Starting phenix.real_space_refine on Mon Jun 16 22:26:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvz_61847/06_2025/9jvz_61847.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvz_61847/06_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_61847/06_2025/9jvz_61847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvz_61847/06_2025/9jvz_61847.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvz_61847/06_2025/9jvz_61847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvz_61847/06_2025/9jvz_61847.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.60, per 1000 atoms: 0.64 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: 5.31 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.61 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: 7.67 Time building geometry restraints manager: 6.28 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: 0.04 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: 1.160 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 49.310 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (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 TRP 0.002 0.001 TRP H 174 HIS 0.005 0.001 HIS H 117 PHE 0.006 0.001 PHE C 175 TYR 0.007 0.001 TYR M 75 ARG 0.002 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.13125 ( 1176) hydrogen bonds : angle 6.19770 ( 3789) covalent geometry : bond 0.00646 (19845) covalent geometry : angle 0.84564 (26824) 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 : 2.227 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: 0.7553 (t0) REVERT: B 58 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8702 (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: 0.8319 (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: 0.7547 (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 59 ASP cc_start: 0.8786 (m-30) cc_final: 0.8439 (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: 0.9009 (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: 0.7110 (t0) REVERT: H 58 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8761 (mtpp) REVERT: H 59 ASP cc_start: 0.8631 (m-30) cc_final: 0.8348 (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: 0.7631 (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: 0.8047 (m-30) 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 165 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8058 (mt-10) REVERT: J 180 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8465 (tpp80) REVERT: J 181 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8750 (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: 0.8190 (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: 0.7955 (m-30) REVERT: M 71 ASP cc_start: 0.8572 (m-30) cc_final: 0.8287 (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: 0.7916 (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: 1.5216 time to fit residues: 1420.9399 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 : 2.330 ------------------------------------------------------------------------------- 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 206 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ** A 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 124 GLN F 117 HIS G 54 ASN G 101 GLN G 129 ASN H 42 ASN H 124 GLN I 54 ASN I 94 GLN I 101 GLN I 129 ASN J 101 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN J 146 GLN K 101 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN L 59 GLN L 94 GLN ** L 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 101 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.072006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.063333 restraints weight = 34058.196| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.31 r_work: 0.2579 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19859 Z= 0.227 Angle : 0.639 11.084 26824 Z= 0.301 Chirality : 0.043 0.229 3087 Planarity : 0.004 0.035 3479 Dihedral : 8.918 59.759 2995 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.73 % Allowed : 17.92 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2478 helix: 0.55 (0.13), residues: 1407 sheet: -2.73 (0.27), residues: 182 loop : -1.25 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 174 HIS 0.004 0.001 HIS J 171 PHE 0.015 0.002 PHE G 147 TYR 0.011 0.001 TYR M 206 ARG 0.008 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1176) hydrogen bonds : angle 4.16923 ( 3789) covalent geometry : bond 0.00495 (19845) covalent geometry : angle 0.63925 (26824) Misc. bond : bond 0.00121 ( 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 739 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 664 time to evaluate : 2.229 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. TARDY: cannot create tardy model for: "SER N 210 " (corrupted residue). Skipping it. REVERT: A 38 ASP cc_start: 0.8887 (m-30) cc_final: 0.7978 (m-30) REVERT: A 42 ASN cc_start: 0.9300 (m110) cc_final: 0.8755 (m110) REVERT: A 55 ASP cc_start: 0.8047 (t0) cc_final: 0.7526 (t0) REVERT: A 59 ASP cc_start: 0.9021 (m-30) cc_final: 0.8642 (m-30) REVERT: A 152 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8785 (ttp80) REVERT: A 170 ASP cc_start: 0.9012 (t70) cc_final: 0.8616 (t70) REVERT: B 38 ASP cc_start: 0.8911 (m-30) cc_final: 0.8510 (m-30) REVERT: B 42 ASN cc_start: 0.9399 (m-40) cc_final: 0.8924 (m110) REVERT: B 55 ASP cc_start: 0.8179 (t70) cc_final: 0.7831 (t0) REVERT: B 59 ASP cc_start: 0.8883 (m-30) cc_final: 0.8430 (m-30) REVERT: B 139 GLN cc_start: 0.8957 (mt0) cc_final: 0.8687 (mt0) REVERT: B 170 ASP cc_start: 0.9027 (t70) cc_final: 0.8644 (t70) REVERT: C 38 ASP cc_start: 0.8903 (m-30) cc_final: 0.8320 (m-30) REVERT: C 42 ASN cc_start: 0.9334 (m-40) cc_final: 0.8881 (m110) REVERT: C 55 ASP cc_start: 0.7962 (t70) cc_final: 0.7525 (t0) REVERT: C 59 ASP cc_start: 0.9002 (m-30) cc_final: 0.8582 (m-30) REVERT: C 139 GLN cc_start: 0.8974 (mt0) cc_final: 0.8731 (mt0) REVERT: C 152 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8872 (ttp80) REVERT: D 18 ASP cc_start: 0.8651 (m-30) cc_final: 0.8437 (m-30) REVERT: D 38 ASP cc_start: 0.9003 (m-30) cc_final: 0.8523 (m-30) REVERT: D 42 ASN cc_start: 0.9371 (m-40) cc_final: 0.9019 (m110) REVERT: D 55 ASP cc_start: 0.8103 (t70) cc_final: 0.7676 (t0) REVERT: D 59 ASP cc_start: 0.9048 (m-30) cc_final: 0.8682 (m-30) REVERT: D 111 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8761 (mttt) REVERT: D 113 TYR cc_start: 0.8955 (m-80) cc_final: 0.8711 (m-80) REVERT: D 152 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8801 (ttp80) REVERT: D 170 ASP cc_start: 0.8755 (t70) cc_final: 0.8524 (t70) REVERT: E 22 GLU cc_start: 0.8694 (tt0) cc_final: 0.7921 (tm-30) REVERT: E 42 ASN cc_start: 0.9195 (m-40) cc_final: 0.8906 (m110) REVERT: E 55 ASP cc_start: 0.8130 (t70) cc_final: 0.7540 (t0) REVERT: E 58 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8572 (mtpp) REVERT: E 59 ASP cc_start: 0.9015 (m-30) cc_final: 0.8605 (m-30) REVERT: E 111 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8780 (ttmt) REVERT: E 135 ASP cc_start: 0.8986 (m-30) cc_final: 0.8489 (m-30) REVERT: E 152 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8851 (ttp80) REVERT: E 170 ASP cc_start: 0.8871 (t70) cc_final: 0.8415 (t0) REVERT: F 38 ASP cc_start: 0.8832 (m-30) cc_final: 0.8371 (m-30) REVERT: F 42 ASN cc_start: 0.9325 (m-40) cc_final: 0.8778 (m-40) REVERT: F 55 ASP cc_start: 0.7884 (t0) cc_final: 0.7564 (t0) REVERT: F 58 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8574 (mtmm) REVERT: F 59 ASP cc_start: 0.9065 (m-30) cc_final: 0.8808 (m-30) REVERT: F 130 THR cc_start: 0.8963 (t) cc_final: 0.8611 (p) REVERT: F 135 