Starting phenix.real_space_refine on Mon Apr 6 05:58:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kh6_62333/04_2026/9kh6_62333.map" } resolution = 2.8 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= 0.005 sd= 0.085 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 18 5.49 5 S 42 5.16 5 C 10404 2.51 5 N 2676 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16206 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "C" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "D" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "E" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "F" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2605 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'4BW': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.39, per 1000 atoms: 0.21 Number of scatterers: 16206 At special positions: 0 Unit cell: (117.03, 161.02, 83.83, 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 18 15.00 O 3066 8.00 N 2676 7.00 C 10404 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: 1.43 Conformation dependent library (CDL) restraints added in 644.2 milliseconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 12 sheets defined 50.8% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 12 through 15 Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.501A pdb=" N PHE A 42 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.535A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.771A pdb=" N LYS A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 182 through 193 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 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 235 through 261 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.917A pdb=" N GLN A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 308 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 12 through 15 Processing helix chain 'B' and resid 16 through 32 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 63 through 74 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.709A pdb=" N ILE B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) No H-bonds generated for '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: 3.556A pdb=" N LEU B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.769A pdb=" N LYS B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.635A pdb=" N LEU B 177 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 178 " --> pdb=" O GLY B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 182 through 193 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 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 235 through 261 Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.882A pdb=" N GLN B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'C' and resid 12 through 15 Processing helix chain 'C' and resid 16 through 33 removed outlier: 3.715A pdb=" N ASN C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 49 through 61 Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.623A pdb=" N LEU C 113 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.628A pdb=" N LYS C 145 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.566A pdb=" N LEU C 177 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 178 " --> pdb=" O GLY C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 182 through 193 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 235 through 261 Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.641A pdb=" N GLN C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 308 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'D' and resid 12 through 15 Processing helix chain 'D' and resid 16 through 33 Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.563A pdb=" N PHE D 42 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 63 through 74 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: 3.660A pdb=" N LEU D 113 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.713A pdb=" N LYS D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.803A pdb=" N LEU D 177 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 178 " --> pdb=" O GLY D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 178' Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.530A pdb=" N GLY D 186 " --> pdb=" O PRO D 182 " (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 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 235 through 261 Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.684A pdb=" N GLN D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'E' and resid 12 through 15 Processing helix chain 'E' and resid 16 through 33 Processing helix chain 'E' and resid 37 through 42 removed outlier: 3.564A pdb=" N PHE E 42 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.636A pdb=" N LEU E 113 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.806A pdb=" N LYS E 145 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.800A pdb=" N LEU E 177 " --> pdb=" O ASP E 174 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE E 178 " --> pdb=" O GLY E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.526A pdb=" N GLY E 186 " --> pdb=" O PRO E 182 " (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 232 through 234 No H-bonds generated for 'chain 'E' and resid 232 through 234' Processing helix chain 'E' and resid 235 through 261 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.739A pdb=" N GLN E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 308 Processing helix chain 'E' and resid 309 through 314 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 16 through 32 Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 63 through 74 