) cc_final: 0.7037 (m-30) REVERT: D 150 ASP cc_start: 0.7901 (m-30) cc_final: 0.7300 (t0) REVERT: D 199 GLN cc_start: 0.8176 (pt0) cc_final: 0.7842 (pm20) REVERT: D 249 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6703 (tm-30) REVERT: E 76 ASP cc_start: 0.6276 (OUTLIER) cc_final: 0.5886 (p0) REVERT: E 102 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8561 (mm-30) REVERT: E 150 ASP cc_start: 0.7934 (m-30) cc_final: 0.7206 (t0) REVERT: E 310 ASP cc_start: 0.7603 (p0) cc_final: 0.6747 (t0) REVERT: F 60 TYR cc_start: 0.8848 (t80) cc_final: 0.8484 (t80) REVERT: F 114 LYS cc_start: 0.8312 (mmtm) cc_final: 0.7589 (ptpt) REVERT: F 143 ASP cc_start: 0.7939 (m-30) cc_final: 0.7700 (m-30) REVERT: F 193 MET cc_start: 0.8724 (mmt) cc_final: 0.8463 (mmt) outliers start: 52 outliers final: 19 residues processed: 223 average time/residue: 0.5559 time to fit residues: 135.3850 Evaluate side-chains 191 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS B 137 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS E 170 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.159651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106217 restraints weight = 16504.476| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.95 r_work: 0.3102 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14286 Z= 0.183 Angle : 0.542 5.639 19374 Z= 0.280 Chirality : 0.044 0.151 2142 Planarity : 0.004 0.038 2460 Dihedral : 18.018 158.680 2206 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.37 % Allowed : 14.84 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1710 helix: 1.46 (0.18), residues: 828 sheet: -0.35 (0.31), residues: 252 loop : -0.53 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 321 TYR 0.015 0.001 TYR A 14 PHE 0.021 0.001 PHE E 251 TRP 0.010 0.001 TRP E 104 HIS 0.002 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00448 (14286) covalent geometry : angle 0.54245 (19374) hydrogen bonds : bond 0.03624 ( 640) hydrogen bonds : angle 4.26303 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 123 ASP cc_start: 0.8382 (t0) cc_final: 0.7936 (t0) REVERT: A 124 PHE cc_start: 0.8350 (t80) cc_final: 0.8038 (t80) REVERT: A 141 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8738 (mtpp) REVERT: B 27 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: B 32 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 123 ASP cc_start: 0.8385 (t0) cc_final: 0.8132 (t0) REVERT: B 239 ASN cc_start: 0.7308 (m-40) cc_final: 0.6922 (p0) REVERT: B 253 GLU cc_start: 0.8510 (tp30) cc_final: 0.8173 (tt0) REVERT: C 63 LYS cc_start: 0.8057 (mppt) cc_final: 0.7662 (mmmt) REVERT: C 74 HIS cc_start: 0.7676 (m170) cc_final: 0.7446 (m170) REVERT: C 114 LYS cc_start: 0.8255 (mttt) cc_final: 0.7847 (ptpt) REVERT: C 142 ARG cc_start: 0.8032 (mmt-90) cc_final: 0.6087 (ptt180) REVERT: C 143 ASP cc_start: 0.8141 (m-30) cc_final: 0.7786 (m-30) REVERT: D 3 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8180 (mtmt) REVERT: D 28 GLN cc_start: 0.6932 (mm-40) cc_final: 0.6413 (mt0) REVERT: D 29 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: D 107 ASP cc_start: 0.7313 (m-30) cc_final: 0.7040 (m-30) REVERT: D 150 ASP cc_start: 0.7927 (m-30) cc_final: 0.7265 (t0) REVERT: D 199 GLN cc_start: 0.8200 (pt0) cc_final: 0.7872 (pm20) REVERT: D 249 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6716 (tm-30) REVERT: D 313 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7417 (mtm110) REVERT: E 3 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8296 (mtmt) REVERT: E 29 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: E 76 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5881 (p0) REVERT: E 102 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8556 (mm-30) REVERT: E 150 ASP cc_start: 0.7961 (m-30) cc_final: 0.7243 (t0) REVERT: E 193 MET cc_start: 0.9127 (mmt) cc_final: 0.8813 (mmt) REVERT: E 310 ASP cc_start: 0.7526 (p0) cc_final: 0.6815 (t0) REVERT: F 114 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7619 (ptpt) REVERT: F 143 ASP cc_start: 0.8138 (m-30) cc_final: 0.7841 (m-30) REVERT: F 193 MET cc_start: 0.8765 (mmt) cc_final: 0.8483 (mmt) outliers start: 50 outliers final: 21 residues processed: 214 average time/residue: 0.5593 time to fit residues: 130.2348 Evaluate side-chains 191 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 2 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS D 170 ASN E 74 HIS E 170 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109200 restraints weight = 16411.517| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.94 r_work: 0.3129 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14286 Z= 0.125 Angle : 0.504 6.025 19374 Z= 0.259 Chirality : 0.043 0.149 2142 Planarity : 0.004 0.043 2460 Dihedral : 17.770 156.416 2206 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.44 % Allowed : 15.52 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1710 helix: 1.66 (0.19), residues: 828 sheet: -0.36 (0.31), residues: 252 loop : -0.47 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 321 TYR 0.015 0.001 TYR A 14 PHE 0.020 0.001 PHE E 251 TRP 0.010 0.001 TRP E 104 HIS 0.002 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00298 (14286) covalent geometry : angle 0.50441 (19374) hydrogen bonds : bond 0.03237 ( 640) hydrogen bonds : angle 4.13566 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7908 (mm-30) REVERT: A 249 GLN cc_start: 0.7881 (tt0) cc_final: 0.7641 (tm-30) REVERT: A 253 GLU cc_start: 0.8514 (tp30) cc_final: 0.8150 (tt0) REVERT: B 27 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: B 32 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 123 ASP cc_start: 0.8254 (t0) cc_final: 0.8003 (t0) REVERT: B 239 ASN cc_start: 0.7316 (m-40) cc_final: 0.6949 (p0) REVERT: B 253 GLU cc_start: 0.8468 (tp30) cc_final: 0.8158 (tt0) REVERT: C 74 HIS cc_start: 0.7639 (m170) cc_final: 0.7369 (m170) REVERT: C 114 LYS cc_start: 0.8267 (mttt) cc_final: 0.7839 (ptpt) REVERT: C 142 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.6068 (ptt180) REVERT: C 143 ASP cc_start: 0.8088 (m-30) cc_final: 0.7694 (m-30) REVERT: D 28 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6337 (mt0) REVERT: D 29 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6569 (mm-30) REVERT: D 107 ASP cc_start: 0.7246 (m-30) cc_final: 0.6992 (m-30) REVERT: D 150 ASP cc_start: 0.7880 (m-30) cc_final: 0.7234 (t0) REVERT: D 199 GLN cc_start: 0.8206 (pt0) cc_final: 0.7891 (pm20) REVERT: D 249 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6713 (tm-30) REVERT: E 27 GLU cc_start: 0.7635 (tp30) cc_final: 0.7376 (tp30) REVERT: E 29 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6519 (mm-30) REVERT: E 76 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5762 (p0) REVERT: E 102 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8573 (mm-30) REVERT: E 150 ASP cc_start: 0.7931 (m-30) cc_final: 0.7235 (t0) REVERT: E 193 MET cc_start: 0.9093 (mmt) cc_final: 0.8763 (mmt) REVERT: E 310 ASP cc_start: 0.7481 (p0) cc_final: 0.6825 (t0) REVERT: F 60 TYR cc_start: 0.8778 (t80) cc_final: 0.8454 (t80) REVERT: F 114 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7583 (ptpt) REVERT: F 143 ASP cc_start: 0.8088 (m-30) cc_final: 0.7789 (m-30) REVERT: F 193 MET cc_start: 0.8745 (mmt) cc_final: 0.8463 (mmt) outliers start: 