ASP cc_start: 0.9008 (m-30) cc_final: 0.8514 (m-30) REVERT: G 34 ASN cc_start: 0.7969 (m110) cc_final: 0.7753 (m-40) REVERT: G 42 ILE cc_start: 0.9375 (mt) cc_final: 0.9135 (mm) REVERT: G 47 GLN cc_start: 0.8668 (tp40) cc_final: 0.8432 (tp40) REVERT: G 50 ASP cc_start: 0.8865 (m-30) cc_final: 0.8522 (m-30) REVERT: G 160 MET cc_start: 0.9168 (mtt) cc_final: 0.8955 (mtp) REVERT: G 192 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8400 (mm-30) REVERT: H 38 ASP cc_start: 0.8937 (m-30) cc_final: 0.8475 (m-30) REVERT: H 42 ASN cc_start: 0.9311 (m110) cc_final: 0.8889 (m110) REVERT: H 55 ASP cc_start: 0.7840 (t70) cc_final: 0.7224 (t0) REVERT: H 58 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8703 (mtpp) REVERT: H 59 ASP cc_start: 0.9046 (m-30) cc_final: 0.8535 (m-30) REVERT: H 135 ASP cc_start: 0.8895 (m-30) cc_final: 0.8491 (m-30) REVERT: H 139 GLN cc_start: 0.8903 (mt0) cc_final: 0.8648 (mt0) REVERT: H 152 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8636 (ttp80) REVERT: H 170 ASP cc_start: 0.8994 (t70) cc_final: 0.8600 (t0) REVERT: I 33 TYR cc_start: 0.8920 (m-80) cc_final: 0.8670 (m-80) REVERT: I 34 ASN cc_start: 0.7959 (m110) cc_final: 0.7421 (m110) REVERT: I 42 ILE cc_start: 0.9533 (mt) cc_final: 0.9296 (mm) REVERT: I 50 ASP cc_start: 0.8920 (m-30) cc_final: 0.8603 (m-30) REVERT: I 205 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: I 207 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7591 (ppt-90) REVERT: J 31 ASN cc_start: 0.8512 (t0) cc_final: 0.8218 (t160) REVERT: J 34 ASN cc_start: 0.8140 (m110) cc_final: 0.7777 (m110) REVERT: J 52 SER cc_start: 0.9396 (OUTLIER) cc_final: 0.9179 (p) REVERT: J 181 LYS cc_start: 0.9231 (mtmm) cc_final: 0.8970 (mtmm) REVERT: J 202 THR cc_start: 0.8999 (t) cc_final: 0.8771 (p) REVERT: K 34 ASN cc_start: 0.7934 (m110) cc_final: 0.7317 (m110) REVERT: K 38 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8239 (mm-30) REVERT: K 50 ASP cc_start: 0.8849 (m-30) cc_final: 0.8437 (m-30) REVERT: K 54 ASN cc_start: 0.8963 (m-40) cc_final: 0.8393 (m110) REVERT: K 129 ASN cc_start: 0.9321 (m-40) cc_final: 0.8931 (m110) REVERT: K 158 GLU cc_start: 0.9182 (tp30) cc_final: 0.8816 (tp30) REVERT: K 180 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8745 (ttm110) REVERT: L 34 ASN cc_start: 0.7804 (m110) cc_final: 0.7447 (m110) REVERT: L 50 ASP cc_start: 0.8756 (m-30) cc_final: 0.8408 (m-30) REVERT: L 123 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8686 (mtmt) REVERT: M 54 ASN cc_start: 0.9258 (m-40) cc_final: 0.9043 (m110) REVERT: M 101 GLN cc_start: 0.8682 (tt0) cc_final: 0.8427 (tt0) REVERT: M 204 LEU cc_start: 0.9029 (mt) cc_final: 0.8756 (mt) REVERT: M 205 GLU cc_start: 0.7771 (pp20) cc_final: 0.7446 (pp20) REVERT: N 47 GLN cc_start: 0.8635 (tp40) cc_final: 0.8308 (tp40) REVERT: N 71 ASP cc_start: 0.9129 (m-30) cc_final: 0.8817 (m-30) REVERT: N 149 ASP cc_start: 0.9006 (m-30) cc_final: 0.8742 (m-30) REVERT: N 151 GLU cc_start: 0.8965 (tt0) cc_final: 0.8247 (tp30) REVERT: N 205 GLU cc_start: 0.7973 (pp20) cc_final: 0.7682 (pp20) outliers start: 75 outliers final: 20 residues processed: 700 average time/residue: 1.3864 time to fit residues: 1084.2425 Evaluate side-chains 627 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 602 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 86 CYS Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 58 LYS 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 86 CYS 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 180 ARG 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 M residue 78 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 81 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 47 GLN B 117 HIS C 42 ASN D 42 ASN D 117 HIS D 142 GLN E 42 ASN E 124 GLN F 42 ASN F 142 GLN G 54 ASN G 101 GLN