Starting phenix.real_space_refine on Sun Aug 24 10:39:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvz_61847/08_2025/9jvz_61847.cif" } resolution = 2.56 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= 0.001 sd= 0.017 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 S 119 5.16 5 B 14 2.79 5 C 12334 2.51 5 N 3325 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 211 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19558 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1382 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.20 Number of scatterers: 19558 At special positions: 0 Unit cell: (111.47, 110.76, 106.5, 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 119 16.00 O 3766 8.00 N 3325 7.00 C 12334 6.00 B 14 5.00 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 559.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 55.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.517A pdb=" N GLU A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 132 through 159 Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.517A pdb=" N GLU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 132 through 159 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.518A pdb=" N GLU C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 132 through 159 Processing helix chain 'C' and resid 161 through 169 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.517A pdb=" N GLU D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 55 Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 132 through 159 Processing helix chain 'D' and resid 161 through 169 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'E' and resid 16 through 27 removed outlier: 3.518A pdb=" N GLU E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 98 through 106 Processing helix chain 'E' and resid 132 through 159 Processing helix chain 'E' and resid 161 through 169 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.517A pdb=" N GLU F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 Processing helix chain 'F' and resid 70 through 84 Processing helix chain 'F' and resid 98 through 106 Processing helix chain 'F' and resid 132 through 159 Processing helix chain 'F' and resid 161 through 169 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'G' and resid 32 through 39 Processing helix chain 'G' and resid 49 through 67 Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 110 through 118 removed outlier: 3.535A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 173 Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.517A pdb=" N GLU H 27 " --> pdb=" O ARG H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 132 through 159 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 176 through 184 Processing helix chain 'I' and resid 32 through 39 Processing helix chain 'I' and resid 49 through 67 Processing helix chain 'I' and resid 82 through 96 Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.759A pdb=" N VAL I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 173 Processing helix chain 'I' and resid 175 through 183 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 49 through 67 Processing helix chain 'J' and resid 82 through 96 Processing helix chain 'J' and resid 110 through 118 removed outlier: 3.660A pdb=" N VAL J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 173 Processing helix chain 'J' and resid 175 through 183 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 49 through 67 Processing helix chain 'K' and resid 82 through 96 Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'K' and resid 147 through 173 Processing helix chain 'K' and resid 175 through 183 Processing helix chain 'K' and resid 190 through 198 Processing helix chain 'L' and resid 32 through 39 Processing helix chain 'L' and resid 49 through 67 Processing helix chain 'L' and resid 82 through 96 Processing helix chain 'L' and resid 110 through 118 Processing helix chain 'L' and resid 147 through 173 Processing helix chain 'L' and resid 175 through 183 Processing helix chain 'L' and resid 190 through 198 Processing helix chain 'M' and resid 32 through 39 Processing helix chain 'M' and resid 49 through 67 Processing helix chain 'M' and resid 82 through 96 Processing helix chain 'M' and resid 110 through 118 Processing helix chain 'M' and resid 147 through 173 Processing helix chain 'M' and resid 175 through 183 Processing helix chain 'M' and resid 190 through 198 Processing helix chain 'N' and resid 32 through 39 Processing helix chain 'N' and resid 49 through 67 Processing helix chain 'N' and resid 82 through 96 Processing helix chain 'N' and resid 110 through 118 Processing helix chain 'N' and resid 147 through 173 Processing helix chain 'N' and resid 175 through 183 Processing helix chain 'N' and resid 190 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER A 66 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET A 95 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG A 119 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 94 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 121 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER A 66 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET A 95 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR A 90 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.537A pdb=" N VAL A 129 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 143 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER B 66 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET B 95 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG B 119 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY B 94 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU B 121 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 96 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER B 66 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET B 95 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR B 113 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR B 90 " --> pdb=" O TYR B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 129 removed outlier: 3.515A pdb=" N VAL B 129 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE M 143 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER C 66 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG C 119 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY C 94 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C 121 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 96 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER C 66 " --> pdb=" O MET C 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET C 95 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 90 " --> pdb=" O TYR C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.703A pdb=" N ILE J 143 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER D 66 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET D 95 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG D 119 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY D 94 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU D 121 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA D 96 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER D 66 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET D 95 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR D 113 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR D 90 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.501A pdb=" N VAL D 129 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I 143 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.494A pdb=" N SER E 66 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG E 119 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLY E 94 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU E 121 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA E 96 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.494A pdb=" N SER E 66 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET E 95 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N THR E 90 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 126 through 129 removed outlier: 3.538A pdb=" N ILE G 143 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER F 66 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET F 95 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG F 119 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY F 94 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU F 121 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA F 96 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER F 66 " --> pdb=" O MET F 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET F 95 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR F 113 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR F 90 " --> pdb=" O TYR F 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 126 through 129 removed outlier: 3.564A pdb=" N ILE N 143 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.439A pdb=" N ILE G 72 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL G 103 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET G 74 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU G 105 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE G 76 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN G 107 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.439A pdb=" N ILE G 72 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL G 103 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET G 74 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU G 105 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE G 76 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN G 107 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 126 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY H 94 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA H 96 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 5.495A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 131 removed outlier: 3.621A pdb=" N ILE K 143 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY H 131 " --> pdb=" O GLY K 141 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY K 141 " --> pdb=" O GLY H 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG I 131 " --> pdb=" O CYS I 104 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY I 106 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU I 133 " --> pdb=" O GLY I 106 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA I 108 " --> pdb=" O LEU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE I 72 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL I 103 " --> pdb=" O ILE I 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET I 74 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU I 105 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE I 76 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN I 107 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET I 125 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR I 102 " --> pdb=" O MET I 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA I 126 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE J 72 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL J 103 " --> pdb=" O ILE J 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET J 74 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU J 105 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE J 76 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLN J 107 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET J 125 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR J 102 " --> pdb=" O MET J 125 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 126 " --> pdb=" O THR J 202 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE K 72 " --> pdb=" O GLN K 101 