51 outliers final: 19 residues processed: 216 average time/residue: 0.5553 time to fit residues: 131.0883 Evaluate side-chains 188 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 322 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 74 HIS B 74 HIS ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS E 170 ASN ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108487 restraints weight = 16397.139| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.95 r_work: 0.3130 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14286 Z= 0.131 Angle : 0.511 7.603 19374 Z= 0.261 Chirality : 0.043 0.151 2142 Planarity : 0.004 0.047 2460 Dihedral : 17.770 156.256 2206 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.17 % Allowed : 15.38 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1710 helix: 1.71 (0.19), residues: 828 sheet: -0.54 (0.31), residues: 276 loop : -0.39 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 321 TYR 0.016 0.001 TYR A 14 PHE 0.021 0.001 PHE E 251 TRP 0.013 0.001 TRP D 104 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00316 (14286) covalent geometry : angle 0.51098 (19374) hydrogen bonds : bond 0.03233 ( 640) hydrogen bonds : angle 4.08863 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7726 (t80) cc_final: 0.7272 (t80) REVERT: A 249 GLN cc_start: 0.7878 (tt0) cc_final: 0.7652 (tm-30) REVERT: A 253 GLU cc_start: 0.8515 (tp30) cc_final: 0.8150 (tt0) REVERT: B 27 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: B 126 ARG cc_start: 0.8561 (mpp80) cc_final: 0.7825 (mtm-85) REVERT: B 239 ASN cc_start: 0.7296 (m-40) cc_final: 0.6943 (p0) REVERT: B 253 GLU cc_start: 0.8504 (tp30) cc_final: 0.8131 (tt0) REVERT: C 74 HIS cc_start: 0.7692 (m170) cc_final: 0.7425 (m170) REVERT: C 114 LYS cc_start: 0.8305 (mttt) cc_final: 0.7881 (ptpt) REVERT: C 142 ARG cc_start: 0.8050 (mmt-90) cc_final: 0.6153 (ptt180) REVERT: C 143 ASP cc_start: 0.8141 (m-30) cc_final: 0.7708 (m-30) REVERT: C 296 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: D 28 GLN cc_start: 0.6818 (mm-40) cc_final: 0.6323 (mt0) REVERT: D 29 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: D 107 ASP cc_start: 0.7186 (m-30) cc_final: 0.6933 (m-30) REVERT: D 150 ASP cc_start: 0.7866 (m-30) cc_final: 0.7214 (t0) REVERT: D 199 GLN cc_start: 0.8228 (pt0) cc_final: 0.7931 (pm20) REVERT: D 249 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6729 (tm-30) REVERT: E 29 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6459 (mm-30) REVERT: E 76 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5793 (p0) REVERT: E 102 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8534 (mm-30) REVERT: E 150 ASP cc_start: 0.7921 (m-30) cc_final: 0.7228 (t0) REVERT: E 310 ASP cc_start: 0.7465 (p0) cc_final: 0.6829 (t0) REVERT: E 321 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7745 (mtt-85) REVERT: F 60 TYR cc_start: 0.8787 (t80) cc_final: 0.8458 (t80) REVERT: F 74 HIS cc_start: 0.7676 (m170) cc_final: 0.7377 (m170) REVERT: F 114 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7590 (ptpt) REVERT: F 142 ARG cc_start: 0.8044 (mmt-90) cc_final: 0.6055 (ptt180) REVERT: F 143 ASP cc_start: 0.8134 (m-30) cc_final: 0.7737 (m-30) REVERT: F 193 MET cc_start: 0.8730 (mmt) cc_final: 0.8476 (mmt) outliers start: 47 outliers final: 18 residues processed: 208 average time/residue: 0.5927 time to fit residues: 134.8788 Evaluate side-chains 184 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Chi-restraints excluded: chain E residue 289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 113 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 0.0470 chunk 170 