G 144 GLN H 117 HIS I 54 ASN I 101 GLN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN J 146 GLN K 101 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 146 GLN K 153 GLN L 31 ASN L 54 ASN L 94 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 129 ASN N 144 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.068475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.060160 restraints weight = 34397.914| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.22 r_work: 0.2522 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19859 Z= 0.283 Angle : 0.660 10.959 26824 Z= 0.309 Chirality : 0.044 0.253 3087 Planarity : 0.004 0.035 3479 Dihedral : 8.415 59.516 2989 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.33 % Allowed : 18.37 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2478 helix: 1.21 (0.13), residues: 1407 sheet: -2.20 (0.31), residues: 182 loop : -1.08 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.004 0.001 HIS I 171 PHE 0.013 0.002 PHE B 102 TYR 0.011 0.001 TYR E 78 ARG 0.007 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 1176) hydrogen bonds : angle 4.04412 ( 3789) covalent geometry : bond 0.00620 (19845) covalent geometry : angle 0.65997 (26824) Misc. bond : bond 0.00200 ( 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: 87 poor density : 626 time to evaluate : 3.077 Fit side-chains revert: symmetry clash 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: 0.8520 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 23 ARG cc_start: 0.9141 (ttp-170) cc_final: 0.8906 (ttm170) REVERT: A 42 ASN cc_start: 0.9314 (m110) cc_final: 0.8695 (m110) REVERT: A 55 ASP cc_start: 0.8212 (t0) cc_final: 0.7551 (t0) REVERT: A 58 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8698 (mtpp) REVERT: A 59 ASP cc_start: 0.8955 (m-30) cc_final: 0.8542 (m-30) REVERT: A 170 ASP cc_start: 0.9026 (t70) cc_final: 0.8772 (t70) REVERT: B 22 GLU cc_start: 0.8630 (tt0) cc_final: 0.7638 (tp30) REVERT: B 38 ASP cc_start: 0.8962 (m-30) cc_final: 0.8390 (m-30) REVERT: B 42 ASN cc_start: 0.9472 (m110) cc_final: 0.8886 (m110) REVERT: B 55 ASP cc_start: 0.8265 (t70) cc_final: 0.7745 (t0) REVERT: B 170 ASP cc_start: 0.9052 (t70) cc_final: 0.8700 (t70) REVERT: C 35 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: C 38 ASP cc_start: 0.9042 (m-30) cc_final: 0.8387 (m-30) REVERT: C 42 ASN cc_start: 0.9373 (m110) cc_final: 0.8979 (m110) REVERT: C 55 ASP cc_start: 0.8092 (t70) cc_final: 0.7596 (t0) REVERT: C 59 ASP cc_start: 0.8946 (m-30) cc_final: 0.8390 (m-30) REVERT: C 139 GLN cc_start: 0.9070 (mt0) cc_final: 0.8832 (mt0) REVERT: C 152 ARG cc_start: 0.9237 (ttp80) cc_final: 0.8967 (ttp80) REVERT: D 18 ASP cc_start: 0.8876 (m-30) cc_final: 0.8668 (m-30) REVERT: D 38 ASP cc_start: 0.9065 (m-30) cc_final: 0.8674 (m-30) REVERT: D 42 ASN cc_start: 0.9433 (m110) cc_final: 0.9029 (m110) REVERT: D 55 ASP cc_start: 0.8265 (t70) cc_final: 0.7894 (t0) REVERT: D 59 ASP cc_start: 0.9013 (m-30) cc_final: 0.8664 (m-30) REVERT: D 152 ARG cc_start: 0.9199 (ttp80) cc_final: 0.8801 (ttp80) REVERT: D 170 ASP cc_start: 0.8754 (t70) cc_final: 0.8554 (t70) REVERT: E 22 GLU cc_start: 0.8720 (tt0) cc_final: 0.7954 (tm-30) REVERT: E 42 ASN cc_start: 0.9231 (m110) cc_final: 0.8919 (m110) REVERT: E 55 ASP cc_start: 0.8276 (t70) cc_final: 0.7663 (t0) REVERT: E 58 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8596 (mtpp) REVERT: E 59 ASP cc_start: 0.8947 (m-30) cc_final: 0.8440 (m-30) REVERT: E 111 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8878 (mtmt) REVERT: E 135 ASP cc_start: 0.9001 (m-30) cc_final: 0.8532 (m-30) REVERT: E 152 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8900 (ttp80) REVERT: E 170 ASP cc_start: 0.8827 (t70) cc_final: 0.8257 (t0) REVERT: F 23 ARG cc_start: 0.9156 (mtp180) cc_final: 