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL K 103 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET K 74 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU K 105 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE K 76 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN K 107 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG K 131 " --> pdb=" O CYS K 104 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY K 106 " --> pdb=" O ARG K 131 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU K 133 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA K 108 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE K 72 " --> pdb=" O GLN K 101 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL K 103 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET K 74 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU K 105 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE K 76 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN K 107 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET K 125 " --> pdb=" O ILE K 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR K 102 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA K 126 " --> pdb=" O THR K 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE L 72 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL L 103 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET L 74 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU L 105 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE L 76 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN L 107 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET L 125 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR L 102 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA L 126 " --> pdb=" O THR L 202 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE M 72 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL M 103 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 74 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU M 105 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE M 76 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN M 107 " --> pdb=" O ILE M 76 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE M 72 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL M 103 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 74 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU M 105 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE M 76 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN M 107 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET M 125 " --> pdb=" O ILE M 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR M 102 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA M 126 " --> pdb=" O THR M 202 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 41 through 44 removed outlier: 6.440A pdb=" N ILE N 72 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 103 " --> pdb=" O ILE N 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET N 74 " --> pdb=" O VAL N 103 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU N 105 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE N 76 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN N 107 " --> pdb=" O ILE N 76 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET N 125 " --> pdb=" O ILE N 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR N 102 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA N 126 " --> pdb=" O THR N 202 " (cutoff:3.500A) 1281 hydrogen bonds defined for protein. 3789 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: 3.26 Time building geometry restraints manager: 1.91 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: 4533 1.33 - 1.45: 3852 1.45 - 1.57: 11229 1.57 - 1.69: 14 1.69 - 1.81: 217 Bond restraints: 19845 Sorted by residual: bond pdb=" B26 BO2 A 201 " pdb=" O28 BO2 A 201 " ideal model delta sigma weight residual 1.356 1.492 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" B26 BO2 C 201 " pdb=" O28 BO2 C 201 " ideal model delta sigma weight residual 1.356 1.491 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" B26 BO2 H 201 " pdb=" O28 BO2 H 201 " ideal model delta sigma weight residual 1.356 1.491 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" B26 BO2 N 301 " pdb=" O28 BO2 N 301 " ideal model delta sigma weight residual 1.356 1.490 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" B26 BO2 L 301 " pdb=" O28 BO2 L 301 " ideal model delta sigma weight residual 1.356 1.489 -0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 19840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 26347 2.59 - 5.17: 408 5.17 - 7.76: 21 7.76 - 10.35: 23 10.35 - 12.93: 25 Bond angle restraints: 26824 Sorted by residual: angle pdb=" C ALA D 96 " pdb=" N ALA D 97 " pdb=" CA ALA D 97 " ideal model delta sigma weight residual 122.93 116.57 6.36 1.45e+00 4.76e-01 1.92e+01 angle pdb=" CA MET B 99 " pdb=" C MET B 99 " pdb=" O MET B 99 " ideal model delta sigma weight residual 120.42 115.79 4.63 1.06e+00 8.90e-01 1.90e+01 angle pdb=" O27 BO2 B 201 " pdb=" B26 BO2 B 201 " pdb=" O28 BO2 B 201 " ideal model delta sigma weight residual 119.22 106.29 12.93 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C ALA B 96 " pdb=" N ALA B 97 " pdb=" CA ALA B 97 " ideal model delta sigma weight residual 122.94 116.52 6.42 1.50e+00 4.44e-01 1.83e+01 angle pdb=" O27 BO2 E 201 " pdb=" B26 BO2 E 201 " pdb=" O28 BO2 E 201 " ideal model delta sigma weight residual 119.22 106.81 12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 26819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 10885 17.34 - 34.67: 939 34.67 - 52.01: 203 52.01 - 69.35: 68 69.35 - 86.68: 50 Dihedral angle restraints: 12145 sinusoidal: 4907 harmonic: 7238 Sorted by residual: dihedral pdb=" CA LEU J 127 " pdb=" C LEU J 127 " pdb=" N PRO J 128 " pdb=" CA PRO J 128 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LEU G 127 " pdb=" C LEU G 127 " pdb=" N PRO G 128 " pdb=" CA PRO G 128 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU N 127 " pdb=" C LEU N 127 " pdb=" N PRO N 128 " pdb=" CA PRO N 128 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 12142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2261 0.042 - 0.083: 552 0.083 - 0.125: 210 0.125 - 0.166: 36 0.166 - 0.208: 28 Chirality restraints: 3087 Sorted by residual: chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3084 not shown) Planarity restraints: 3479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 B 201 " -0.317 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C2 BO2 B 201 " -0.128 2.00e-02 2.50e+03 pdb=" C7 BO2 B 201 " 0.058 2.00e-02 2.50e+03 pdb=" N9 BO2 B 201 " 0.494 2.00e-02 2.50e+03 pdb=" O8 BO2 B 201 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 H 201 " 0.221 2.00e-02 2.50e+03 2.60e-01 8.46e+02 pdb=" C18 BO2 H 201 " -0.127 2.00e-02 2.50e+03 pdb=" C21 BO2 H 201 " 0.317 2.00e-02 2.50e+03 pdb=" N20 BO2 H 201 " -0.416 2.00e-02 2.50e+03 pdb=" O19 BO2 H 201 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 A 201 " -0.215 2.00e-02 2.50e+03 2.55e-01 8.13e+02 pdb=" C18 BO2 A 201 " 0.119 2.00e-02 2.50e+03 pdb=" C21 BO2 A 201 " -0.310 2.00e-02 2.50e+03 pdb=" N20 BO2 A 201 " 0.410 2.00e-02 2.50e+03 pdb=" O19 BO2 A 201 " -0.003 2.00e-02 2.50e+03 ... (remaining 3476 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1410 2.74 - 3.28: 20350 3.28 - 3.82: 36934 3.82 - 4.36: 45707 4.36 - 4.90: 75187 Nonbonded interactions: 179588 Sorted by model distance: nonbonded pdb=" O ILE H 165 " pdb=" OG SER H 169 " model vdw 2.197 3.040 nonbonded pdb=" O ILE E 165 " pdb=" OG SER E 169 " model vdw 2.197 3.040 nonbonded pdb=" O ILE A 165 " pdb=" OG SER A 169 " model vdw 2.197 3.040 nonbonded pdb=" O ILE C 165 " pdb=" OG SER C 169 " model vdw 2.197 3.040 nonbonded pdb=" O ILE F 165 " pdb=" OG SER F 169 " model vdw 2.197 3.040 ... (remaining 179583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.230 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.260 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 19859 Z= 0.373 Angle : 0.846 12.931 26824 Z= 0.487 Chirality : 0.047 0.208 3087 Planarity : 0.014 0.274 3479 Dihedral : 15.096 86.685 7483 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.60 % Allowed : 9.81 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.14), residues: 2478 helix: -1.11 (0.11), residues: 1386 sheet: -3.03 (0.25), residues: 189 loop : -1.77 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 28 TYR 0.007 0.001 TYR M 75 PHE 0.006 0.001 PHE C 175 TRP 0.002 0.001 TRP H 174 HIS 0.005 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00646 (19845) covalent geometry : angle 0.84564 (26824) hydrogen bonds : bond 0.13125 ( 1176) hydrogen bonds : angle 6.19770 ( 3789) Misc. bond : bond 0.02328 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 840 time to evaluate : 0.649 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER N 210 " (corrupted residue). Skipping it. REVERT: A 42 ASN cc_start: 0.9059 (m-40) cc_final: 0.8584 (m110) REVERT: A 59 ASP cc_start: 0.8548 (m-30) cc_final: 0.8282 (m-30) REVERT: A 113 TYR cc_start: 0.8396 (m-80) cc_final: 0.8048 (m-80) REVERT: A 152 ARG cc_start: 0.8650 (ttp80) cc_final: 0.7961 (ttp80) REVERT: A 170 ASP cc_start: 0.8025 (t70) cc_final: 0.7367 (OUTLIER) REVERT: A 183 TYR cc_start: 0.8444 (t80) cc_final: 0.7904 (t80) REVERT: A 188 HIS cc_start: 0.7816 (m90) cc_final: 0.7596 (m90) REVERT: B 38 ASP cc_start: 0.8413 (m-30) cc_final: 0.8098 (m-30) REVERT: B 42 ASN cc_start: 0.9117 (m-40) cc_final: 0.8667 (m-40) REVERT: B 55 ASP cc_start: 0.7912 (t70) cc_final: 0.7579 (t0) REVERT: B 58 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8713 (mtmm) REVERT: B 59 ASP cc_start: 0.8553 (m-30) cc_final: 0.8053 (m-30) REVERT: B 139 GLN cc_start: 0.8645 (mt0) cc_final: 0.8318 (mt0) REVERT: B 170 ASP cc_start: 0.8364 (t70) cc_final: 0.7874 (t70) REVERT: B 182 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7941 (mm-30) REVERT: C 38 ASP cc_start: 0.8149 (m-30) cc_final: 0.7652 (m-30) REVERT: C 42 ASN cc_start: 0.8898 (m-40) cc_final: 0.8563 (m110) REVERT: C 55 ASP cc_start: 0.7603 (t70) cc_final: 0.7288 (t0) REVERT: C 59 ASP cc_start: 0.8678 (m-30) cc_final: 0.8264 (m-30) REVERT: C 124 GLN cc_start: 0.8831 (pt0) cc_final: 0.8527 (pt0) REVERT: C 139 GLN cc_start: 0.8716 (mt0) cc_final: 0.8314 (mt0) REVERT: C 149 GLU cc_start: 0.8194 (tp30) cc_final: 0.7592 (tp30) REVERT: C 152 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8072 (ttp80) REVERT: C 168 ASP cc_start: 0.8918 (m-30) cc_final: 0.8702 (m-30) REVERT: C 170 ASP cc_start: 0.8218 (t70) cc_final: 0.7730 (t70) REVERT: C 183 TYR cc_start: 0.8836 (t80) cc_final: 0.8477 (t80) REVERT: C 188 HIS cc_start: 0.7818 (m90) cc_final: 0.7399 (m-70) REVERT: D 18 ASP cc_start: 0.8062 (m-30) cc_final: 0.7810 (m-30) REVERT: D 38 ASP cc_start: 0.8352 (m-30) cc_final: 0.7840 (m-30) REVERT: D 42 ASN cc_start: 0.8946 (m-40) cc_final: 0.8707 (m-40) REVERT: D 55 ASP cc_start: 0.7817 (t70) cc_final: 0.7548 (t0) REVERT: D 59 ASP cc_start: 0.8683 (m-30) cc_final: 0.8386 (m-30) REVERT: D 152 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8055 (ttp80) REVERT: D 170 ASP cc_start: 0.8090 (t70) cc_final: 0.7689 (t70) REVERT: D 183 TYR cc_start: 0.8494 (t80) cc_final: 0.8108 (t80) REVERT: D 188 HIS cc_start: 0.7949 (m90) cc_final: 0.7579 (m-70) REVERT: E 18 ASP cc_start: 0.8103 (m-30) cc_final: 0.7854 (m-30) REVERT: E 22 GLU cc_start: 0.8052 (tt0) cc_final: 0.7619 (tm-30) REVERT: E 37 ASN cc_start: 0.9139 (p0) cc_final: 0.8938 (p0) REVERT: E 42 ASN cc_start: 0.8984 (m-40) cc_final: 0.8635 (m-40) REVERT: E 55 ASP cc_start: 0.7758 (t70) cc_final: 0.7314 (t0) REVERT: E 58 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8605 (mtmm) REVERT: E 59 ASP cc_start: 0.8665 (m-30) cc_final: 0.8195 (m-30) REVERT: E 135 ASP cc_start: 0.8275 (m-30) cc_final: 