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: 3.599A pdb=" N LEU F 113 " --> pdb=" O LEU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.708A pdb=" N LYS F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.594A pdb=" N LEU F 177 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE F 178 " --> pdb=" O GLY F 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 178' Processing helix chain 'F' and resid 182 through 193 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 235 through 261 Processing helix chain 'F' and resid 275 through 280 removed outlier: 3.936A pdb=" N GLN F 280 " --> pdb=" O GLN F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 133 removed outlier: 6.999A pdb=" N ILE A 45 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY A 47 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N ILE A 122 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE A 4 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 204 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 6 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 206 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 8 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR A 268 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE A 203 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 270 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER A 205 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 128 through 133 removed outlier: 3.710A 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: 6.937A pdb=" N ILE B 45 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 47 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ILE B 122 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN B 5 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR B 46 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 7 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 4 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 204 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 6 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE B 206 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA B 8 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N TYR B 268 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 203 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 270 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER B 205 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 128 through 133 removed outlier: 3.825A pdb=" N ILE C 122 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 170 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 133 removed outlier: 6.824A pdb=" N ILE C 45 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLY C 47 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N ILE C 122 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 4 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU C 204 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 6 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE C 206 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 8 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N TYR C 268 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 203 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ILE C 270 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER C 205 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 128 through 133 removed outlier: 3.687A 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: 6.852A pdb=" N ILE D 45 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY D 47 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ILE D 122 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN D 5 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR D 46 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU D 7 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE D 4 " --> pdb=" O HIS D 202 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU D 204 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 6 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE D 206 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA D 8 " --> pdb=" O ILE D 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 128 through 133 Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 133 removed outlier: 6.894A pdb=" N ILE E 45 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY E 47 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ILE E 122 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN E 5 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR E 46 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU E 7 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE E 4 " --> pdb=" O HIS E 202 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU E 204 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE E 6 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 206 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA E 8 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 128 through 133 removed outlier: 3.782A pdb=" N ILE F 122 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN F 170 " --> pdb=" O ILE F 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 128 through 133 removed outlier: 6.794A pdb=" N ILE F 45 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY F 47 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ILE F 122 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE F 4 " --> pdb=" O HIS F 202 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU F 204 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE F 6 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE F 206 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA F 8 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR F 268 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 203 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE F 270 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER F 205 " --> pdb=" O ILE F 270 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2007 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: 2.80 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3708 1.33 - 1.45: 3348 1.45 - 1.57: 9426 1.57 - 1.69: 42 1.69 - 1.81: 72 Bond restraints: 16596 Sorted by residual: bond pdb=" C18 PEE B 402 " pdb=" C19 PEE B 402 " ideal model delta sigma weight residual 1.523 1.299 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C18 PEE A 402 " pdb=" C19 PEE A 402 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C18 PEE C 402 " pdb=" C19 PEE C 402 " ideal model delta sigma weight residual 1.523 1.304 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C18 PEE D 402 " pdb=" C19 PEE D 402 " ideal model delta sigma weight residual 1.523 1.304 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C38 PEE F 402 " pdb=" C39 PEE F 402 " ideal model delta sigma weight residual 1.523 1.304 0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 16591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 21919 3.52 - 7.04: 352 7.04 - 10.55: 97 10.55 - 14.07: 35 14.07 - 17.59: 31 Bond angle restraints: 22434 Sorted by residual: angle pdb=" OAD 4BW F 401 " pdb=" PBR 4BW F 401 " pdb=" OAH 4BW F 401 " ideal model delta sigma weight residual 122.13 104.54 17.59 3.00e+00 1.11e-01 3.44e+01 angle pdb=" OAD 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sigma weight residual 122.13 104.54 17.59 3.00e+00 1.11e-01 3.44e+01 angle pdb=" OAD 4BW A 401 " pdb=" PBR 4BW A 401 " pdb=" OAH 4BW A 401 " ideal model delta sigma weight residual 122.13 104.59 17.54 3.00e+00 1.11e-01 3.42e+01 angle pdb=" OAD 4BW E 401 " pdb=" PBR 4BW E 401 " pdb=" OAH 4BW E 401 " ideal model delta sigma weight residual 122.13 104.65 17.48 3.00e+00 1.11e-01 3.39e+01 angle pdb=" OAD 4BW B 401 " pdb=" PBR 4BW B 401 " pdb=" OAH 4BW B 401 " ideal model delta sigma weight residual 122.13 104.67 17.46 3.00e+00 1.11e-01 3.39e+01 ... (remaining 22429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 9892 35.54 - 71.07: 271 71.07 - 106.61: 27 106.61 - 142.15: 10 142.15 - 177.68: 42 Dihedral angle restraints: 10242 sinusoidal: 4536 harmonic: 5706 Sorted by residual: dihedral pdb=" CD ARG D 126 " pdb=" NE ARG D 126 " pdb=" CZ ARG D 126 " pdb=" NH1 ARG D 126 " ideal model delta sinusoidal sigma weight residual 0.00 65.89 -65.89 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CD ARG E 126 " pdb=" NE ARG E 126 " pdb=" CZ ARG E 126 " pdb=" NH1 ARG E 126 " ideal model delta sinusoidal sigma weight residual 0.00 52.53 -52.53 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CD ARG D 164 " pdb=" NE ARG D 164 " pdb=" CZ ARG D 164 " pdb=" NH1 ARG D 164 " ideal model delta sinusoidal sigma weight residual 0.00 -44.39 44.39 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2006 0.063 - 0.125: 361 0.125 - 0.188: 25 0.188 - 0.251: 17 0.251 - 0.313: 9 Chirality restraints: 2418 Sorted by residual: chirality pdb=" C2' 4BW C 401 " pdb=" C1' 4BW C 401 " pdb=" C3' 4BW C 401 " pdb=" O2' 4BW C 401 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C2' 4BW F 401 " pdb=" C1' 4BW F 401 " pdb=" C3' 4BW F 401 " pdb=" O2' 4BW F 401 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C2' 4BW B 401 " pdb=" C1' 4BW B 401 " pdb=" C3' 4BW B 401 " pdb=" O2' 4BW B 401 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2415 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 126 " -0.998 9.50e-02 1.11e+02 4.47e-01 1.21e+02 pdb=" NE ARG D 126 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG D 126 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 126 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 126 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 126 " 0.882 9.50e-02 1.11e+02 3.95e-01 9.49e+01 pdb=" NE ARG E 126 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG E 126 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 126 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 126 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " -0.763 9.50e-02 1.11e+02 3.42e-01 7.12e+01 pdb=" NE ARG B 126 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " -0.023 2.00e-02 2.50e+03 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1852 2.75 - 3.29: 15880 3.29 - 3.82: 28086 3.82 - 4.36: 36592 4.36 - 4.90: 60296 Nonbonded interactions: 142706 Sorted by model distance: nonbonded pdb=" OH TYR E 92 " pdb=" OD2 ASP E 285 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR D 92 " pdb=" OD2 ASP D 285 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR F 92 " pdb=" OD2 ASP F 285 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR C 92 " pdb=" OD2 ASP C 285 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR E 14 " pdb=" O PHE E 71 " model vdw 2.302 3.040 ... (remaining 142701 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: 1.400 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.310 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.224 16596 Z= 0.605 Angle : 1.283 17.590 22434 Z= 0.558 Chirality : 0.053 0.313 2418 Planarity : 0.017 0.447 2832 Dihedral : 20.915 177.684 6582 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.47 % Allowed : 0.53 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1986 helix: 1.03 (0.19), residues: 798 sheet: -0.23 (0.31), residues: 246 loop : -0.20 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 126 TYR 0.023 0.001 TYR F 192 PHE 0.039 0.002 PHE