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS C 5 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN D 170 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108223 restraints weight = 16417.437| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.96 r_work: 0.3123 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14286 Z= 0.137 Angle : 0.525 7.694 19374 Z= 0.265 Chirality : 0.043 0.182 2142 Planarity : 0.004 0.047 2460 Dihedral : 17.767 156.170 2206 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.77 % Allowed : 16.67 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1710 helix: 1.77 (0.19), residues: 798 sheet: -0.54 (0.31), residues: 276 loop : -0.44 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 126 TYR 0.015 0.001 TYR A 14 PHE 0.021 0.001 PHE E 251 TRP 0.013 0.001 TRP D 104 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00330 (14286) covalent geometry : angle 0.52468 (19374) hydrogen bonds : bond 0.03269 ( 640) hydrogen bonds : angle 4.08877 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7806 (t80) cc_final: 0.7419 (t80) REVERT: A 141 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8484 (mtpp) REVERT: A 249 GLN cc_start: 0.7894 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 253 GLU cc_start: 0.8508 (tp30) cc_final: 0.8156 (tt0) REVERT: B 27 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: B 239 ASN cc_start: 0.7263 (m-40) cc_final: 0.6942 (p0) REVERT: B 253 GLU cc_start: 0.8501 (tp30) cc_final: 0.8148 (tt0) REVERT: C 74 HIS cc_start: 0.7676 (m170) cc_final: 0.7413 (m170) REVERT: C 114 LYS cc_start: 0.8308 (mttt) cc_final: 0.7884 (ptpt) REVERT: C 142 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.6166 (ptt180) REVERT: C 143 ASP cc_start: 0.8168 (m-30) cc_final: 0.7719 (m-30) REVERT: D 15 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7835 (mtp85) REVERT: D 28 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6313 (mt0) REVERT: D 107 ASP cc_start: 0.7208 (m-30) cc_final: 0.6955 (m-30) REVERT: D 150 ASP cc_start: 0.7877 (m-30) cc_final: 0.7182 (t0) REVERT: D 199 GLN cc_start: 0.8223 (pt0) cc_final: 0.7928 (pm20) REVERT: D 249 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6755 (tm-30) REVERT: E 27 GLU cc_start: 0.7591 (tp30) cc_final: 0.7338 (tp30) REVERT: E 29 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: E 76 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5785 (p0) REVERT: E 150 ASP cc_start: 0.7888 (m-30) cc_final: 0.7210 (t0) REVERT: E 310 ASP cc_start: 0.7460 (p0) cc_final: 0.6831 (t0) REVERT: F 60 TYR cc_start: 0.8781 (t80) cc_final: 0.8460 (t80) REVERT: F 74 HIS cc_start: 0.7669 (m170) cc_final: 0.7397 (m170) REVERT: F 114 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7633 (ptpt) REVERT: F 142 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.6068 (ptt180) REVERT: F 143 ASP cc_start: 0.8180 (m-30) cc_final: 0.7782 (m-30) REVERT: F 193 MET cc_start: 0.8730 (mmt) cc_final: 0.8481 (mmt) outliers start: 41 outliers final: 16 residues processed: 201 average time/residue: 0.6102 time to fit residues: 134.0376 Evaluate side-chains 182 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 58 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS B 74 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS D 170 ASN ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106187 restraints weight = 16433.968| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.86 r_work: 0.3082 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14286 Z= 0.169 Angle : 0.557 10.143 19374 Z= 0.279 Chirality : 0.044 0.202 2142 Planarity : 0.004 0.048 2460 Dihedral : 17.882 156.973 2206 