0.7688 (m-30) REVERT: E 139 GLN cc_start: 0.8766 (mt0) cc_final: 0.8539 (mt0) REVERT: E 152 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8176 (ttp80) REVERT: E 170 ASP cc_start: 0.8190 (t70) cc_final: 0.7686 (t70) REVERT: E 188 HIS cc_start: 0.7641 (m90) cc_final: 0.6976 (m90) REVERT: F 18 ASP cc_start: 0.8399 (m-30) cc_final: 0.8190 (m-30) REVERT: F 42 ASN cc_start: 0.9006 (m-40) cc_final: 0.8734 (m110) REVERT: F 58 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8450 (mtmm) REVERT: F 59 ASP cc_start: 0.8786 (m-30) cc_final: 0.8438 (m-30) REVERT: F 124 GLN cc_start: 0.8716 (pt0) cc_final: 0.8449 (pt0) REVERT: F 135 ASP cc_start: 0.8326 (m-30) cc_final: 0.7658 (m-30) REVERT: F 149 GLU cc_start: 0.8215 (tp30) cc_final: 0.7737 (tp30) REVERT: F 152 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8094 (ttp80) REVERT: F 170 ASP cc_start: 0.8431 (t70) cc_final: 0.7595 (t70) REVERT: F 182 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7780 (mm-30) REVERT: F 188 HIS cc_start: 0.7737 (m90) cc_final: 0.7294 (m-70) REVERT: G 34 ASN cc_start: 0.7461 (m110) cc_final: 0.6451 (m-40) REVERT: G 38 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7762 (mm-30) REVERT: G 42 ILE cc_start: 0.9213 (mt) cc_final: 0.8988 (mm) REVERT: G 50 ASP cc_start: 0.8434 (m-30) cc_final: 0.8126 (m-30) REVERT: H 38 ASP cc_start: 0.8299 (m-30) cc_final: 0.8060 (m-30) REVERT: H 42 ASN cc_start: 0.8985 (m-40) cc_final: 0.8716 (m110) REVERT: H 47 GLN cc_start: 0.9235 (mt0) cc_final: 0.8859 (mt0) REVERT: H 55 ASP cc_start: 0.7631 (t70) cc_final: 0.7194 (t0) REVERT: H 58 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8725 (mtmm) REVERT: H 59 ASP cc_start: 0.8631 (m-30) cc_final: 0.8349 (m-30) REVERT: H 130 THR cc_start: 0.8414 (t) cc_final: 0.8176 (p) REVERT: H 135 ASP cc_start: 0.8162 (m-30) cc_final: 0.7765 (m-30) REVERT: H 139 GLN cc_start: 0.8627 (mt0) cc_final: 0.8253 (mt0) REVERT: H 152 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8316 (ttp80) REVERT: H 168 ASP cc_start: 0.8999 (m-30) cc_final: 0.8730 (m-30) REVERT: H 170 ASP cc_start: 0.8224 (t70) cc_final: 0.7731 (t70) REVERT: H 183 TYR cc_start: 0.8729 (t80) cc_final: 0.8450 (t80) REVERT: H 188 HIS cc_start: 0.7899 (m90) cc_final: 0.7630 (m90) REVERT: I 34 ASN cc_start: 0.7677 (m110) cc_final: 0.7141 (m110) REVERT: I 50 ASP cc_start: 0.8397 (m-30) cc_final: 0.8048 (m-30) REVERT: I 54 ASN cc_start: 0.8759 (m-40) cc_final: 0.8539 (m110) REVERT: I 59 GLN cc_start: 0.8760 (mt0) cc_final: 0.8508 (mt0) REVERT: I 180 ARG cc_start: 0.8761 (ttt90) cc_final: 0.8468 (ttt-90) REVERT: I 181 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8670 (mttp) REVERT: J 34 ASN cc_start: 0.7685 (m110) cc_final: 0.7092 (m110) REVERT: J 71 ASP cc_start: 0.8711 (m-30) cc_final: 0.8505 (m-30) REVERT: J 146 GLN cc_start: 0.8580 (mt0) cc_final: 0.8351 (mt0) REVERT: J 164 MET cc_start: 0.8979 (ttp) cc_final: 0.8778 (ttp) REVERT: J 165 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8053 (mt-10) REVERT: J 180 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8495 (tpp80) REVERT: J 181 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8751 (mtmm) REVERT: K 31 ASN cc_start: 0.7780 (t0) cc_final: 0.7381 (t0) REVERT: K 34 ASN cc_start: 0.7175 (m110) cc_final: 0.6459 (m110) REVERT: K 50 ASP cc_start: 0.8087 (m-30) cc_final: 0.7731 (m-30) REVERT: K 54 ASN cc_start: 0.8413 (m-40) cc_final: 0.7869 (m110) REVERT: K 71 ASP cc_start: 0.8655 (m-30) cc_final: 0.8436 (m-30) REVERT: K 94 GLN cc_start: 0.8853 (mm110) cc_final: 0.8648 (mm110) REVERT: K 158 GLU cc_start: 0.8692 (tp30) cc_final: 0.8326 (tp30) REVERT: L 31 ASN cc_start: 0.7706 (t0) cc_final: 0.7402 (t0) REVERT: L 33 TYR cc_start: 0.8596 (m-80) cc_final: 0.8362 (m-80) REVERT: L 34 ASN cc_start: 0.6974 (m110) cc_final: 0.6424 (m110) REVERT: L 50 ASP cc_start: 0.7793 (m-30) cc_final: 0.7362 (m-30) REVERT: L 54 ASN cc_start: 0.8699 (m-40) cc_final: 0.8183 (m110) REVERT: L 101 GLN cc_start: 0.8409 (tt0) cc_final: 0.8203 (tt0) REVERT: M 54 ASN cc_start: 0.9133 (m-40) cc_final: 0.8830 (m110) REVERT: M 55 ASP cc_start: 0.8225 (m-30) cc_final: 0.8008 (m-30) REVERT: M 71 ASP cc_start: 0.8572 (m-30) cc_final: 0.8288 (m-30) REVERT: M 101 GLN cc_start: 0.8566 (tt0) cc_final: 0.8240 (tt0) REVERT: M 181 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8645 (mttp) REVERT: N 55 ASP cc_start: 0.8201 (m-30) cc_final: 0.7915 (m-30) REVERT: N 71 ASP cc_start: 0.8658 (m-30) cc_final: 0.8103 (m-30) REVERT: N 151 GLU cc_start: 0.8300 (tt0) cc_final: 0.7691 (tp30) REVERT: N 180 ARG cc_start: 0.8780 (ttt90) cc_final: 0.8578 (tpp-160) outliers start: 12 outliers final: 4 residues processed: 842 average time/residue: 0.6208 time to fit residues: 578.7299 Evaluate side-chains 632 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 629 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain H residue 98 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 117 HIS B 117 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS D 42 ASN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN E 117 HIS E 124 GLN F 117 HIS G 54 ASN G 101 GLN G 129 ASN H 42 ASN H 117 HIS H 124 GLN I 94 GLN I 101 GLN I 129 ASN J 101 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN K 101 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 153 GLN L 59 GLN L 94 GLN ** L 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 94 GLN N 101 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.069584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.061170 restraints weight = 34440.317| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.26 r_work: 0.2541 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 19859 Z= 0.301 Angle : 0.688 11.361 26824 Z= 0.324 Chirality : 0.044 0.232 3087 Planarity : 0.004 0.039 3479 Dihedral : 8.848 59.825 2995 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.08 % Allowed : 17.12 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 2478 helix: 0.52 (0.13), residues: 1407 sheet: -2.63 (0.28), residues: 182 loop : -1.25 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 161 TYR 0.014 0.002 TYR M 206 PHE 0.015 0.002 PHE G 147 TRP 0.002 0.001 TRP E 174 HIS 0.004 0.001 HIS J 171 Details of bonding type rmsd covalent geometry : bond 0.00657 (19845) covalent geometry : angle 0.68841 (26824) hydrogen bonds : bond 0.03855 ( 1176) hydrogen bonds : angle 4.21592 ( 3789) Misc. bond : bond 0.00120 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 646 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER N 210 " (corrupted residue). Skipping it. REVERT: A 38 ASP cc_start: 0.8886 (m-30) cc_final: 0.8001 (m-30) REVERT: A 42 ASN cc_start: 0.9350 (m110) cc_final: 0.8823 (m110) REVERT: A 55 ASP cc_start: 0.8208 (t0) cc_final: 0.7686 (t0) REVERT: A 59 ASP cc_start: 0.9046 (m-30) cc_final: 0.8654 (m-30) REVERT: A 111 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8944 (mttt) REVERT: A 170 ASP cc_start: 0.9060 (t70) cc_final: 0.8776 (t70) REVERT: B 38 ASP cc_start: 0.8935 (m-30) cc_final: 0.8681 (m-30) REVERT: B 42 ASN cc_start: 0.9470 (m-40) cc_final: 0.9052 (m110) REVERT: B 55 ASP cc_start: 0.8340 (t70) cc_final: 0.7808 (t0) REVERT: B 59 ASP cc_start: 0.8883 (m-30) cc_final: 0.8468 (m-30) REVERT: B 170 ASP cc_start: 0.9095 (t70) cc_final: 0.8741 (t70) REVERT: C 35 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: C 38 ASP cc_start: 0.8963 (m-30) cc_final: 0.8463 (m-30) REVERT: C 42 ASN cc_start: 0.9351 (m-40) cc_final: 0.8973 (m110) REVERT: C 55 ASP cc_start: 0.8066 (t70) cc_final: 0.7639 (t0) REVERT: C 59 ASP cc_start: 0.9012 (m-30) cc_final: 0.8611 (m-30) REVERT: C 139 GLN cc_start: 0.9124 (mt0) cc_final: 0.8857 (mt0) REVERT: C 152 ARG cc_start: 0.9225 (ttp80) cc_final: 0.9007 (ttp80) REVERT: C 164 ARG cc_start: 0.9047 (tpt-90) cc_final: 0.8567 (tpt-90) REVERT: C 168 ASP cc_start: 0.9058 (m-30) cc_final: 0.8716 (m-30) REVERT: D 18 ASP cc_start: 0.8712 (m-30) cc_final: 0.8497 (m-30) REVERT: D 38 ASP cc_start: 0.9040 (m-30) cc_final: 0.8627 (m-30) REVERT: D 42 ASN cc_start: 0.9393 (m110) cc_final: 0.9055 (m110) REVERT: D 55 ASP cc_start: 0.8311 (t70) cc_final: 0.7939 (t0) REVERT: D 59 ASP cc_start: 0.9052 (m-30) cc_final: 0.8666 (m-30) REVERT: D 152 ARG cc_start: 0.9201 (ttp80) cc_final: 0.8878 (ttp80) REVERT: D 170 ASP cc_start: 0.8848 (t70) cc_final: 0.8647 (t70) REVERT: E 22 GLU cc_start: 0.8755 (tt0) cc_final: 0.8005 (tm-30) REVERT: E 42 ASN cc_start: 0.9208 (m110) cc_final: 0.8934 (m110) REVERT: E 55 ASP cc_start: 0.8298 (t70) cc_final: 0.7797 (t0) REVERT: E 58 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8672 (mtmm) REVERT: E 59 ASP cc_start: 0.9033 (m-30) cc_final: 0.8657 (m-30) REVERT: E 135 ASP cc_start: 0.9042 (m-30) cc_final: 0.8577 (m-30) REVERT: E 152 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8889 (ttp80) REVERT: E 170 ASP cc_start: 0.8943 (t70) cc_final: 0.8540 (t0) REVERT: F 38 ASP cc_start: 0.8843 (m-30) cc_final: 0.8478 (m-30) REVERT: F 42 ASN cc_start: 0.9386 (m-40) cc_final: 0.8877 (m-40) REVERT: F 58 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8527 (mtmt) REVERT: F 59 ASP cc_start: 0.9090 (m-30) cc_final: 0.8845 (m-30) REVERT: F 135 ASP cc_start: 0.9077 (m-30) cc_final: 0.8598 (m-30) REVERT: G 47 GLN cc_start: 0.8782 (tp40) cc_final: 0.8564 (tp40) REVERT: G 50 ASP cc_start: 0.8858 (m-30) cc_final: 0.8563 (m-30) REVERT: G 192 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8527 (mm-30) REVERT: H 38 ASP cc_start: 0.8943 (m-30) cc_final: 0.8522 (m-30) REVERT: H 42 ASN cc_start: 0.9354 (m110) cc_final: 0.8974 (m110) REVERT: H 55 ASP cc_start: 0.8018 (t70) cc_final: 0.7492 (t0) REVERT: H 58 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8726 (mtmm) REVERT: H 59 ASP cc_start: 0.9081 (m-30) cc_final: 0.8594 (m-30) REVERT: H 135 ASP cc_start: 0.8964 (m-30) cc_final: 0.8581 (m-30) REVERT: H 139 GLN cc_start: 0.9046 (mt0) cc_final: 0.8816 (mt0) REVERT: H 152 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8726 (ttp80) REVERT: H 170 ASP cc_start: 0.9036 (t70) cc_final: 0.8681 (t0) REVERT: I 34 ASN cc_start: 0.8137 (m110) cc_final: 0.7626 (m110) REVERT: I 50 ASP cc_start: 0.8982 (m-30) cc_final: 0.8698 (m-30) REVERT: I 54 ASN cc_start: 0.9090 (m-40) cc_final: 0.8879 (m110) REVERT: I 205 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8270 (pm20) REVERT: I 207 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7747 (ppt-90) REVERT: J 31 ASN cc_start: 0.8671 (t0) cc_final: 0.8385 (t160) REVERT: J 34 ASN cc_start: 0.8281 (m110) cc_final: 0.7929 (m110) REVERT: J 181 LYS cc_start: 0.9271 (mtmm) cc_final: 0.9051 (mttp) REVERT: K 34 ASN cc_start: 0.8098 (m110) cc_final: 0.7511 (m110) REVERT: K 39 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8671 (mt-10) REVERT: K 47 GLN cc_start: 0.8632 (tp40) cc_final: 0.8403 (tp40) REVERT: K 50 ASP cc_start: 0.8891 (m-30) cc_final: 0.8660 (m-30) REVERT: K 129 ASN cc_start: 0.9378 (m-40) cc_final: 0.8989 (m110) REVERT: K 158 GLU cc_start: 0.9223 (tp30) cc_final: 0.8945 (tp30) REVERT: K 180 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (ttm110) REVERT: L 34 ASN cc_start: 0.7979 (m110) cc_final: 0.7653 (m110) REVERT: L 50 ASP cc_start: 0.8818 (m-30) cc_final: 0.8521 (m-30) REVERT: L 123 LYS cc_start: 0.9040 (mtmt) cc_final: 0.8825 (mtmt) REVERT: M 34 ASN cc_start: 0.8190 (m110) cc_final: 0.7925 (m110) REVERT: M 54 ASN cc_start: 0.9363 (m-40) cc_final: 0.9080 (m110) REVERT: M 101 GLN cc_start: 0.8819 (tt0) cc_final: 0.8544 (tt0) REVERT: M 204 LEU cc_start: 0.9184 (mt) cc_final: 0.8928 (mt) REVERT: N 34 ASN cc_start: 0.8127 (t0) cc_final: 0.7922 (m110) REVERT: N 47 GLN cc_start: 0.8724 (tp40) cc_final: 0.8522 (tp40) REVERT: N 71 ASP cc_start: 0.9154 (m-30) cc_final: 0.8908 (m-30) REVERT: N 149 ASP cc_start: 0.9080 (m-30) cc_final: 0.8831 (m-30) REVERT: N 151 GLU cc_start: 0.9008 (tt0) cc_final: 