F 251 TRP 0.018 0.002 TRP D 104 HIS 0.005 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.01178 (16596) covalent geometry : angle 1.28307 (22434) hydrogen bonds : bond 0.17273 ( 691) hydrogen bonds : angle 7.10121 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.484 Fit side-chains REVERT: A 174 ASP cc_start: 0.7812 (m-30) cc_final: 0.7510 (m-30) REVERT: B 98 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7686 (ttpp) REVERT: B 161 TYR cc_start: 0.8947 (m-80) cc_final: 0.8679 (m-80) REVERT: C 126 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6216 (mpt180) REVERT: C 143 ASP cc_start: 0.7970 (m-30) cc_final: 0.7738 (m-30) REVERT: D 257 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8346 (mtmm) REVERT: F 126 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6474 (mpt180) REVERT: F 281 PHE cc_start: 0.8885 (m-80) cc_final: 0.8680 (m-80) outliers start: 8 outliers final: 3 residues processed: 261 average time/residue: 0.5980 time to fit residues: 171.8731 Evaluate side-chains 180 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 126 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN C 180 ASN C 249 GLN C 273 GLN D 74 HIS F 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100152 restraints weight = 19545.937| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.34 r_work: 0.3016 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16596 Z= 0.130 Angle : 0.519 5.143 22434 Z= 0.269 Chirality : 0.044 0.212 2418 Planarity : 0.005 0.050 2832 Dihedral : 24.628 178.258 2753 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 6.89 % Favored : 91.76 % 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: 0.67 (0.19), residues: 1986 helix: 1.36 (0.19), residues: 816 sheet: -0.19 (0.31), residues: 246 loop : -0.11 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 126 TYR 0.014 0.001 TYR F 192 PHE 0.032 0.001 PHE C 251 TRP 0.013 0.001 TRP D 104 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00303 (16596) covalent geometry : angle 0.51946 (22434) hydrogen bonds : bond 0.03911 ( 691) hydrogen bonds : angle 4.97835 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.485 Fit side-chains REVERT: B 98 LYS cc_start: 0.8032 (ttmt) cc_final: 0.7800 (ttpt) REVERT: C 126 ARG cc_start: 0.7842 (mtm110) cc_final: 0.6164 (mpt180) REVERT: D 257 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8469 (mtpt) REVERT: E 28 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7442 (pt0) REVERT: E 49 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8206 (t) REVERT: E 253 GLU cc_start: 0.8348 (tt0) cc_final: 0.8066 (tt0) REVERT: F 78 ILE cc_start: 0.8255 (mt) cc_final: 0.7966 (mp) REVERT: F 123 ASP cc_start: 0.8656 (t0) cc_final: 0.8407 (t0) REVERT: F 126 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6137 (mpt180) outliers start: 23 outliers final: 8 residues processed: 207 average time/residue: 0.6278 time to fit residues: 142.6986 Evaluate side-chains 186 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 173 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN F 137 ASN F 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096387 restraints weight = 19920.413| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.34 r_work: 0.2972 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16596 Z= 0.219 Angle : 0.551 5.105 22434 Z= 0.284 Chirality : 0.046 0.224 2418 Planarity : 0.005 0.041 2832 Dihedral : 23.772 178.680 2748 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.65 % Allowed : 8.72 % Favored : 89.63 % 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: 0.75 (0.18), residues: 1986 helix: 1.62 (0.18), residues: 780 sheet: -0.36 (0.30), residues: 246 loop : -0.13 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 15 TYR 0.012 0.001 TYR B 192 PHE 0.021 0.002 PHE C 251 TRP 0.011 0.001 TRP D 104 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00533 (16596) covalent geometry : angle 0.55064 (22434) hydrogen bonds : bond 0.04368 ( 691) hydrogen bonds : angle 4.84274 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.600 Fit side-chains REVERT: B 15 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8311 (ttp-170) REVERT: B 98 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7785 (ttpp) REVERT: C 126 ARG cc_start: 0.8017 (mtm110) cc_final: 0.6096 (mpt180) REVERT: E 28 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7442 (pt0) REVERT: E 49 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8283 (t) REVERT: F 49 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8543 (m) REVERT: F 78 ILE cc_start: 0.8239 (mt) cc_final: 0.7924 (mp) REVERT: F 123 ASP cc_start: 0.8642 (t0) cc_final: 0.8439 (t0) REVERT: F 126 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6130 (mpt180) REVERT: F 273 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7860 (mt0) outliers start: 28 outliers final: 10 residues processed: 200 average time/residue: 0.6302 time to fit residues: 138.6033 Evaluate side-chains 183 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 273 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 29 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN C 137 ASN C 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101020 restraints weight = 19740.769| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.34 r_work: 0.3050 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16596 Z= 0.108 Angle : 0.477 5.188 22434 Z= 0.247 Chirality : 0.043 0.223 2418 Planarity : 0.004 0.039 2832 Dihedral : 22.672 171.068 2748 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.18 % Allowed : 9.72 % Favored : 88.10 % 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: 1.04 (0.19), residues: 1986 helix: 1.92 (0.19), residues: 780 sheet: -0.30 (0.30), residues: 246 loop : 0.00 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 15 TYR 0.009 0.001 TYR B 192 PHE 0.025 0.001 PHE F 251 TRP 0.010 0.001 TRP D 104 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00249 (16596) covalent geometry : angle 0.47679 (22434) hydrogen bonds : bond 0.03362 ( 691) hydrogen bonds : angle 4.54640 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.473 Fit side-chains REVERT: A 91 LYS cc_start: 0.8710 (ttmt) cc_final: 0.8510 (ttmt) REVERT: B 15 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8639 (ttm110) REVERT: B 126 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6694 (mtt180) REVERT: B 242 ASP cc_start: 0.8562 (t0) cc_final: 0.8315 (m-30) REVERT: C 70 LEU cc_start: 0.7986 (mp) cc_final: 0.7541 (tt) REVERT: C 126 ARG cc_start: 0.7914 (mtm110) cc_final: 0.5965 (mpt180) REVERT: D 71 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7865 (t80) REVERT: E 28 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7540 (pt0) REVERT: E 49 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8251 (t) REVERT: E 171 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: F 32 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8103 (mm-30) REVERT: F 78 ILE cc_start: 0.8219 (mt) cc_final: 0.7908 (mp) REVERT: F 92 TYR cc_start: 0.8679 (m-80) cc_final: 0.8451 (m-80) REVERT: F 126 ARG cc_start: 0.8028 (mtm110) cc_final: 0.6154 (mpt180) REVERT: F 221 LYS cc_start: 0.8002 (mttm) cc_final: 0.7589 (mmtp) outliers start: 37 outliers final: 12 residues processed: 203 average time/residue: 0.6117 time to fit residues: 136.5725 Evaluate side-chains 188 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 173 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 187 optimal weight: 0.0170 chunk 1 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN C 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100659 restraints weight = 19673.456| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.33 r_work: 0.3019 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16596 Z= 0.144 Angle : 0.494 5.369 22434 Z= 0.254 Chirality : 0.043 0.215 2418 Planarity : 0.004 0.035 2832 Dihedral : 22.462 170.098 2744 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.94 % Allowed : 10.48 % Favored : 87.57 % 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: 1.05 (0.19), residues: 1986 helix: 1.92 (0.18), residues: 780 sheet: -0.33 (0.30), residues: 246 loop : 0.03 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.012 0.001 TYR D 192 PHE 0.026 0.001 PHE C 251 TRP 0.009 0.001 TRP D 104 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00345 (16596) covalent geometry : angle 0.49434 (22434) hydrogen bonds : bond 0.03647 ( 691) hydrogen bonds : angle 4.55011 ( 2007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.613 Fit side-chains REVERT: A 15 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8684 (ttm110) REVERT: A 91 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8486 (ttmt) REVERT: B 15 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (ttm110) REVERT: C 126 ARG cc_start: 0.7881 (mtm110) cc_final: 0.5954 (mpt180) REVERT: D 15 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7973 (ttm-80) REVERT: D 71 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7806 (t80) REVERT: E 28 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7546 (pt0) REVERT: E 49 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8292 (t) REVERT: E 171 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: F 32 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8076 (mm-30) REVERT: F 49 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8535 (m) REVERT: F 78 ILE cc_start: 0.8208 (mt) cc_final: 0.7885 (mp) REVERT: F 123 ASP cc_start: 0.8752 (t0) cc_final: 0.8478 (t0) REVERT: F 126 ARG cc_start: 0.8032 (mtm110) cc_final: 0.6120 (mpt180) REVERT: F 221 LYS cc_start: 0.8013 (mttm) cc_final: 0.7719 (mmtp) outliers start: 33 outliers final: 15 residues processed: 198 average time/residue: 0.6185 time to fit residues: 134.6253 Evaluate side-chains 192 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 85 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN C 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099328 restraints weight = 19607.516| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.34 r_work: 0.3006 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16596 Z= 0.137 Angle : 0.490 5.358 22434 Z= 0.252 Chirality : 0.043 0.220 2418 Planarity : 0.004 0.036 2832 Dihedral : 22.117 174.367 2744 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.00 % Allowed : 10.95 % Favored : 87.04 % 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: 0.94 (0.19), residues: 1986 helix: 1.68 (0.18), residues: 816 sheet: -0.35 (0.30), residues: 246 loop : 0.04 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.013 0.001 TYR D 192 PHE 0.027 0.001 PHE C 251 TRP 0.009 0.001 TRP D 104 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00327 (16596) covalent geometry : angle 0.48984 (22434) hydrogen bonds : bond 0.03572 ( 691) hydrogen bonds : angle 4.51792 ( 2007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.650 Fit side-chains REVERT: A 15 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8666 (ttm110) REVERT: A 321 ARG cc_start: 0.8874 (mpt90) cc_final: 0.8665 (mpt180) REVERT: B 15 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8703 (ttm110) REVERT: B 147 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8391 (mttm) REVERT: C 32 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 70 LEU cc_start: 0.8013 (mp) cc_final: 