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.36 % Allowed : 17.48 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1710 helix: 1.68 (0.19), residues: 798 sheet: -0.58 (0.30), residues: 276 loop : -0.42 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.015 0.001 TYR A 192 PHE 0.022 0.001 PHE E 251 TRP 0.017 0.001 TRP D 104 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00412 (14286) covalent geometry : angle 0.55655 (19374) hydrogen bonds : bond 0.03473 ( 640) hydrogen bonds : angle 4.14851 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7895 (t80) cc_final: 0.7443 (t80) REVERT: A 141 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: A 253 GLU cc_start: 0.8522 (tp30) cc_final: 0.8148 (tt0) REVERT: B 27 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: B 123 ASP cc_start: 0.8165 (t0) cc_final: 0.7874 (t0) REVERT: B 239 ASN cc_start: 0.7203 (m-40) cc_final: 0.6889 (p0) REVERT: B 253 GLU cc_start: 0.8480 (tp30) cc_final: 0.8101 (tt0) REVERT: C 74 HIS cc_start: 0.7601 (m170) cc_final: 0.7344 (m170) REVERT: C 114 LYS cc_start: 0.8268 (mttt) cc_final: 0.7804 (ptpt) REVERT: C 142 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.6067 (ptt180) REVERT: C 143 ASP cc_start: 0.8315 (m-30) cc_final: 0.7762 (m-30) REVERT: D 15 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7793 (mtp85) REVERT: D 28 GLN cc_start: 0.6712 (mm-40) cc_final: 0.6214 (mt0) REVERT: D 107 ASP cc_start: 0.7336 (m-30) cc_final: 0.7076 (m-30) REVERT: D 150 ASP cc_start: 0.7878 (m-30) cc_final: 0.7090 (t0) REVERT: D 193 MET cc_start: 0.9089 (mmt) cc_final: 0.8832 (mmt) REVERT: D 199 GLN cc_start: 0.8193 (pt0) cc_final: 0.7883 (pm20) REVERT: D 249 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6629 (tm-30) REVERT: D 321 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7705 (mtt-85) REVERT: E 28 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6245 (mt0) REVERT: E 29 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6462 (mm-30) REVERT: E 76 ASP cc_start: 0.6229 (OUTLIER) cc_final: 0.5931 (p0) REVERT: E 150 ASP cc_start: 0.7901 (m-30) cc_final: 0.7128 (t0) REVERT: E 310 ASP cc_start: 0.7349 (p0) cc_final: 0.6736 (t0) REVERT: F 60 TYR cc_start: 0.8773 (t80) cc_final: 0.8490 (t80) REVERT: F 74 HIS cc_start: 0.7604 (m170) cc_final: 0.7345 (m170) REVERT: F 114 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7558 (ptpt) REVERT: F 142 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.5925 (ptt-90) REVERT: F 143 ASP cc_start: 0.8266 (m-30) cc_final: 0.7773 (m-30) REVERT: F 193 MET cc_start: 0.8705 (mmt) cc_final: 0.8440 (mmt) outliers start: 35 outliers final: 19 residues processed: 192 average time/residue: 0.6204 time to fit residues: 129.4031 Evaluate side-chains 184 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106344 restraints weight = 16424.619| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.86 r_work: 0.3083 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14286 Z= 0.171 Angle : 0.566 8.679 19374 Z= 0.284 Chirality : 0.044 0.208 2142 Planarity : 0.004 0.047 2460 Dihedral : 17.866 156.822 2206 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.96 % Allowed : 18.02 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1710 helix: 1.57 (0.19), residues: 828 sheet: -0.59 (0.30), residues: 276 loop : -0.28 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.015 0.001 TYR A 14 PHE 0.023 0.001 PHE E 251 TRP 0.021 0.001 TRP D 104 HIS 0.005 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00418 (14286) covalent geometry : angle 0.56568 (19374) hydrogen bonds : bond 0.03499 ( 640) hydrogen bonds : angle 4.17860 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 