0.8348 (tp30) outliers start: 82 outliers final: 24 residues processed: 688 average time/residue: 0.5748 time to fit residues: 441.3027 Evaluate side-chains 616 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 588 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 207 ARG Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 180 ARG Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN E 124 GLN F 42 ASN F 142 GLN G 34 ASN G 54 ASN G 59 GLN G 101 GLN G 144 GLN I 101 GLN I 136 GLN J 144 GLN J 146 GLN K 101 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 153 GLN L 31 ASN L 54 ASN L 94 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 101 GLN N 129 ASN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.071093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.062856 restraints weight = 34545.427| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.25 r_work: 0.2583 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19859 Z= 0.179 Angle : 0.602 10.505 26824 Z= 0.281 Chirality : 0.042 0.209 3087 Planarity : 0.003 0.028 3479 Dihedral : 8.400 59.498 2989 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.53 % Allowed : 18.87 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.16), residues: 2478 helix: 1.36 (0.13), residues: 1400 sheet: -2.26 (0.31), residues: 182 loop : -1.05 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 43 TYR 0.010 0.001 TYR I 197 PHE 0.012 0.001 PHE B 102 TRP 0.005 0.001 TRP C 174 HIS 0.004 0.001 HIS N 171 Details of bonding type rmsd covalent geometry : bond 0.00395 (19845) covalent geometry : angle 0.60229 (26824) hydrogen bonds : bond 0.03366 ( 1176) hydrogen bonds : angle 3.93010 ( 3789) Misc. bond : bond 0.00142 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 642 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. REVERT: A 22 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 42 ASN cc_start: 0.9342 (m110) cc_final: 0.8704 (m110) REVERT: A 55 ASP cc_start: 0.8240 (t0) cc_final: 0.7799 (t0) REVERT: A 58 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8870 (mtmm) REVERT: A 59 ASP cc_start: 0.9029 (m-30) cc_final: 0.8583 (m-30) REVERT: A 170 ASP cc_start: 0.9062 (t70) cc_final: 0.8616 (t70) REVERT: B 22 GLU cc_start: 0.8629 (tt0) cc_final: 0.7621 (tp30) REVERT: B 38 ASP cc_start: 0.8929 (m-30) cc_final: 0.8403 (m-30) REVERT: B 42 ASN cc_start: 0.9490 (m-40) cc_final: 0.8984 (m110) REVERT: B 55 ASP cc_start: 0.8279 (t70) cc_final: 0.7765 (t0) REVERT: B 59 ASP cc_start: 0.8817 (m-30) cc_final: 0.8611 (m-30) REVERT: B 164 ARG cc_start: 0.8935 (tpt-90) cc_final: 0.8550 (tpt-90) REVERT: B 170 ASP cc_start: 0.9087 (t70) cc_final: 0.8721 (t70) REVERT: C 38 ASP cc_start: 0.9001 (m-30) cc_final: 0.8318 (m-30) REVERT: C 42 ASN cc_start: 0.9403 (m-40) cc_final: 0.9013 (m110) REVERT: C 55 ASP cc_start: 0.8131 (t70) cc_final: 0.7655 (t0) REVERT: C 59 ASP cc_start: 0.8938 (m-30) cc_final: 0.8564 (m-30) REVERT: C 139 GLN cc_start: 0.9093 (mt0) cc_final: 0.8813 (mt0) REVERT: C 152 ARG cc_start: 0.9230 (ttp80) cc_final: 0.9028 (ttp80) REVERT: D 18 ASP cc_start: 0.8772 (m-30) cc_final: 0.8571 (m-30) REVERT: D 38 ASP cc_start: 0.8996 (m-30) cc_final: 0.8583 (m-30) REVERT: D 42 ASN cc_start: 0.9405 (m110) cc_final: 0.9018 (m110) REVERT: D 55 ASP cc_start: 0.8317 (t70) cc_final: 0.7937 (t0) REVERT: D 59 ASP cc_start: 0.9023 (m-30) cc_final: 0.8685 (m-30) REVERT: D 152 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8818 (ttp80) REVERT: D 170 ASP cc_start: 0.8785 (t70) cc_final: 0.8584 (t70) REVERT: E 22 GLU cc_start: 0.8712 (tt0) cc_final: 0.7960 (tm-30) REVERT: E 38 ASP cc_start: 0.8820 (m-30) cc_final: 0.8525 (m-30) REVERT: E 42 ASN cc_start: 0.9173 (m110) cc_final: 0.8795 (m110) REVERT: E 55 ASP cc_start: 0.8311 (t70) cc_final: 0.7789 (t0) REVERT: E 58 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8643 (mtmm) REVERT: E 59 ASP cc_start: 0.8934 (m-30) cc_final: 0.8530 (m-30) REVERT: E 104 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9001 (tp) REVERT: E 135 ASP cc_start: 0.8995 (m-30) cc_final: 0.8541 (m-30) REVERT: E 147 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8649 (ttpt) REVERT: E 152 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8853 (ttp80) REVERT: E 170 ASP cc_start: 0.8889 (t70) cc_final: 0.8341 (t0) REVERT: F 23 ARG cc_start: 0.9136 (mtp180) cc_final: 0.8925 (mtp180) REVERT: F 42 ASN cc_start: 0.9401 (m110) cc_final: 0.8990 (m-40) REVERT: F 55 ASP cc_start: 0.8043 (t0) cc_final: 0.7824 (t0) REVERT: F 58 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8520 (mtmt) REVERT: F 59 ASP cc_start: 0.9104 (m-30) cc_final: 0.8802 (m-30) REVERT: F 130 THR cc_start: 0.8988 (t) cc_final: 0.8664 (p) REVERT: F 135 ASP cc_start: 0.9046 (m-30) cc_final: 0.8538 (m-30) REVERT: F 147 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8691 (ttpt) REVERT: G 50 ASP cc_start: 0.8834 (m-30) cc_final: 0.8471 (m-30) REVERT: G 192 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8550 (mm-30) REVERT: H 23 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8752 (mtp180) REVERT: H 38 ASP cc_start: 0.8905 (m-30) cc_final: 0.8404 (m-30) REVERT: H 42 ASN cc_start: 0.9363 (m110) cc_final: 0.8910 (m110) REVERT: H 55 ASP cc_start: 0.8109 (t70) cc_final: 0.7547 (t0) REVERT: H 58 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8695 (mtmm) REVERT: H 59 ASP cc_start: 0.9034 (m-30) cc_final: 0.8567 (m-30) REVERT: H 135 ASP cc_start: 0.8914 (m-30) cc_final: 0.8516 (m-30) REVERT: H 139 GLN cc_start: 0.8996 (mt0) cc_final: 0.8746 (mt0) REVERT: H 152 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8673 (ttp80) REVERT: H 170 ASP cc_start: 0.9079 (t70) cc_final: 0.8719 (t0) REVERT: I 34 ASN cc_start: 0.8261 (m110) cc_final: 0.7781 (m110) REVERT: I 50 ASP cc_start: 0.8994 (m-30) cc_final: 0.8662 (m-30) REVERT: I 59 GLN cc_start: 0.9185 (mt0) cc_final: 0.8796 (mt0) REVERT: I 205 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: I 207 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (ppt-90) REVERT: J 31 ASN cc_start: 0.8664 (t0) cc_final: 0.8416 (t160) REVERT: J 34 ASN cc_start: 0.8342 (m110) cc_final: 0.7995 (m110) REVERT: J 187 LYS cc_start: 0.8497 (tppt) cc_final: 0.8292 (tppt) REVERT: K 34 ASN cc_start: 0.8030 (m110) cc_final: 0.7787 (m110) REVERT: K 39 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8703 (mt-10) REVERT: K 47 GLN cc_start: 0.8565 (tp40) cc_final: 0.8352 (tp40) REVERT: K 50 ASP cc_start: 0.8877 (m-30) cc_final: 0.8451 (m-30) REVERT: K 54 ASN cc_start: 0.9056 (m-40) cc_final: 0.8845 (m110) REVERT: K 129 ASN cc_start: 0.9332 (m-40) cc_final: 0.9023 (m110) REVERT: K 158 GLU cc_start: 0.9234 (tp30) cc_final: 0.8995 (tp30) REVERT: K 160 MET cc_start: 0.9363 (mtt) cc_final: 0.9149 (mtp) REVERT: L 31 ASN cc_start: 0.8464 (t0) cc_final: 0.8248 (t0) REVERT: L 34 ASN cc_start: 0.8372 (m110) cc_final: 0.7965 (m110) REVERT: L 50 ASP cc_start: 0.8820 (m-30) cc_final: 0.8571 (m-30) REVERT: M 54 ASN cc_start: 0.9385 (m-40) cc_final: 0.9056 (m110) REVERT: M 101 GLN cc_start: 0.8803 (tt0) cc_final: 0.8570 (tt0) REVERT: M 138 SER cc_start: 0.8988 (p) cc_final: 0.8636 (m) REVERT: M 202 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9048 (p) REVERT: M 204 LEU cc_start: 0.9247 (mt) cc_final: 0.8961 (mp) REVERT: M 205 GLU cc_start: 0.7751 (pp20) cc_final: 0.7431 (pp20) REVERT: N 34 ASN cc_start: 0.8271 (t0) cc_final: 0.8068 (m110) REVERT: N 47 GLN cc_start: 0.8592 (tp40) cc_final: 0.8387 (tp40) REVERT: N 71 ASP cc_start: 0.9111 (m-30) cc_final: 0.8816 (m-30) REVERT: N 151 GLU cc_start: 0.8986 (tt0) cc_final: 0.8308 (tp30) REVERT: N 205 GLU cc_start: 0.8623 (pm20) cc_final: 0.8391 (pp20) REVERT: N 206 TYR cc_start: 0.8741 (m-80) cc_final: 0.8517 (m-10) outliers start: 71 outliers final: 28 residues processed: 671 average time/residue: 0.5550 time to fit residues: 418.1112 Evaluate side-chains 630 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 598 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 207 ARG Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 150 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 169 optimal weight: 0.0270 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 overall best weight: 1.8444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN G 47 GLN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 101 GLN J 94 GLN J 101 GLN J 144 GLN K 101 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 153 GLN L 54 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN M 107 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 107 GLN N 144 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.071365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.063061 restraints weight = 34353.497| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.25 r_work: 0.2588 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19859 Z= 0.163 Angle : 0.581 10.331 26824 Z= 0.272 Chirality : 0.042 0.207 3087 Planarity : 0.003 0.038 3479 Dihedral : 8.151 59.772 2989 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.68 % Allowed : 19.51 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.17), residues: 2478 helix: 1.78 (0.13), residues: 1407 sheet: -2.04 (0.32), residues: 182 loop : -0.98 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 43 TYR 0.020 0.001 TYR C 113 PHE 0.008 0.001 PHE F 143 TRP 0.002 0.001 TRP E 174 HIS 0.003 0.001 HIS M 171 Details of bonding type rmsd covalent geometry : bond 0.00360 (19845) covalent geometry : angle 0.58111 (26824) hydrogen bonds : bond 0.03227 ( 1176) hydrogen bonds : angle 3.81447 ( 3789) Misc. bond : bond 0.00152 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 637 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. REVERT: A 22 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 23 ARG cc_start: 0.9152 (ttm170) cc_final: 0.8947 (ttm170) REVERT: A 42 ASN cc_start: 0.9335 (m110) cc_final: 0.8695 (m110) REVERT: A 55 ASP cc_start: 0.8264 (t0) cc_final: 0.7762 (t0) REVERT: A 59 ASP cc_start: 0.8955 (m-30) cc_final: 0.8502 (m-30) REVERT: A 163 GLU cc_start: 0.9254 (pm20) cc_final: 0.9041 (mp0) REVERT: A 164 ARG cc_start: 0.9007 (tpt-90) cc_final: 0.8700 (tpt-90) REVERT: A 170 ASP cc_start: 0.9036 (t70) cc_final: 0.8717 (t70) REVERT: B 22 GLU cc_start: 0.8559 (tt0) cc_final: 0.7551 (tp30) REVERT: B 38 ASP cc_start: 0.8944 (m-30) cc_final: 0.8364 (m-30) REVERT: B 42 ASN cc_start: 0.9490 (m-40) cc_final: 0.9003 (m110) REVERT: B 55 ASP cc_start: 0.8298 (t70) cc_final: 0.7767 (t0) REVERT: B 59 ASP cc_start: 0.8838 (m-30) cc_final: 0.8436 (m-30) REVERT: B 111 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8925 (mttt) REVERT: B 170 ASP cc_start: 0.9089 (t70) cc_final: 0.8723 (t70) REVERT: C 38 ASP cc_start: 0.9025 (m-30) cc_final: 0.8574 (m-30) REVERT: C 42 ASN cc_start: 0.9392 (m-40) cc_final: 0.8998 (m110) REVERT: C 55 ASP cc_start: 0.8213 (t70) cc_final: 0.7695 (t0) REVERT: C 59 ASP cc_start: 0.8928 (m-30) cc_final: 0.8436 (m-30) REVERT: C 111 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8987 (mttt) REVERT: C 139 GLN cc_start: 0.9093 (mt0) cc_final: 0.8888 (mt0) REVERT: C 152 ARG cc_start: 0.9213 (ttp80) cc_final: 0.8979 (ttp80) REVERT: D 18 ASP cc_start: 0.8830 (m-30) cc_final: 0.8629 (m-30) REVERT: D 38 ASP cc_start: 0.9032 (m-30) cc_final: 0.8648 (m-30) REVERT: D 42 ASN cc_start: 0.9398 (m110) cc_final: 0.9007 (m110) REVERT: D 55 ASP cc_start: 0.8342 (t70) cc_final: 0.8132 (t0) REVERT: D 59 ASP cc_start: 0.9012 (m-30) cc_final: 0.8782 (m-30) REVERT: D 152 ARG cc_start: 0.9135 (ttp80) cc_final: 0.8822 (ttp80) REVERT: E 22 GLU cc_start: 0.8725 (tt0) cc_final: 0.7899 (tm-30) REVERT: E 38 ASP cc_start: 0.8802 (m-30) cc_final: 0.8512 (m-30) REVERT: E 42 ASN cc_start: 0.9163 (m110) cc_final: 0.8756 (m110) REVERT: E 55 ASP cc_start: 0.8350 (t70) cc_final: 0.7859 (t0) REVERT: E 58 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8819 (mtmt) REVERT: E 59 ASP cc_start: 0.8914 (m-30) cc_final: 0.8518 (m-30) REVERT: E 104 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8985 (tp) REVERT: E 135 ASP cc_start: 0.8971 (m-30) cc_final: 0.8509 (m-30) REVERT: E 147 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8658 (ttpt) REVERT: E 152 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8857 (ttp80) REVERT: E 170 ASP cc_start: 0.8943 (t70) cc_final: 0.8529 (t0) REVERT: F 42 ASN cc_start: 0.9384 (m110) cc_final: 0.9130 (m110) REVERT: F 55 ASP cc_start: 0.8051 (t0) cc_final: 0.7654 (t0) REVERT: F 58 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8414 (mtmt) REVERT: F 59 ASP cc_start: 0.9104 (m-30) cc_final: 0.8799 (m-30) REVERT: F 135 ASP cc_start: 0.9014 (m-30) cc_final: 0.8512 (m-30) REVERT: G 50 ASP cc_start: 0.8801 (m-30) cc_final: 0.8447 (m-30) REVERT: G 71 ASP cc_start: 0.8927 (m-30) cc_final: 0.8695 (m-30) REVERT: G 165 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8622 (mt-10) REVERT: G 192 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8566 (mm-30) REVERT: H 23 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8836 (mtp180) REVERT: H 38 ASP cc_start: 0.8902 (m-30) cc_final: 0.8460 (m-30) REVERT: H 42 ASN cc_start: 0.9371 (m110) cc_final: 0.8928 (m110) REVERT: H 55 ASP cc_start: 0.8147 (t70) cc_final: 0.7571 (t0) REVERT: H 58 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8789 (mtpp) REVERT: H 59 ASP cc_start: 0.9009 (m-30) cc_final: 0.8492 (m-30) REVERT: H 135 ASP cc_start: 0.8884 (m-30) cc_final: 0.8462 (m-30) REVERT: H 139 GLN cc_start: 0.8998 (mt0) cc_final: 0.8757 (mt0) REVERT: H 152 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8694 (ttp80) REVERT: H 170 ASP cc_start: 0.9109 (t70) cc_final: 0.8777 (t0) REVERT: I 31 ASN cc_start: 0.8523 (t0) cc_final: 0.8195 (t0) REVERT: I 34 ASN cc_start: 0.8349 (m110) cc_final: 0.7788 (m110) REVERT: I 50 ASP cc_start: 0.9027 (m-30) cc_final: 0.8702 (m-30) REVERT: I 59 GLN cc_start: 0.9146 (mt0) cc_final: 0.8758 (mt0) REVERT: I 138 SER cc_start: 0.8935 (p) cc_final: 0.8725 (m) REVERT: I 205 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: I 207 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7840 (ppt-90) REVERT: J 31 ASN cc_start: 0.8708 (t0) cc_final: 0.8487 (t160) REVERT: J 34 ASN cc_start: 0.8407 (m110) cc_final: 0.8091 (m110) REVERT: K 39 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8704 (mt-10) REVERT: K 50 ASP cc_start: 0.8927 (m-30) cc_final: 0.8470 (m-30) REVERT: K 54 ASN cc_start: 0.9085 (m-40) cc_final: 0.8870 (m110) REVERT: K 129 ASN cc_start: 0.9336 (m-40) cc_final: 0.9042 (m110) REVERT: K 158 GLU cc_start: 0.9230 (tp30) cc_final: 0.8993 (tp30) REVERT: L 34 ASN cc_start: 0.8459 (m110) cc_final: 0.8148 (m110) REVERT: L 50 ASP cc_start: 0.8892 (m-30) cc_final: 0.8600 (m-30) REVERT: M 54 ASN cc_start: 0.9381 (m-40) cc_final: 0.9023 (m110) REVERT: M 138 SER cc_start: 0.9042 (p) cc_final: 0.8686 (m) REVERT: M 202 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9050 (p) REVERT: M 204 LEU cc_start: 0.9226 (mt) cc_final: 0.9022 (mp) REVERT: M 205 GLU cc_start: 0.7796 (pp20) cc_final: 0.7436 (pp20) REVERT: N 34 ASN cc_start: 0.8295 (t0) cc_final: 0.8078 (m110) REVERT: N 47 GLN cc_start: 0.8597 (tp40) cc_final: 0.8387 (tp40) REVERT: N 71 ASP cc_start: 0.9083 (m-30) cc_final: 0.8795 (m-30) REVERT: N 151 GLU cc_start: 0.8976 (tt0) cc_final: 0.8288 (tp30) outliers start: 74 outliers final: 33 residues processed: 668 average time/residue: 0.5799 time to fit residues: 433.3977 Evaluate side-chains 640 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 603 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 207 ARG Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 143 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 60 optimal weight: 0.0000 chunk 89 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 101 GLN J 101 GLN J 144 GLN K 47 GLN K 101 GLN K 144 GLN K 153 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 107 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.072948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.064402 restraints weight = 33983.596| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.31 r_work: 0.2606 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19859 Z= 0.130 Angle : 0.570 10.017 26824 Z= 0.267 Chirality : 0.042 0.233 3087 Planarity : 0.003 0.047 3479 Dihedral : 7.899 59.535 2989 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.43 % Allowed : 19.96 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2478 helix: 2.01 (0.13), residues: 1407 sheet: -1.78 (0.34), residues: 182 loop : -0.87 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 164 TYR 0.018 0.001 TYR C 113 PHE 0.008 0.001 PHE B 185 TRP 0.002 0.001 TRP C 174 HIS 0.003 0.001 HIS M 171 Details of bonding type rmsd covalent geometry : bond 0.00287 (19845) covalent geometry : angle 0.56961 (26824) hydrogen bonds : bond 0.03038 ( 1176) hydrogen bonds : angle 3.71402 ( 3789) Misc. bond : bond 0.00129 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 656 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 42 ASN cc_start: 0.9293 (m110) cc_final: 0.8626 (m110) REVERT: A 55 ASP cc_start: 0.8105 (t0) cc_final: 0.7547 (t0) REVERT: A 58 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8670 (mtmp) REVERT: A 59 ASP cc_start: 0.8939 (m-30) cc_final: 0.8412 (m-30) REVERT: A 152 ARG cc_start: 0.8993 (ttp80) cc_final: 0.8721 (ttp80) REVERT: A 164 ARG cc_start: 0.8884 (tpt-90) cc_final: 0.8606 (tpt-90) REVERT: A 170 ASP cc_start: 0.9027 (t70) cc_final: 0.8648 (t0) REVERT: B 22 GLU cc_start: 0.8421 (tt0) cc_final: 0.7443 (tp30) REVERT: B 38 ASP cc_start: 0.8937 (m-30) cc_final: 0.8304 (m-30) REVERT: B 42 ASN cc_start: 0.9465 (m-40) cc_final: 0.8935 (m110) REVERT: B 47 GLN cc_start: 0.9489 (mt0) cc_final: 0.9247 (mt0) REVERT: B 55 ASP cc_start: 0.8129 (t70) cc_final: 0.7613 (t0) REVERT: B 59 ASP cc_start: 0.8814 (m-30) cc_final: 0.8504 (m-30) REVERT: B 164 ARG cc_start: 0.8870 (tpt-90) cc_final: 0.8662 (tpt-90) REVERT: B 170 ASP cc_start: 0.9030 (t70) cc_final: 0.8575 (t70) REVERT: C 35 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: C 38 ASP cc_start: 0.9028 (m-30) cc_final: 0.8536 (m-30) REVERT: C 42 ASN cc_start: 0.9350 (m-40) cc_final: 0.8898 (m110) REVERT: C 55 ASP cc_start: 0.8091 (t70) cc_final: 0.7559 (t0) REVERT: C 59 ASP cc_start: 0.8920 (m-30) cc_final: 0.8280 (m-30) REVERT: C 111 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8837 (mttt) REVERT: C 139 GLN cc_start: 0.8935 (mt0) cc_final: 0.8656 (mt0) REVERT: C 152 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8869 (ttp80) REVERT: C 164 ARG cc_start: 0.9055 (tpt-90) cc_final: 0.8740 (tpt-90) REVERT: C 168 ASP cc_start: 0.9189 (m-30) cc_final: 0.8902 (m-30) REVERT: D 18 ASP cc_start: 0.8845 (m-30) cc_final: 0.8619 (m-30) REVERT: D 38 ASP cc_start: 0.8994 (m-30) cc_final: 0.8565 (m-30) REVERT: D 42 ASN cc_start: 0.9364 (m110) cc_final: 0.8917 (m110) REVERT: D 55 ASP cc_start: 0.8176 (t70) cc_final: 0.7910 (t0) REVERT: D 59 ASP cc_start: 0.8986 (m-30) cc_final: 0.8575 (m-30) REVERT: D 152 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8785 (ttp80) REVERT: E 21 TYR cc_start: 0.8899 (m-10) cc_final: 0.8668 (m-10) REVERT: E 22 GLU cc_start: 0.8665 (tt0) cc_final: 0.7762 (tm-30) REVERT: E 38 ASP cc_start: 0.8809 (m-30) cc_final: 0.8520 (m-30) REVERT: E 42 ASN cc_start: 0.9114 (m110) cc_final: 0.8646 (m110) REVERT: E 55 ASP cc_start: 0.8234 (t70) cc_final: 0.7760 (t0) REVERT: E 58 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8684 (mtmm) REVERT: E 59 ASP cc_start: 0.8877 (m-30) cc_final: 0.8454 (m-30) REVERT: E 104 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8855 (tp) REVERT: E 111 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8669 (ttmt) REVERT: E 135 ASP cc_start: 0.8893 (m-30) cc_final: 0.8393 (m-30) REVERT: E 152 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8472 (ttp80) REVERT: E 170 ASP cc_start: 0.8841 (t70) cc_final: 0.8409 (t0) REVERT: F 38 ASP cc_start: 0.8858 (m-30) cc_final: 0.8520 (m-30) REVERT: F 42 ASN cc_start: 0.9328 (m110) cc_final: 0.9044 (m110) REVERT: F 55 ASP cc_start: 0.7852 (t0) cc_final: 0.7492 (t0) REVERT: F 58 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8274 (mtmt) REVERT: F 59 ASP cc_start: 0.9058 (m-30) cc_final: 0.8732 (m-30) REVERT: G 50 ASP cc_start: 0.8785 (m-30) cc_final: 0.8374 (m-30) REVERT: G 71 ASP cc_start: 0.8925 (m-30) cc_final: 0.8670 (m-30) REVERT: G 125 MET cc_start: 0.8617 (mmm) cc_final: 0.8416 (mmt) REVERT: G 165 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8454 (mt-10) REVERT: H 23 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8679 (mtp180) REVERT: H 38 ASP cc_start: 0.8911 (m-30) cc_final: 0.8408 (m-30) REVERT: H 42 ASN cc_start: 0.9315 (m110) cc_final: 0.8815 (m110) REVERT: H 55 ASP cc_start: 0.7961 (t70) cc_final: 0.7428 (t0) REVERT: H 58 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8510 (ttmm) REVERT: H 59 ASP cc_start: 0.8993 (m-30) cc_final: 0.8395 (m-30) REVERT: H 135 ASP cc_start: 0.8801 (m-30) cc_final: 0.8337 (m-30) REVERT: H 139 GLN cc_start: 0.8817 (mt0) cc_final: 0.8541 (mt0) REVERT: H 152 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8628 (ttp80) REVERT: H 170 ASP cc_start: 0.9020 (t70) cc_final: 0.8673 (t0) REVERT: I 31 ASN cc_start: 0.8383 (t0) cc_final: 0.8140 (t160) REVERT: I 34 ASN cc_start: 0.8276 (m110) cc_final: 0.7743 (m110) REVERT: I 50 ASP cc_start: 0.8977 (m-30) cc_final: 0.8595 (m-30) REVERT: I 59 GLN cc_start: 0.8922 (mt0) cc_final: 0.8590 (mt0) REVERT: I 205 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: J 31 ASN cc_start: 0.8621 (t0) cc_final: 0.8398 (t160) REVERT: J 34 ASN cc_start: 0.8266 (m110) cc_final: 0.7944 (m110) REVERT: J 54 ASN cc_start: 0.8968 (m-40) cc_final: 0.8267 (m110) REVERT: J 138 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8541 (m) REVERT: K 39 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8646 (mt-10) REVERT: K 47 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: K 50 ASP cc_start: 0.8890 (m-30) cc_final: 0.8406 (m-30) REVERT: K 52 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9079 (p) REVERT: K 54 ASN cc_start: 0.9019 (m-40) cc_final: 0.8775 (m110) REVERT: K 129 ASN cc_start: 0.9238 (m-40) cc_final: 0.8967 (m110) REVERT: K 158 GLU cc_start: 0.9187 (tp30) cc_final: 0.8956 (tp30) REVERT: L 34 ASN cc_start: 0.8340 (m110) cc_final: 0.8075 (m110) REVERT: L 50 ASP cc_start: 0.8902 (m-30) cc_final: 0.8594 (m-30) REVERT: L 52 SER cc_start: 0.9472 (OUTLIER) cc_final: 0.9224 (p) REVERT: M 54 ASN cc_start: 0.9334 (m-40) cc_final: 0.8908 (m110) REVERT: M 138 SER cc_start: 0.8878 (p) cc_final: 0.8527 (m) REVERT: M 202 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8914 (p) REVERT: M 204 LEU cc_start: 0.9198 (mt) cc_final: 0.8908 (mp) REVERT: M 205 GLU cc_start: 0.7825 (pp20) cc_final: 0.7512 (pp20) REVERT: N 34 ASN cc_start: 0.8079 (t0) cc_final: 0.7876 (m110) REVERT: N 71 ASP cc_start: 0.9096 (m-30) cc_final: 0.8764 (m-30) REVERT: N 151 GLU cc_start: 0.8963 (tt0) cc_final: 0.8205 (tp30) REVERT: N 205 GLU cc_start: 0.8630 (pm20) cc_final: 0.8330 (pp20) outliers start: 69 outliers final: 30 residues processed: 687 average time/residue: 0.5458 time to fit residues: 421.1825 Evaluate side-chains 659 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 620 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 47 GLN Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 28 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 225 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN G 47 GLN G 54 ASN G 77 ASN G 101 GLN G 144 GLN G 146 GLN I 54 ASN I 101 GLN J 101 GLN J 144 GLN K 101 GLN K 144 GLN K 153 GLN L 31 ASN L 54 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN M 129 