0.7584 (tt) REVERT: C 126 ARG cc_start: 0.7867 (mtm110) cc_final: 0.5907 (mpt180) REVERT: D 49 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8250 (t) REVERT: D 71 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7910 (t80) REVERT: D 160 THR cc_start: 0.8039 (m) cc_final: 0.7725 (p) REVERT: E 28 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7537 (pt0) REVERT: E 49 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8273 (t) REVERT: F 32 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8018 (mm-30) REVERT: F 49 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8533 (m) REVERT: F 78 ILE cc_start: 0.8135 (mt) cc_final: 0.7804 (mp) REVERT: F 123 ASP cc_start: 0.8636 (t0) cc_final: 0.8381 (t0) REVERT: F 126 ARG cc_start: 0.8040 (mtm110) cc_final: 0.6061 (mpt180) outliers start: 34 outliers final: 15 residues processed: 202 average time/residue: 0.6026 time to fit residues: 134.2920 Evaluate side-chains 191 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 192 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN C 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101133 restraints weight = 19582.318| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.34 r_work: 0.3052 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16596 Z= 0.112 Angle : 0.473 5.447 22434 Z= 0.244 Chirality : 0.043 0.216 2418 Planarity : 0.004 0.037 2832 Dihedral : 21.579 178.163 2744 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 11.13 % Favored : 87.04 % 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: 1.03 (0.19), residues: 1986 helix: 1.78 (0.18), residues: 816 sheet: -0.35 (0.30), residues: 246 loop : 0.09 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.013 0.001 TYR D 192 PHE 0.024 0.001 PHE C 251 TRP 0.010 0.001 TRP D 104 HIS 0.003 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00262 (16596) covalent geometry : angle 0.47337 (22434) hydrogen bonds : bond 0.03312 ( 691) hydrogen bonds : angle 4.42994 ( 2007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.592 Fit side-chains REVERT: A 15 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8679 (ttm110) REVERT: B 15 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: B 281 PHE cc_start: 0.8370 (m-80) cc_final: 0.7883 (m-80) REVERT: C 70 LEU cc_start: 0.7925 (mp) cc_final: 0.7514 (tt) REVERT: C 126 ARG cc_start: 0.7867 (mtm110) cc_final: 0.6127 (mmm160) REVERT: D 49 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8223 (t) REVERT: D 71 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7903 (t80) REVERT: E 28 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7581 (pt0) REVERT: E 31 LYS cc_start: 0.7772 (mttp) cc_final: 0.7448 (mmtm) REVERT: E 49 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8256 (t) REVERT: E 126 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7543 (ttt-90) REVERT: F 32 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8070 (mm-30) REVERT: F 49 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8516 (m) REVERT: F 92 TYR cc_start: 0.8576 (m-80) cc_final: 0.8356 (m-80) REVERT: F 126 ARG cc_start: 0.8057 (mtm110) cc_final: 0.6005 (mpt180) outliers start: 31 outliers final: 15 residues processed: 198 average time/residue: 0.5880 time to fit residues: 128.7569 Evaluate side-chains 189 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 192 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 178 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN C 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098742 restraints weight = 19791.009| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.33 r_work: 0.3017 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16596 Z= 0.155 Angle : 0.507 6.269 22434 Z= 0.260 Chirality : 0.044 0.204 2418 Planarity : 0.004 0.039 2832 Dihedral : 21.303 165.723 2744 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.71 % Allowed : 11.78 % Favored : 86.51 % 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: 1.12 (0.18), residues: 1986 helix: 2.00 (0.18), residues: 780 sheet: -0.40 (0.30), residues: 246 loop : 0.09 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.016 0.001 TYR D 192 PHE 0.024 0.001 PHE C 251 TRP 0.011 0.001 TRP D 104 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00374 (16596) covalent geometry : angle 0.50680 (22434) hydrogen bonds : bond 0.03711 ( 691) hydrogen bonds : angle 4.50131 ( 2007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.461 Fit side-chains REVERT: A 15 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8671 (ttm110) REVERT: B 15 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8685 (ttm110) REVERT: B 281 PHE cc_start: 0.8390 (m-80) cc_final: 0.7920 (m-80) REVERT: C 70 LEU cc_start: 0.7991 (mp) cc_final: 0.7551 (tt) REVERT: C 126 ARG cc_start: 0.7959 (mtm110) cc_final: 0.5981 (mpt180) REVERT: D 71 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7886 (t80) REVERT: D 213 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7373 (ttmm) REVERT: E 28 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7596 (pt0) REVERT: E 31 LYS cc_start: 0.7800 (mttp) cc_final: 0.7455 (mmtm) REVERT: E 49 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8292 (t) REVERT: F 32 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8043 (mm-30) REVERT: F 49 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8605 (m) REVERT: F 126 ARG cc_start: 0.7963 (mtm110) cc_final: 0.6019 (mpt180) outliers start: 29 outliers final: 18 residues processed: 192 average time/residue: 0.5731 time to fit residues: 122.1343 Evaluate side-chains 184 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 192 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN C 273 GLN F 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.146719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103468 restraints weight = 19531.209| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.33 r_work: 0.3040 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16596 Z= 0.109 Angle : 0.476 5.954 22434 Z= 0.245 Chirality : 0.043 0.199 2418 Planarity : 0.004 0.039 2832 Dihedral : 20.746 156.445 2744 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.65 % Allowed : 12.19 % Favored : 86.16 % 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: 1.09 (0.19), residues: 1986 helix: 1.83 (0.18), residues: 816 sheet: -0.36 (0.30), residues: 246 loop : 0.12 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.015 0.001 TYR D 192 PHE 0.025 0.001 PHE C 251 TRP 0.011 0.001 TRP D 104 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00256 (16596) covalent geometry : angle 0.47610 (22434) hydrogen bonds : bond 0.03263 ( 691) hydrogen bonds : angle 4.41434 ( 2007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.619 Fit side-chains REVERT: A 15 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8670 (ttm110) REVERT: A 321 ARG cc_start: 0.8829 (mpt90) cc_final: 0.8603 (mpt180) REVERT: B 15 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8646 (ttm110) REVERT: B 242 ASP cc_start: 0.8594 (t0) cc_final: 0.8332 (m-30) REVERT: C 15 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8629 (ttp80) REVERT: C 70 LEU cc_start: 0.7887 (mp) cc_final: 0.7490 (tt) REVERT: C 126 ARG cc_start: 0.7868 (mtm110) cc_final: 0.6159 (mmm160) REVERT: D 71 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7983 (t80) REVERT: E 28 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7577 (pt0) REVERT: E 31 LYS cc_start: 0.7744 (mttp) cc_final: 0.7423 (mmtm) REVERT: E 49 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8234 (t) REVERT: E 126 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7522 (ttt-90) REVERT: F 32 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 49 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8537 (m) REVERT: F 126 ARG cc_start: 0.7927 (mtm110) cc_final: 0.5956 (mpt180) outliers start: 28 outliers final: 18 residues processed: 189 average time/residue: 0.5735 time to fit residues: 120.2742 Evaluate side-chains 181 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 191 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097411 restraints weight = 19718.188| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.33 r_work: 0.2977 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16596 Z= 0.196 Angle : 0.542 7.036 22434 Z= 0.277 Chirality : 0.046 0.207 2418 Planarity : 0.004 0.039 2832 Dihedral : 20.938 159.345 2744 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 12.54 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 1986 helix: 1.93 (0.18), residues: 780 sheet: -0.40 (0.30), residues: 246 loop : 0.09 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 15 TYR 0.018 0.001 TYR D 192 PHE 0.023 0.002 PHE C 251 TRP 0.012 0.001 TRP D 104 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00476 (16596) covalent geometry : angle 0.54174 (22434) hydrogen bonds : bond 0.04004 ( 691) hydrogen bonds : angle 4.58528 ( 2007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.512 Fit side-chains REVERT: B 281 PHE cc_start: 0.8432 (m-80) cc_final: 0.8218 (m-80) REVERT: C 65 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: C 126 ARG cc_start: 0.7984 (mtm110) cc_final: 0.5992 (mpt180) REVERT: D 71 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7896 (t80) REVERT: D 213 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7323 (ttmm) REVERT: E 28 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7599 (pt0) REVERT: E 49 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8340 (t) REVERT: F 32 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8032 (mm-30) REVERT: F 49 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8667 (m) REVERT: F 126 ARG cc_start: 0.8041 (mtm110) cc_final: 0.6055 (mpt180) outliers start: 28 outliers final: 18 residues processed: 185 average time/residue: 0.6025 time to fit residues: 122.7459 Evaluate side-chains 178 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 192 TYR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 192 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 10.0000 chunk 178 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 0.0010 chunk 132 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 80 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 273 GLN ** F 94 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102917 restraints weight = 19550.419| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.32 r_work: 0.3083 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16596 Z= 0.098 Angle : 0.480 6.260 22434 Z= 0.248 Chirality : 0.043 0.187 2418 Planarity : 0.004 0.039 2832 Dihedral : 20.344 163.064 2744 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.53 % Allowed : 12.84 % Favored : 85.63 % 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: 1.17 (0.19), residues: 1986 helix: 1.86 (0.19), residues: 816 sheet: -0.40 (0.29), residues: 258 loop : 0.25 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 15 TYR 0.015 0.001 TYR D 192 PHE 0.028 0.001 PHE C 251 TRP 0.012 0.001 TRP D 104 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00220 (16596) covalent geometry : angle 0.48029 (22434) hydrogen bonds : bond 0.03166 ( 691) hydrogen bonds : angle 4.42307 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5890.05 seconds wall clock time: 101 minutes 6.11 seconds (6066.11 seconds total)