14 TYR cc_start: 0.7696 (t80) cc_final: 0.7479 (t80) REVERT: A 141 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8514 (mtpp) REVERT: A 253 GLU cc_start: 0.8514 (tp30) cc_final: 0.8140 (tt0) REVERT: B 27 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: B 123 ASP cc_start: 0.8240 (t0) cc_final: 0.7924 (t0) REVERT: B 239 ASN cc_start: 0.7230 (m-40) cc_final: 0.6978 (p0) REVERT: B 253 GLU cc_start: 0.8471 (tp30) cc_final: 0.8100 (tt0) REVERT: C 74 HIS cc_start: 0.7646 (m170) cc_final: 0.7393 (m170) REVERT: C 114 LYS cc_start: 0.8271 (mttt) cc_final: 0.7760 (mmtm) REVERT: C 142 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.6066 (ptt180) REVERT: C 143 ASP cc_start: 0.8314 (m-30) cc_final: 0.7754 (m-30) REVERT: D 15 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7808 (mtp85) REVERT: D 25 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6520 (tm-30) REVERT: D 28 GLN cc_start: 0.6719 (mm-40) cc_final: 0.6246 (mt0) REVERT: D 107 ASP cc_start: 0.7332 (m-30) cc_final: 0.7062 (m-30) REVERT: D 150 ASP cc_start: 0.7886 (m-30) cc_final: 0.7092 (t0) REVERT: D 199 GLN cc_start: 0.8188 (pt0) cc_final: 0.7879 (pm20) REVERT: D 249 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6678 (tm-30) REVERT: D 321 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7567 (mtt-85) REVERT: E 25 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6603 (tm-30) REVERT: E 28 GLN cc_start: 0.6754 (mm-40) cc_final: 0.6152 (mt0) REVERT: E 29 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6372 (mm-30) REVERT: E 76 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.5978 (p0) REVERT: E 124 PHE cc_start: 0.8337 (t80) cc_final: 0.8095 (t80) REVERT: E 150 ASP cc_start: 0.7923 (m-30) cc_final: 0.7117 (t0) REVERT: E 310 ASP cc_start: 0.7314 (p0) cc_final: 0.6710 (t0) REVERT: F 60 TYR cc_start: 0.8782 (t80) cc_final: 0.8486 (t80) REVERT: F 74 HIS cc_start: 0.7613 (m170) cc_final: 0.7363 (m170) REVERT: F 114 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7555 (ptpt) REVERT: F 142 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.6007 (ptt180) REVERT: F 143 ASP cc_start: 0.8303 (m-30) cc_final: 0.7801 (m-30) REVERT: F 193 MET cc_start: 0.8713 (mmt) cc_final: 0.8453 (mmt) outliers start: 29 outliers final: 18 residues processed: 189 average time/residue: 0.5758 time to fit residues: 118.9991 Evaluate side-chains 183 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 0.0980 chunk 127 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 74 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** D 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 HIS E 170 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109598 restraints weight = 16284.661| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.85 r_work: 0.3132 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14286 Z= 0.110 Angle : 0.531 7.992 19374 Z= 0.268 Chirality : 0.043 0.202 2142 Planarity : 0.004 0.048 2460 Dihedral : 17.605 154.684 2206 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.02 % Allowed : 18.22 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1710 helix: 1.74 (0.19), residues: 828 sheet: -0.60 (0.30), residues: 276 loop : -0.21 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 126 TYR 0.016 0.001 TYR A 14 PHE 0.022 0.001 PHE E 251 TRP 0.024 0.002 TRP D 104 HIS 0.006 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00259 (14286) covalent geometry : angle 0.53053 (19374) hydrogen bonds : bond 0.03071 ( 640) hydrogen bonds : angle 4.10755 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.25 seconds wall clock time: 70 minutes 50.59 seconds (4250.59 seconds total)