ASN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 107 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.061602 restraints weight = 34221.148| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.23 r_work: 0.2555 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19859 Z= 0.222 Angle : 0.633 11.655 26824 Z= 0.294 Chirality : 0.044 0.273 3087 Planarity : 0.003 0.039 3479 Dihedral : 7.810 58.200 2989 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.03 % Allowed : 20.26 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2478 helix: 1.99 (0.13), residues: 1407 sheet: -1.65 (0.33), residues: 196 loop : -0.90 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 43 TYR 0.018 0.001 TYR C 113 PHE 0.007 0.001 PHE H 102 TRP 0.001 0.000 TRP A 174 HIS 0.004 0.001 HIS I 171 Details of bonding type rmsd covalent geometry : bond 0.00487 (19845) covalent geometry : angle 0.63309 (26824) hydrogen bonds : bond 0.03462 ( 1176) hydrogen bonds : angle 3.79802 ( 3789) Misc. bond : bond 0.00180 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 633 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 39 GLU cc_start: 0.9088 (tt0) cc_final: 0.8869 (tt0) REVERT: A 42 ASN cc_start: 0.9354 (m110) cc_final: 0.8839 (m110) REVERT: A 43 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8472 (ttp80) REVERT: A 55 ASP cc_start: 0.8228 (t0) cc_final: 0.7708 (t0) REVERT: A 59 ASP cc_start: 0.8934 (m-30) cc_final: 0.8474 (m-30) REVERT: A 164 ARG cc_start: 0.9007 (tpt-90) cc_final: 0.8676 (tpt-90) REVERT: A 170 ASP cc_start: 0.9027 (t70) cc_final: 0.8798 (t70) REVERT: B 22 GLU cc_start: 0.8510 (tt0) cc_final: 0.7614 (tp30) REVERT: B 23 ARG cc_start: 0.9114 (mtm-85) cc_final: 0.8913 (mtp180) REVERT: B 38 ASP cc_start: 0.8964 (m-30) cc_final: 0.8212 (m-30) REVERT: B 42 ASN cc_start: 0.9500 (m-40) cc_final: 0.9047 (m110) REVERT: B 55 ASP cc_start: 0.8263 (t70) cc_final: 0.7731 (t0) REVERT: B 59 ASP cc_start: 0.8859 (m-30) cc_final: 0.8393 (m-30) REVERT: B 164 ARG cc_start: 0.8923 (tpt-90) cc_final: 0.8602 (tpt-90) REVERT: B 170 ASP cc_start: 0.9044 (t70) cc_final: 0.8689 (t70) REVERT: C 38 ASP cc_start: 0.9057 (m-30) cc_final: 0.8623 (m-30) REVERT: C 42 ASN cc_start: 0.9389 (m-40) cc_final: 0.8997 (m110) REVERT: C 55 ASP cc_start: 0.8131 (t70) cc_final: 0.7665 (t0) REVERT: C 59 ASP cc_start: 0.8933 (m-30) cc_final: 0.8577 (m-30) REVERT: C 139 GLN cc_start: 0.9073 (mt0) cc_final: 0.8827 (mt0) REVERT: C 152 ARG cc_start: 0.9243 (ttp80) cc_final: 0.9023 (ttp80) REVERT: C 164 ARG cc_start: 0.9123 (tpt-90) cc_final: 0.8882 (tpt-90) REVERT: C 168 ASP cc_start: 0.9211 (m-30) cc_final: 0.8941 (m-30) REVERT: D 18 ASP cc_start: 0.8911 (m-30) cc_final: 0.8702 (m-30) REVERT: D 38 ASP cc_start: 0.9046 (m-30) cc_final: 0.8707 (m-30) REVERT: D 42 ASN cc_start: 0.9396 (m110) cc_final: 0.8973 (m110) REVERT: D 55 ASP cc_start: 0.8346 (t70) cc_final: 0.7957 (t0) REVERT: D 59 ASP cc_start: 0.8975 (m-30) cc_final: 0.8645 (m-30) REVERT: D 152 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8816 (ttp80) REVERT: E 22 GLU cc_start: 0.8789 (tt0) cc_final: 0.7909 (tm-30) REVERT: E 38 ASP cc_start: 0.8828 (m-30) cc_final: 0.8615 (m-30) REVERT: E 42 ASN cc_start: 0.9164 (m110) cc_final: 0.8790 (m110) REVERT: E 55 ASP cc_start: 0.8353 (t70) cc_final: 0.7872 (t0) REVERT: E 58 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8768 (mtmt) REVERT: E 59 ASP cc_start: 0.8897 (m-30) cc_final: 0.8411 (m-30) REVERT: E 104 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.8963 (tp) REVERT: E 111 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8790 (mtmt) REVERT: E 135 ASP cc_start: 0.8987 (m-30) cc_final: 0.8495 (m-30) REVERT: E 170 ASP cc_start: 0.8930 (t70) cc_final: 0.8552 (t0) REVERT: F 38 ASP cc_start: 0.8890 (m-30) cc_final: 0.8641 (m-30) REVERT: F 42 ASN cc_start: 0.9395 (m110) cc_final: 0.9153 (m110) REVERT: F 58 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8679 (ttmt) REVERT: F 59 ASP cc_start: 0.9052 (m-30) cc_final: 0.8770 (m-30) REVERT: G 50 ASP cc_start: 0.8809 (m-30) cc_final: 0.8451 (m-30) REVERT: G 71 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8723 (m-30) REVERT: G 192 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8649 (mm-30) REVERT: H 23 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8741 (mtp180) REVERT: H 38 ASP cc_start: 0.8931 (m-30) cc_final: 0.8444 (m-30) REVERT: H 42 ASN cc_start: 0.9382 (m110) cc_final: 0.8913 (m110) REVERT: H 55 ASP cc_start: 0.8095 (t70) cc_final: 0.7598 (t0) REVERT: H 58 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8563 (ttmm) REVERT: H 59 ASP cc_start: 0.8971 (m-30) cc_final: 0.8414 (m-30) REVERT: H 135 ASP cc_start: 0.8883 (m-30) cc_final: 0.8429 (m-30) REVERT: H 139 GLN cc_start: 0.8971 (mt0) cc_final: 0.8722 (mt0) REVERT: H 152 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8716 (ttp80) REVERT: H 170 ASP cc_start: 0.9096 (t70) cc_final: 0.8776 (t0) REVERT: H 182 GLU cc_start: 0.9158 (tp30) cc_final: 0.8928 (tp30) REVERT: I 31 ASN cc_start: 0.8522 (t0) cc_final: 0.8289 (t160) REVERT: I 34 ASN cc_start: 0.8404 (m110) cc_final: 0.7907 (m110) REVERT: I 50 ASP cc_start: 0.9023 (m-30) cc_final: 0.8637 (m-30) REVERT: I 59 GLN cc_start: 0.9148 (mt0) cc_final: 0.8765 (mt0) REVERT: I 205 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: J 34 ASN cc_start: 0.8425 (m110) cc_final: 0.8149 (m110) REVERT: J 54 ASN cc_start: 0.9105 (m-40) cc_final: 0.8860 (m110) REVERT: J 66 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9063 (mp) REVERT: K 47 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8305 (tp40) REVERT: K 50 ASP cc_start: 0.8949 (m-30) cc_final: 0.8544 (m-30) REVERT: K 52 SER cc_start: 0.9465 (OUTLIER) cc_final: 0.9212 (p) REVERT: K 54 ASN cc_start: 0.9127 (m-40) cc_final: 0.8923 (m110) REVERT: K 158 GLU cc_start: 0.9204 (tp30) cc_final: 0.9000 (tp30) REVERT: L 34 ASN cc_start: 0.8396 (m110) cc_final: 0.7869 (m110) REVERT: L 50 ASP cc_start: 0.8922 (m-30) cc_final: 0.8642 (m-30) REVERT: L 52 SER cc_start: 0.9572 (OUTLIER) cc_final: 0.9362 (p) REVERT: M 54 ASN cc_start: 0.9362 (m-40) cc_final: 0.9015 (m110) REVERT: M 202 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9040 (p) REVERT: M 204 LEU cc_start: 0.9289 (mt) cc_final: 0.9013 (mp) REVERT: M 205 GLU cc_start: 0.7913 (pp20) cc_final: 0.7640 (pp20) REVERT: N 47 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8329 (tp40) REVERT: N 71 ASP cc_start: 0.9066 (m-30) cc_final: 0.8754 (m-30) REVERT: N 151 GLU cc_start: 0.8976 (tt0) cc_final: 0.8287 (tp30) outliers start: 81 outliers final: 40 residues processed: 666 average time/residue: 0.5681 time to fit residues: 424.2224 Evaluate side-chains 669 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 620 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 125 MET Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 47 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 125 MET Chi-restraints excluded: chain N residue 138 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 116 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS G 31 ASN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 101 GLN I 136 GLN J 101 GLN J 144 GLN K 47 GLN K 101 GLN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 129 ASN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 GLN N 54 ASN N 101 GLN N 107 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.067791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.059382 restraints weight = 34755.236| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.25 r_work: 0.2499 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2366 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19859 Z= 0.322 Angle : 0.706 12.649 26824 Z= 0.328 Chirality : 0.046 0.297 3087 Planarity : 0.004 0.042 3479 Dihedral : 8.067 59.968 2989 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.23 % Allowed : 19.96 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.17), residues: 2478 helix: 1.81 (0.13), residues: 1407 sheet: -1.63 (0.34), residues: 196 loop : -0.94 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 164 TYR 0.018 0.001 TYR C 113 PHE 0.009 0.001 PHE H 102 TRP 0.002 0.000 TRP A 174 HIS 0.005 0.002 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00708 (19845) covalent geometry : angle 0.70578 (26824) hydrogen bonds : bond 0.03901 ( 1176) hydrogen bonds : angle 3.95022 ( 3789) Misc. bond : bond 0.00218 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 615 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 42 ASN cc_start: 0.9349 (m110) cc_final: 0.9045 (m110) REVERT: A 43 ARG cc_start: 0.8705 (tmm-80) cc_final: 0.8461 (ttp80) REVERT: A 55 ASP cc_start: 0.8241 (t0) cc_final: 0.7708 (t0) REVERT: A 59 ASP cc_start: 0.8972 (m-30) cc_final: 0.8514 (m-30) REVERT: A 164 ARG cc_start: 0.8969 (tpt-90) cc_final: 0.8718 (tpt-90) REVERT: A 170 ASP cc_start: 0.9028 (t70) cc_final: 0.8813 (t70) REVERT: B 22 GLU cc_start: 0.8548 (tt0) cc_final: 0.7696 (tp30) REVERT: B 38 ASP cc_start: 0.8993 (m-30) cc_final: 0.8268 (m-30) REVERT: B 42 ASN cc_start: 0.9524 (m-40) cc_final: 0.9089 (m110) REVERT: B 55 ASP cc_start: 0.8299 (t70) cc_final: 0.7760 (t0) REVERT: B 59 ASP cc_start: 0.8829 (m-30) cc_final: 0.8431 (m-30) REVERT: B 170 ASP cc_start: 0.9034 (t70) cc_final: 0.8786 (t0) REVERT: C 38 ASP cc_start: 0.9100 (m-30) cc_final: 0.8718 (m-30) REVERT: C 42 ASN cc_start: 0.9413 (m-40) cc_final: 0.9067 (m110) REVERT: C 55 ASP cc_start: 0.8146 (t70) cc_final: 0.7699 (t0) REVERT: C 59 ASP cc_start: 0.8919 (m-30) cc_final: 0.8632 (m-30) REVERT: C 139 GLN cc_start: 0.9160 (mt0) cc_final: 0.8888 (mt0) REVERT: C 152 ARG cc_start: 0.9271 (ttp80) cc_final: 0.9032 (ttp80) REVERT: C 168 ASP cc_start: 0.9213 (m-30) cc_final: 0.8901 (m-30) REVERT: D 38 ASP cc_start: 0.9087 (m-30) cc_final: 0.8816 (m-30) REVERT: D 42 ASN cc_start: 0.9405 (m110) cc_final: 0.8976 (m110) REVERT: D 55 ASP cc_start: 0.8350 (t70) cc_final: 0.7858 (t0) REVERT: D 59 ASP cc_start: 0.8915 (m-30) cc_final: 0.8621 (m-30) REVERT: D 152 ARG cc_start: 0.9202 (ttp80) cc_final: 0.8826 (ttp80) REVERT: E 22 GLU cc_start: 0.8853 (tt0) cc_final: 0.7980 (tm-30) REVERT: E 42 ASN cc_start: 0.9195 (m110) cc_final: 0.8890 (m110) REVERT: E 55 ASP cc_start: 0.8402 (t70) cc_final: 0.7952 (t0) REVERT: E 58 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8806 (mtmt) REVERT: E 59 ASP cc_start: 0.8863 (m-30) cc_final: 0.8510 (m-30) REVERT: E 104 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9047 (tp) REVERT: E 135 ASP cc_start: 0.8985 (m-30) cc_final: 0.8514 (m-30) REVERT: E 170 ASP cc_start: 0.8923 (t70) cc_final: 0.8615 (t0) REVERT: F 38 ASP cc_start: 0.8980 (m-30) cc_final: 0.8768 (m-30) REVERT: F 42 ASN cc_start: 0.9389 (m110) cc_final: 0.9150 (m110) REVERT: F 58 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8591 (mtmm) REVERT: F 59 ASP cc_start: 0.9088 (m-30) cc_final: 0.8610 (m-30) REVERT: F 111 LYS cc_start: 0.9266 (mtmm) cc_final: 0.9006 (mttt) REVERT: G 50 ASP cc_start: 0.8873 (m-30) cc_final: 0.8541 (m-30) REVERT: G 192 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8707 (mm-30) REVERT: H 23 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8715 (mtp180) REVERT: H 38 ASP cc_start: 0.8942 (m-30) cc_final: 0.8520 (m-30) REVERT: H 42 ASN cc_start: 0.9368 (m110) cc_final: 0.8896 (m110) REVERT: H 55 ASP cc_start: 0.8158 (t70) cc_final: 0.7655 (t0) REVERT: H 58 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8573 (ttmm) REVERT: H 59 ASP cc_start: 0.9005 (m-30) cc_final: 0.8453 (m-30) REVERT: H 135 ASP cc_start: 0.8923 (m-30) cc_final: 0.8517 (m-30) REVERT: H 152 ARG cc_start: 0.9235 (ttp80) cc_final: 0.8882 (ttp80) REVERT: H 170 ASP cc_start: 0.9089 (t70) cc_final: 0.8786 (t0) REVERT: H 182 GLU cc_start: 0.9179 (tp30) cc_final: 0.8929 (tp30) REVERT: I 31 ASN cc_start: 0.8535 (t0) cc_final: 0.8322 (t160) REVERT: I 34 ASN cc_start: 0.8497 (m110) cc_final: 0.8032 (m110) REVERT: I 50 ASP cc_start: 0.9012 (m-30) cc_final: 0.8683 (m-30) REVERT: I 205 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: J 34 ASN cc_start: 0.8539 (m110) cc_final: 0.8286 (m110) REVERT: J 54 ASN cc_start: 0.9157 (m-40) cc_final: 0.8930 (m110) REVERT: K 50 ASP cc_start: 0.8984 (m-30) cc_final: 0.8636 (m-30) REVERT: K 52 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.9252 (p) REVERT: L 34 ASN cc_start: 0.8426 (m110) cc_final: 0.8180 (m110) REVERT: L 50 ASP cc_start: 0.9015 (m-30) cc_final: 0.8763 (m-30) REVERT: M 54 ASN cc_start: 0.9422 (m-40) cc_final: 0.9084 (m110) REVERT: M 202 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9164 (p) REVERT: M 205 GLU cc_start: 0.7942 (pp20) cc_final: 0.7701 (pp20) REVERT: N 125 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8878 (mtm) REVERT: N 151 GLU cc_start: 0.8997 (tt0) cc_final: 0.8341 (tp30) outliers start: 85 outliers final: 40 residues processed: 647 average time/residue: 0.6351 time to fit residues: 459.6878 Evaluate side-chains 647 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 601 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 191 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 125 MET Chi-restraints excluded: chain N residue 138 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN G 31 ASN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 101 GLN J 144 GLN K 54 ASN K 101 GLN K 153 GLN L 136 GLN L 144 GLN N 54 ASN N 101 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.065314 restraints weight = 34077.820| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.22 r_work: 0.2630 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19859 Z= 0.123 Angle : 0.600 10.999 26824 Z= 0.281 Chirality : 0.042 0.247 3087 Planarity : 0.003 0.037 3479 Dihedral : 8.009 59.898 2989 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.43 % Allowed : 21.01 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.17), residues: 2478 helix: 1.98 (0.13), residues: 1414 sheet: -1.45 (0.37), residues: 182 loop : -0.78 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 164 TYR 0.017 0.001 TYR C 113 PHE 0.009 0.001 PHE D 102 TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00276 (19845) covalent geometry : angle 0.59990 (26824) hydrogen bonds : bond 0.03123 ( 1176) hydrogen bonds : angle 3.78137 ( 3789) Misc. bond : bond 0.00110 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 649 time to evaluate : 0.822 Fit side-chains TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 39 GLU cc_start: 0.9070 (tt0) cc_final: 0.8857 (tt0) REVERT: A 42 ASN cc_start: 0.9363 (m110) cc_final: 0.8831 (m110) REVERT: A 43 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8408 (ttp80) REVERT: A 55 ASP cc_start: 0.8335 (t0) cc_final: 0.7889 (t0) REVERT: A 58 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8839 (mtmp) REVERT: A 59 ASP cc_start: 0.8920 (m-30) cc_final: 0.8464 (m-30) REVERT: A 152 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8796 (ttp80) REVERT: A 164 ARG cc_start: 0.9018 (tpt-90) cc_final: 0.8782 (tpt-90) REVERT: A 170 ASP cc_start: 0.9048 (t70) cc_final: 0.8799 (t70) REVERT: B 22 GLU cc_start: 0.8462 (tt0) cc_final: 0.7565 (tp30) REVERT: B 23 ARG cc_start: 0.9081 (mtm180) cc_final: 0.8865 (mtp180) REVERT: B 38 ASP cc_start: 0.8857 (m-30) cc_final: 0.8108 (m-30) REVERT: B 42 ASN cc_start: 0.9513 (m110) cc_final: 0.9006 (m110) REVERT: B 47 GLN cc_start: 0.9599 (mt0) cc_final: 0.9328 (mt0) REVERT: B 55 ASP cc_start: 0.8363 (t70) cc_final: 0.7763 (t0) REVERT: B 58 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8350 (ttmm) REVERT: B 164 ARG cc_start: 0.8922 (tpt-90) cc_final: 0.8696 (tpt-90) REVERT: B 170 ASP cc_start: 0.8999 (t70) cc_final: 0.8689 (t70) REVERT: C 38 ASP cc_start: 0.9015 (m-30) cc_final: 0.8634 (m-30) REVERT: C 42 ASN cc_start: 0.9399 (m-40) cc_final: 0.9035 (m110) REVERT: C 55 ASP cc_start: 0.8290 (t70) cc_final: 0.7811 (t0) REVERT: C 58 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8739 (mtmt) REVERT: C 59 ASP cc_start: 0.8845 (m-30) cc_final: 0.8617 (m-30) REVERT: C 139 GLN cc_start: 0.9112 (mt0) cc_final: 0.8835 (mt0) REVERT: C 168 ASP cc_start: 0.9247 (m-30) cc_final: 0.9039 (m-30) REVERT: D 38 ASP cc_start: 0.8964 (m-30) cc_final: 0.8604 (m-30) REVERT: D 42 ASN cc_start: 0.9389 (m110) cc_final: 0.8967 (m110) REVERT: D 55 ASP cc_start: 0.8464 (t70) cc_final: 0.8008 (t0) REVERT: D 59 ASP cc_start: 0.8924 (m-30) cc_final: 0.8662 (m-30) REVERT: D 152 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8880 (ttp80) REVERT: E 17 THR cc_start: 0.9071 (m) cc_final: 0.8764 (t) REVERT: E 22 GLU cc_start: 0.8791 (tt0) cc_final: 0.7858 (tp30) REVERT: E 42 ASN cc_start: 0.9166 (m110) cc_final: 0.8774 (m110) REVERT: E 55 ASP cc_start: 0.8455 (t70) cc_final: 0.8018 (t0) REVERT: E 59 ASP cc_start: 0.8829 (m-30) cc_final: 0.8368 (m-30) REVERT: E 104 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9089 (tp) REVERT: E 135 ASP cc_start: 0.8935 (m-30) cc_final: 0.8474 (m-30) REVERT: E 170 ASP cc_start: 0.8951 (t70) cc_final: 0.8561 (t0) REVERT: F 38 ASP cc_start: 0.8871 (m-30) cc_final: 0.8612 (m-30) REVERT: F 42 ASN cc_start: 0.9394 (m110) cc_final: 0.9146 (m110) REVERT: F 43 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8600 (ttp80) REVERT: F 58 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8591 (mtmt) REVERT: F 59 ASP cc_start: 0.9055 (m-30) cc_final: 0.8779 (m-30) REVERT: F 152 ARG cc_start: 0.8996 (ttp80) cc_final: 0.8773 (ttp80) REVERT: F 164 ARG cc_start: 0.8986 (tpt-90) cc_final: 0.8743 (tpt-90) REVERT: G 50 ASP cc_start: 0.8798 (m-30) cc_final: 0.8435 (m-30) REVERT: G 192 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8680 (mm-30) REVERT: H 23 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8830 (mtp85) REVERT: H 38 ASP cc_start: 0.8889 (m-30) cc_final: 0.8381 (m-30) REVERT: H 42 ASN cc_start: 0.9359 (m110) cc_final: 0.8891 (m110) REVERT: H 55 ASP cc_start: 0.8203 (t70) cc_final: 0.7581 (t0) REVERT: H 58 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8545 (ttmm) REVERT: H 59 ASP cc_start: 0.8930 (m-30) cc_final: 0.8596 (m-30) REVERT: H 135 ASP cc_start: 0.8860 (m-30) cc_final: 0.8411 (m-30) REVERT: H 139 GLN cc_start: 0.8867 (mt0) cc_final: 0.8659 (mt0) REVERT: H 152 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8686 (ttp80) REVERT: H 170 ASP cc_start: 0.9120 (t70) cc_final: 0.8801 (t0) REVERT: H 182 GLU cc_start: 0.9164 (tp30) cc_final: 0.8901 (tp30) REVERT: I 31 ASN cc_start: 0.8519 (t0) cc_final: 0.8252 (t160) REVERT: I 34 ASN cc_start: 0.8427 (m110) cc_final: 0.7879 (m110) REVERT: I 50 ASP cc_start: 0.8937 (m-30) cc_final: 0.8572 (m-30) REVERT: I 59 GLN cc_start: 0.9155 (mt0) cc_final: 0.8820 (mt0) REVERT: I 123 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8940 (ttmt) REVERT: I 125 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: I 129 ASN cc_start: 0.9252 (m-40) cc_final: 0.8997 (m-40) REVERT: I 204 LEU cc_start: 0.8670 (tp) cc_final: 0.8412 (pp) REVERT: I 205 GLU cc_start: 0.8140 (mp0) cc_final: 0.7899 (pm20) REVERT: I 207 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7692 (ptt90) REVERT: J 31 ASN cc_start: 0.8755 (t0) cc_final: 0.8541 (t160) REVERT: J 34 ASN cc_start: 0.8477 (m110) cc_final: 0.8160 (m110) REVERT: J 54 ASN cc_start: 0.9038 (m-40) cc_final: 0.8812 (m110) REVERT: K 50 ASP cc_start: 0.8919 (m-30) cc_final: 0.8531 (m-30) REVERT: K 52 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9294 (p) REVERT: K 187 LYS cc_start: 0.8447 (tptt) cc_final: 0.8197 (tptt) REVERT: L 34 ASN cc_start: 0.8429 (m110) cc_final: 0.8175 (m110) REVERT: L 50 ASP cc_start: 0.8917 (m-30) cc_final: 0.8671 (m-30) REVERT: M 54 ASN cc_start: 0.9297 (m-40) cc_final: 0.8944 (m110) REVERT: M 202 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9050 (p) REVERT: M 205 GLU cc_start: 0.7913 (pp20) cc_final: 0.7700 (pp20) REVERT: N 151 GLU cc_start: 0.8962 (tt0) cc_final: 0.8278 (tp30) outliers start: 69 outliers final: 31 residues processed: 680 average time/residue: 0.6020 time to fit residues: 459.3847 Evaluate side-chains 675 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 638 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 207 ARG Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 224 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 ASN G 101 GLN G 144 GLN I 54 ASN J 144 GLN K 54 ASN K 101 GLN L 136 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 101 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.072372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.064145 restraints weight = 33928.219| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.24 r_work: 0.2607 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19859 Z= 0.157 Angle : 0.618 12.297 26824 Z= 0.290 Chirality : 0.043 0.236 3087 Planarity : 0.004 0.042 3479 Dihedral : 7.764 59.844 2989 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.74 % Allowed : 22.95 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.17), residues: 2478 helix: 2.00 (0.13), residues: 1414 sheet: -1.37 (0.37), residues: 182 loop : -0.74 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 164 TYR 0.019 0.001 TYR C 113 PHE 0.009 0.001 PHE D 102 TRP 0.003 0.000 TRP B 174 HIS 0.003 0.001 HIS I 171 Details of bonding type rmsd covalent geometry : bond 0.00355 (19845) covalent geometry : angle 0.61805 (26824) hydrogen bonds : bond 0.03230 ( 1176) hydrogen bonds : angle 3.74882 ( 3789) Misc. bond : bond 0.00139 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 646 time to evaluate : 0.766 Fit side-chains TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER I 210 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER M 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 39 GLU cc_start: 0.9080 (tt0) cc_final: 0.8870 (tt0) REVERT: A 42 ASN cc_start: 0.9346 (m110) cc_final: 0.8794 (m110) REVERT: A 43 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8323 (tmm-80) REVERT: A 55 ASP cc_start: 0.8305 (t0) cc_final: 0.7882 (t0) REVERT: A 59 ASP cc_start: 0.8904 (m-30) cc_final: 0.8485 (m-30) REVERT: A 164 ARG cc_start: 0.8984 (tpt-90) cc_final: 0.8752 (tpt-90) REVERT: A 170 ASP cc_start: 0.9064 (t70) cc_final: 0.8840 (t70) REVERT: B 22 GLU cc_start: 0.8432 (tt0) cc_final: 0.7591 (tp30) REVERT: B 38 ASP cc_start: 0.8825 (m-30) cc_final: 0.8077 (m-30) REVERT: B 42 ASN cc_start: 0.9498 (m110) cc_final: 0.8962 (m110) REVERT: B 55 ASP cc_start: 0.8372 (t70) cc_final: 0.7772 (t0) REVERT: B 58 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8318 (ttmm) REVERT: B 59 ASP cc_start: 0.8869 (m-30) cc_final: 0.8462 (m-30) REVERT: B 164 ARG cc_start: 0.8884 (tpt-90) cc_final: 0.8652 (tpt-90) REVERT: B 170 ASP cc_start: 0.9033 (t70) cc_final: 0.8725 (t70) REVERT: C 38 ASP cc_start: 0.9016 (m-30) cc_final: 0.8644 (m-30) REVERT: C 42 ASN cc_start: 0.9398 (m-40) cc_final: 0.9050 (m110) REVERT: C 55 ASP cc_start: 0.8256 (t70) cc_final: 0.7661 (t0) REVERT: C 58 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8502 (mtmm) REVERT: C 59 ASP cc_start: 0.8853 (m-30) cc_final: 0.8609 (m-30) REVERT: C 139 GLN cc_start: 0.9110 (mt0) cc_final: 0.8892 (mt0) REVERT: C 152 ARG cc_start: 0.9218 (ttp80) cc_final: 0.8779 (ttp80) REVERT: C 164 ARG cc_start: 0.9145 (tpt-90) cc_final: 0.8934 (tpt-90) REVERT: D 38 ASP cc_start: 0.8964 (m-30) cc_final: 0.8617 (m-30) REVERT: D 42 ASN cc_start: 0.9404 (m110) cc_final: 0.8958 (m110) REVERT: D 54 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8703 (mt-10) REVERT: D 55 ASP cc_start: 0.8434 (t70) cc_final: 0.7979 (t0) REVERT: D 59 ASP cc_start: 0.8907 (m-30) cc_final: 0.8567 (m-30) REVERT: D 152 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8897 (ttp80) REVERT: E 17 THR cc_start: 0.9052 (m) cc_final: 0.8761 (t) REVERT: E 22 GLU cc_start: 0.8772 (tt0) cc_final: 0.7836 (tp30) REVERT: E 42 ASN cc_start: 0.9164 (m110) cc_final: 0.8786 (m110) REVERT: E 55 ASP cc_start: 0.8525 (t70) cc_final: 0.7981 (t0) REVERT: E 59 ASP cc_start: 0.8807 (m-30) cc_final: 0.8385 (m-30) REVERT: E 104 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8975 (tp) REVERT: E 109 LYS cc_start: 0.9237 (tppt) cc_final: 0.8967 (mmtp) REVERT: E 135 ASP cc_start: 0.8895 (m-30) cc_final: 0.8424 (m-30) REVERT: E 170 ASP cc_start: 0.8954 (t70) cc_final: 0.8568 (t0) REVERT: F 38 ASP cc_start: 0.8848 (m-30) cc_final: 0.8544 (m-30) REVERT: F 42 ASN cc_start: 0.9384 (m110) cc_final: 0.9134 (m110) REVERT: F 43 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8638 (ttp80) REVERT: F 59 ASP cc_start: 0.9065 (m-30) cc_final: 0.8588 (m-30) REVERT: F 111 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8951 (mtmt) REVERT: G 50 ASP cc_start: 0.8822 (m-30) cc_final: 0.8437 (m-30) REVERT: G 71 ASP cc_start: 0.8883 (m-30) cc_final: 0.8639 (m-30) REVERT: G 125 MET cc_start: 0.8791 (mmt) cc_final: 0.8340 (mmt) REVERT: G 192 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8691 (mm-30) REVERT: H 23 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8791 (mtp85) REVERT: H 38 ASP cc_start: 0.8882 (m-30) cc_final: 0.8360 (m-30) REVERT: H 42 ASN cc_start: 0.9368 (m110) cc_final: 0.8882 (m110) REVERT: H 55 ASP cc_start: 0.8210 (t70) cc_final: 0.7573 (t0) REVERT: H 58 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8542 (ttmm) REVERT: H 59 ASP cc_start: 0.8965 (m-30) cc_final: 0.8403 (m-30) REVERT: H 111 LYS cc_start: 0.9285 (ttmt) cc_final: 0.8982 (ttmt) REVERT: H 135 ASP cc_start: 0.8889 (m-30) cc_final: 0.8434 (m-30) REVERT: H 152 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8782 (ttp80) REVERT: H 170 ASP cc_start: 0.9135 (t70) cc_final: 0.8828 (t0) REVERT: H 182 GLU cc_start: 0.9146 (tp30) cc_final: 0.8877 (tp30) REVERT: I 31 ASN cc_start: 0.8555 (t0) cc_final: 0.8308 (t160) REVERT: I 34 ASN cc_start: 0.8409 (m110) cc_final: 0.7900 (m110) REVERT: I 50 ASP cc_start: 0.8951 (m-30) cc_final: 0.8599 (m-30) REVERT: I 59 GLN cc_start: 0.9055 (mt0) cc_final: 0.8712 (mt0) REVERT: I 125 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8596 (mpp) REVERT: I 129 ASN cc_start: 0.9230 (m-40) cc_final: 0.8960 (m-40) REVERT: I 181 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8920 (mtmp) REVERT: I 205 GLU cc_start: 0.8270 (mp0) cc_final: 0.7908 (pm20) REVERT: J 34 ASN cc_start: 0.8439 (m110) cc_final: 0.8157 (m110) REVERT: J 54 ASN cc_start: 0.9067 (m-40) cc_final: 0.8835 (m110) REVERT: K 50 ASP cc_start: 0.8946 (m-30) cc_final: 0.8197 (m-30) REVERT: K 54 ASN cc_start: 0.9074 (m-40) cc_final: 0.8463 (m110) REVERT: K 187 LYS cc_start: 0.8420 (tptt) cc_final: 0.8165 (tptt) REVERT: K 207 ARG cc_start: 0.8227 (ptt180) cc_final: 0.7934 (ptt180) REVERT: L 34 ASN cc_start: 0.8413 (m110) cc_final: 0.8182 (m110) REVERT: L 50 ASP cc_start: 0.8926 (m-30) cc_final: 0.8677 (m-30) REVERT: M 54 ASN cc_start: 0.9274 (m-40) cc_final: 0.8944 (m110) REVERT: M 202 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9134 (p) REVERT: M 205 GLU cc_start: 0.7764 (pp20) cc_final: 0.7553 (pp20) REVERT: N 151 GLU cc_start: 0.8990 (tt0) cc_final: 0.8312 (tp30) REVERT: N 204 LEU cc_start: 0.8849 (tp) cc_final: 0.8576 (pp) REVERT: N 205 GLU cc_start: 0.8058 (pp20) cc_final: 0.7797 (pp20) outliers start: 55 outliers final: 30 residues processed: 669 average time/residue: 0.6030 time to fit residues: 451.4326 Evaluate side-chains 662 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 628 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 143 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 195 optimal weight: 5.9990 chunk 230 optimal weight: 0.6980 chunk 233 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 101 GLN J 144 GLN K 47 GLN K 101 GLN L 153 GLN N 54 ASN N 101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066107 restraints weight = 34241.521| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.26 r_work: 0.2650 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19859 Z= 0.136 Angle : 0.614 12.052 26824 Z= 0.290 Chirality : 0.043 0.226 3087 Planarity : 0.004 0.044 3479 Dihedral : 7.672 58.342 2989 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.69 % Allowed : 23.59 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.17), residues: 2478 helix: 2.03 (0.13), residues: 1400 sheet: -1.33 (0.37), residues: 182 loop : -0.66 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 164 TYR 0.019 0.001 TYR C 113 PHE 0.011 0.001 PHE D 102 TRP 0.003 0.001 TRP C 174 HIS 0.003 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00310 (19845) covalent geometry : angle 0.61423 (26824) hydrogen bonds : bond 0.03130 ( 1176) hydrogen bonds : angle 3.74825 ( 3789) Misc. bond : bond 0.00119 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 652 time to evaluate : 0.502 Fit side-chains TARDY: cannot create tardy model for: "SER G 210 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 39 GLU cc_start: 0.9053 (tt0) cc_final: 0.8833 (tt0) REVERT: A 42 ASN cc_start: 0.9340 (m110) cc_final: 0.8726 (m110) REVERT: A 43 ARG cc_start: 0.8716 (tmm-80) cc_final: 0.8331 (tmm-80) REVERT: A 55 ASP cc_start: 0.8348 (t0) cc_final: 0.7950 (t0) REVERT: A 59 ASP cc_start: 0.8921 (m-30) cc_final: 0.8524 (m-30) REVERT: A 152 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8829 (ttp80) REVERT: A 164 ARG cc_start: 0.8982 (tpt-90) cc_final: 0.8642 (tpt-90) REVERT: A 170 ASP cc_start: 0.9062 (t70) cc_final: 0.8826 (t70) REVERT: B 22 GLU cc_start: 0.8385 (tt0) cc_final: 0.7520 (tp30) REVERT: B 23 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8726 (ptm160) REVERT: B 38 ASP cc_start: 0.8782 (m-30) cc_final: 0.8199 (m-30) REVERT: B 42 ASN cc_start: 0.9512 (m110) cc_final: 0.9024 (m-40) REVERT: B 43 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8376 (tmm160) REVERT: B 47 GLN cc_start: 0.9583 (mt0) cc_final: 0.9332 (mt0) REVERT: B 55 ASP cc_start: 0.8391 (t70) cc_final: 0.7775 (t0) REVERT: B 58 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8310 (ttmm) REVERT: B 59 ASP cc_start: 0.8901 (m-30) cc_final: 0.8453 (m-30) REVERT: B 170 ASP cc_start: 0.9014 (t70) cc_final: 0.8744 (t0) REVERT: C 38 ASP cc_start: 0.8966 (m-30) cc_final: 0.8585 (m-30) REVERT: C 42 ASN cc_start: 0.9390 (m-40) cc_final: 0.9043 (m110) REVERT: C 55 ASP cc_start: 0.8289 (t70) cc_final: 0.7718 (t0) REVERT: C 58 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8503 (mtmm) REVERT: C 59 ASP cc_start: 0.8834 (m-30) cc_final: 0.8535 (m-30) REVERT: C 139 GLN cc_start: 0.9108 (mt0) cc_final: 0.8831 (mt0) REVERT: C 152 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8787 (ttp80) REVERT: D 38 ASP cc_start: 0.8915 (m-30) cc_final: 0.8560 (m-30) REVERT: D 42 ASN cc_start: 0.9403 (m110) cc_final: 0.8976 (m110) REVERT: D 54 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 55 ASP cc_start: 0.8461 (t70) cc_final: 0.8014 (t0) REVERT: D 59 ASP cc_start: 0.8913 (m-30) cc_final: 0.8659 (m-30) REVERT: D 152 ARG cc_start: 0.9196 (ttp80) cc_final: 0.8897 (ttp80) REVERT: E 22 GLU cc_start: 0.8752 (tt0) cc_final: 0.7788 (tp30) REVERT: E 42 ASN cc_start: 0.9197 (m110) cc_final: 0.8816 (m110) REVERT: E 55 ASP cc_start: 0.8557 (t70) cc_final: 0.8013 (t0) REVERT: E 59 ASP cc_start: 0.8808 (m-30) cc_final: 0.8402 (m-30) REVERT: E 109 LYS cc_start: 0.9178 (tppt) cc_final: 0.8894 (mmtp) REVERT: E 135 ASP cc_start: 0.8871 (m-30) cc_final: 0.8416 (m-30) REVERT: E 152 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8611 (ttp80) REVERT: E 170 ASP cc_start: 0.8946 (t70) cc_final: 0.8533 (t0) REVERT: F 38 ASP cc_start: 0.8822 (m-30) cc_final: 0.8512 (m-30) REVERT: F 42 ASN cc_start: 0.9390 (m110) cc_final: 0.9071 (m110) REVERT: F 58 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8533 (mtmt) REVERT: F 59 ASP cc_start: 0.9034 (m-30) cc_final: 0.8541 (m-30) REVERT: F 111 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8924 (mtmt) REVERT: G 50 ASP cc_start: 0.8803 (m-30) cc_final: 0.8468 (m-30) REVERT: G 71 ASP cc_start: 0.8881 (m-30) cc_final: 0.8670 (m-30) REVERT: H 23 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8784 (mtp85) REVERT: H 38 ASP cc_start: 0.8882 (m-30) cc_final: 0.8343 (m-30) REVERT: H 42 ASN cc_start: 0.9368 (m110) cc_final: 0.8879 (m110) REVERT: H 55 ASP cc_start: 0.8217 (t70) cc_final: 0.7585 (t0) REVERT: H 58 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8559 (ttmm) REVERT: H 59 ASP cc_start: 0.8967 (m-30) cc_final: 0.8585 (m-30) REVERT: H 135 ASP cc_start: 0.8852 (m-30) cc_final: 0.8410 (m-30) REVERT: H 152 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8807 (ttp80) REVERT: H 170 ASP cc_start: 0.9123 (t70) cc_final: 0.8811 (t0) REVERT: I 31 ASN cc_start: 0.8555 (t0) cc_final: 0.8287 (t160) REVERT: I 34 ASN cc_start: 0.8405 (m110) cc_final: 0.7882 (m110) REVERT: I 50 ASP cc_start: 0.8923 (m-30) cc_final: 0.8533 (m-30) REVERT: I 125 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: I 129 ASN cc_start: 0.9163 (m-40) cc_final: 0.8941 (m-40) REVERT: I 205 GLU cc_start: 0.8130 (mp0) cc_final: 0.7811 (pm20) REVERT: J 31 ASN cc_start: 0.8732 (t0) cc_final: 0.8525 (t160) REVERT: J 34 ASN cc_start: 0.8427 (m110) cc_final: 0.8100 (m110) REVERT: J 54 ASN cc_start: 0.9048 (m-40) cc_final: 0.8823 (m110) REVERT: K 50 ASP cc_start: 0.8949 (m-30) cc_final: 0.8486 (m-30) REVERT: K 54 ASN cc_start: 0.9030 (m-40) cc_final: 0.8590 (m110) REVERT: K 144 GLN cc_start: 0.9313 (mm110) cc_final: 0.9072 (mp-120) REVERT: K 187 LYS cc_start: 0.8426 (tptt) cc_final: 0.8170 (tptt) REVERT: L 34 ASN cc_start: 0.8422 (m110) cc_final: 0.8187 (m110) REVERT: L 50 ASP cc_start: 0.8907 (m-30) cc_final: 0.8660 (m-30) REVERT: M 54 ASN cc_start: 0.9247 (m-40) cc_final: 0.8890 (m110) REVERT: M 138 SER cc_start: 0.9000 (p) cc_final: 0.8593 (m) REVERT: M 202 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9067 (p) REVERT: N 34 ASN cc_start: 0.8271 (t0) cc_final: 0.7808 (m110) REVERT: N 151 GLU cc_start: 0.8976 (tt0) cc_final: 0.8268 (tp30) REVERT: N 205 GLU cc_start: 0.8085 (pp20) cc_final: 0.7803 (pp20) outliers start: 54 outliers final: 33 residues processed: 673 average time/residue: 0.5993 time to fit residues: 451.5981 Evaluate side-chains 667 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 631 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 47 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 209 LEU Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 20 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 ASN G 101 GLN G 144 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN J 101 GLN J 144 GLN J 153 GLN K 47 GLN K 101 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 101 GLN N 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.073303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.065039 restraints weight = 34199.044| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.25 r_work: 0.2626 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19859 Z= 0.160 Angle : 0.638 12.757 26824 Z= 0.300 Chirality : 0.044 0.224 3087 Planarity : 0.003 0.044 3479 Dihedral : 7.600 59.922 2989 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.34 % Allowed : 24.39 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.17), residues: 2478 helix: 1.99 (0.13), residues: 1407 sheet: -1.41 (0.34), residues: 196 loop : -0.75 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 43 TYR 0.025 0.001 TYR J 95 PHE 0.010 0.001 PHE F 102 TRP 0.002 0.000 TRP B 174 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00363 (19845) covalent geometry : angle 0.63762 (26824) hydrogen bonds : bond 0.03234 ( 1176) hydrogen bonds : angle 3.76161 ( 3789) Misc. bond : bond 0.00134 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7795.37 seconds wall clock time: 133 minutes 13.55 seconds (7993.55 seconds total)