0.8927 (mtp180) REVERT: F 42 ASN cc_start: 0.9392 (m110) cc_final: 0.9073 (m-40) REVERT: F 55 ASP cc_start: 0.8048 (t0) cc_final: 0.7806 (t0) REVERT: F 58 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: F 59 ASP cc_start: 0.9089 (m-30) cc_final: 0.8746 (m-30) REVERT: F 111 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8921 (mttp) REVERT: G 42 ILE cc_start: 0.9398 (mt) cc_final: 0.9190 (mm) REVERT: G 50 ASP cc_start: 0.8846 (m-30) cc_final: 0.8469 (m-30) REVERT: G 192 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8534 (mm-30) REVERT: H 23 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8802 (mtp180) REVERT: H 38 ASP cc_start: 0.8893 (m-30) cc_final: 0.8393 (m-30) REVERT: H 42 ASN cc_start: 0.9343 (m110) cc_final: 0.8909 (m110) REVERT: H 55 ASP cc_start: 0.8080 (t70) cc_final: 0.7432 (t0) REVERT: H 58 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8698 (mtpp) REVERT: H 59 ASP cc_start: 0.9075 (m-30) cc_final: 0.8558 (m-30) REVERT: H 135 ASP cc_start: 0.8928 (m-30) cc_final: 0.8517 (m-30) REVERT: H 152 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8839 (ttp80) REVERT: H 170 ASP cc_start: 0.9072 (t70) cc_final: 0.8746 (t0) REVERT: I 34 ASN cc_start: 0.8319 (m110) cc_final: 0.7842 (m110) REVERT: I 50 ASP cc_start: 0.8981 (m-30) cc_final: 0.8619 (m-30) REVERT: I 205 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: I 207 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (ppt-90) REVERT: J 34 ASN cc_start: 0.8395 (m110) cc_final: 0.8133 (m110) REVERT: J 52 SER cc_start: 0.9549 (OUTLIER) cc_final: 0.9312 (p) REVERT: K 34 ASN cc_start: 0.8224 (m110) cc_final: 0.7801 (m110) REVERT: K 38 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8294 (mm-30) REVERT: K 39 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8703 (mt-10) REVERT: K 47 GLN cc_start: 0.8619 (tp40) cc_final: 0.8358 (tp40) REVERT: K 50 ASP cc_start: 0.8886 (m-30) cc_final: 0.8450 (m-30) REVERT: K 52 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.9188 (p) REVERT: K 54 ASN cc_start: 0.9120 (m-40) cc_final: 0.8900 (m110) REVERT: K 129 ASN cc_start: 0.9348 (m-40) cc_final: 0.9001 (m110) REVERT: K 158 GLU cc_start: 0.9222 (tp30) cc_final: 0.8972 (tp30) REVERT: K 160 MET cc_start: 0.9377 (mtt) cc_final: 0.9130 (mtp) REVERT: K 206 TYR cc_start: 0.8913 (m-80) cc_final: 0.8643 (m-10) REVERT: L 34 ASN cc_start: 0.8398 (m110) cc_final: 0.8134 (m110) REVERT: L 50 ASP cc_start: 0.8859 (m-30) cc_final: 0.8620 (m-30) REVERT: M 47 GLN cc_start: 0.8470 (tp40) cc_final: 0.8245 (tp40) REVERT: M 54 ASN cc_start: 0.9373 (m-40) cc_final: 0.9084 (m110) REVERT: M 101 GLN cc_start: 0.8789 (tt0) cc_final: 0.8418 (tt0) REVERT: M 125 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (mpp) REVERT: M 204 LEU cc_start: 0.9309 (mt) cc_final: 0.9006 (mp) REVERT: N 71 ASP cc_start: 0.9105 (m-30) cc_final: 0.8819 (m-30) REVERT: N 125 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8903 (mtm) REVERT: N 151 GLU cc_start: 0.8986 (tt0) cc_final: 0.8314 (tp30) outliers start: 87 outliers final: 30 residues processed: 663 average time/residue: 1.5872 time to fit residues: 1179.6684 Evaluate side-chains 630 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 592 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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 B residue 126 LEU Chi-restraints excluded: chain C residue 35 GLU 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 D residue 126 LEU Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain F residue 58 LYS 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 207 ARG 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 J residue 138 SER 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 138 SER Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 125 MET Chi-restraints excluded: chain N residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 129 optimal weight: 0.0070 chunk 120 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 0.1980 chunk 226 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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** B 47 GLN G 31 ASN G 54 ASN G 77 ASN G 101 GLN G 144 GLN G 146 GLN I 54 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 144 GLN K 101 GLN K 136 GLN K 144 GLN K 146 GLN K 153 GLN L 31 ASN L 136 GLN L 144 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 54 ASN N 146 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066773 restraints weight = 34095.993| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.22 r_work: 0.2664 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19859 Z= 0.105 Angle : 0.548 10.083 26824 Z= 0.260 Chirality : 0.041 0.208 3087 Planarity : 0.003 0.036 3479 Dihedral : 8.171 59.657 2989 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.09 % Allowed : 20.76 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2478 helix: 1.78 (0.13), residues: 1400 sheet: -1.71 (0.33), residues: 175 loop : -0.95 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 174 HIS 0.003 0.001 HIS J 171 PHE 0.008 0.001 PHE F 143 TYR 0.016 0.001 TYR C 113 ARG 0.008 0.001 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 1176) hydrogen bonds : angle 3.76971 ( 3789) covalent geometry : bond 0.00221 (19845) covalent geometry : angle 0.54840 (26824) Misc. bond : bond 0.00102 ( 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 741 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 679 time to evaluate : 3.384 Fit side-chains 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: 0.8498 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 42 ASN cc_start: 0.9342 (m110) cc_final: 0.8757 (m110) REVERT: A 43 ARG cc_start: 0.8747 (tmm-80) cc_final: 0.8438 (ttp80) REVERT: A 55 ASP cc_start: 0.8267 (t0) cc_final: 0.7936 (t0) REVERT: A 59 ASP cc_start: 0.8929 (m-30) cc_final: 0.8506 (m-30) REVERT: A 152 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8854 (ttp80) REVERT: A 164 ARG cc_start: 0.9028 (tpt-90) cc_final: 0.8676 (tpt-90) REVERT: A 170 ASP cc_start: 0.9083 (t70) cc_final: 0.8702 (t70) REVERT: B 22 GLU cc_start: 0.8515 (tt0) cc_final: 0.7528 (tp30) REVERT: B 38 ASP cc_start: 0.8864 (m-30) cc_final: 0.8280 (m-30) REVERT: B 42 ASN cc_start: 0.9400 (m110) cc_final: 0.8880 (m110) REVERT: B 43 ARG cc_start: 0.8784 (tmm-80) cc_final: 0.8565 (ttp80) REVERT: B 47 GLN cc_start: 0.9500 (mt0) cc_final: 0.9225 (mt0) REVERT: B 55 ASP cc_start: 0.8373 (t70) cc_final: 0.7756 (t0) REVERT: B 58 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8440 (ttmm) REVERT: B 170 ASP cc_start: 0.9072 (t70) cc_final: 0.8764 (t0) REVERT: C 38 ASP cc_start: 0.8974 (m-30) cc_final: 0.8512 (m-30) REVERT: C 42 ASN cc_start: 0.9351 (m110) cc_final: 0.8930 (m110) REVERT: C 55 ASP cc_start: 0.8289 (t70) cc_final: 0.7785 (t0) REVERT: C 59 ASP cc_start: 0.8905 (m-30) cc_final: 0.8473 (m-30) REVERT: C 139 GLN cc_start: 0.9116 (mt0) cc_final: 0.8836 (mt0) REVERT: C 164 ARG cc_start: 0.9167 (tpt-90) cc_final: 0.8653 (tpt-90) REVERT: C 168 ASP cc_start: 0.9230 (m-30) cc_final: 0.8822 (m-30) REVERT: C 170 ASP cc_start: 0.8925 (t70) cc_final: 0.8610 (t0) REVERT: D 18 ASP cc_start: 0.8829 (m-30) cc_final: 0.8601 (m-30) REVERT: D 38 ASP cc_start: 0.8973 (m-30) cc_final: 0.8560 (m-30) REVERT: D 42 ASN cc_start: 0.9411 (m110) cc_final: 0.9030 (m110) REVERT: D 55 ASP cc_start: 0.8341 (t70) cc_final: 0.7921 (t0) REVERT: D 59 ASP cc_start: 0.9002 (m-30) cc_final: 0.8645 (m-30) REVERT: D 111 LYS cc_start: 0.9031 (mttt) cc_final: 0.8805 (mttt) REVERT: D 135 ASP cc_start: 0.9027 (m-30) cc_final: 0.8769 (m-30) REVERT: E 22 GLU cc_start: 0.8690 (tt0) cc_final: 0.8042 (tm-30) REVERT: E 23 ARG cc_start: 0.8945 (ttp-170) cc_final: 0.8534 (ttp-170) REVERT: E 38 ASP cc_start: 0.8790 (m-30) cc_final: 0.8498 (m-30) REVERT: E 42 ASN cc_start: 0.9169 (m110) cc_final: 0.8684 (m110) REVERT: E 55 ASP cc_start: 0.8383 (t70) cc_final: 0.7738 (t0) REVERT: E 58 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8610 (mtpp) REVERT: E 59 ASP cc_start: 0.8929 (m-30) cc_final: 0.8457 (m-30) REVERT: E 111 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8846 (mtmt) REVERT: E 135 ASP cc_start: 0.8926 (m-30) cc_final: 0.8482 (m-30) REVERT: E 147 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8677 (ttpt) REVERT: E 152 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8755 (ttp80) REVERT: E 170 ASP cc_start: 0.8920 (t70) cc_final: 0.8488 (t0) REVERT: F 23 ARG cc_start: 0.9101 (mtp180) cc_final: 0.8876 (ttm170) REVERT: F 38 ASP cc_start: 0.8809 (m-30) cc_final: 0.8424 (m-30) REVERT: F 42 ASN cc_start: 0.9367 (m110) cc_final: 0.9120 (m110) REVERT: F 58 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8767 (mtmm) REVERT: F 59 ASP cc_start: 0.9079 (m-30) cc_final: 0.8849 (m-30) REVERT: F 147 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8719 (ttmt) REVERT: F 173 ARG cc_start: 0.8513 (tpt90) cc_final: 0.8253 (tpt90) REVERT: G 42 ILE cc_start: 0.9307 (mt) cc_final: 0.9055 (mm) REVERT: G 47 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: G 50 ASP cc_start: 0.8777 (m-30) cc_final: 0.8402 (m-30) REVERT: G 71 ASP cc_start: 0.8900 (m-30) cc_final: 0.8676 (m-30) REVERT: G 165 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8604 (mt-10) REVERT: G 192 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8667 (mm-30) REVERT: H 23 ARG cc_start: 0.9154 (ttp80) cc_final: 0.8793 (mtp180) REVERT: H 38 ASP cc_start: 0.8877 (m-30) cc_final: 0.8389 (m-30) REVERT: H 42 ASN cc_start: 0.9346 (m110) cc_final: 0.8887 (m110) REVERT: H 55 ASP cc_start: 0.8189 (t70) cc_final: 0.7543 (t0) REVERT: H 58 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8679 (mtpp) REVERT: H 59 ASP cc_start: 0.8990 (m-30) cc_final: 0.8508 (m-30) REVERT: H 135 ASP cc_start: 0.8791 (m-30) cc_final: 0.8386 (m-30) REVERT: H 152 ARG cc_start: 0.9139 (ttp80) cc_final: 0.8858 (ttp80) REVERT: H 168 ASP cc_start: 0.9168 (m-30) cc_final: 0.8933 (m-30) REVERT: H 170 ASP cc_start: 0.9092 (t70) cc_final: 0.8750 (t0) REVERT: I 31 ASN cc_start: 0.8546 (t0) cc_final: 0.8146 (t0) REVERT: I 34 ASN cc_start: 0.8405 (m110) cc_final: 0.7750 (m110) REVERT: I 50 ASP cc_start: 0.9005 (m-30) cc_final: 0.8571 (m-30) REVERT: I 59 GLN cc_start: 0.9083 (mt0) cc_final: 0.8533 (mt0) REVERT: I 101 GLN cc_start: 0.8658 (tt0) cc_final: 0.8351 (tm-30) REVERT: I 123 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8792 (mttt) REVERT: I 125 MET cc_start: 0.9164 (mpp) cc_final: 0.8731 (mpt) REVERT: I 160 MET cc_start: 0.9248 (mtt) cc_final: 0.8997 (mtm) REVERT: I 205 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: I 207 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7758 (ppt-90) REVERT: J 34 ASN cc_start: 0.8481 (m110) cc_final: 0.8161 (m110) REVERT: J 35 LYS cc_start: 0.9077 (tptm) cc_final: 0.8337 (mttt) REVERT: J 52 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9351 (p) REVERT: J 138 SER cc_start: 0.8837 (p) cc_final: 0.8606 (m) REVERT: K 34 ASN cc_start: 0.8302 (m110) cc_final: 0.7817 (m110) REVERT: K 38 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 39 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8681 (mt-10) REVERT: K 47 GLN cc_start: 0.8477 (tp40) cc_final: 0.8170 (tp40) REVERT: K 50 ASP cc_start: 0.8870 (m-30) cc_final: 0.8430 (m-30) REVERT: K 52 SER cc_start: 0.9454 (OUTLIER) cc_final: 0.9207 (p) REVERT: K 54 ASN cc_start: 0.9035 (m-40) cc_final: 0.8814 (m110) REVERT: K 129 ASN cc_start: 0.9305 (m-40) cc_final: 0.9071 (m110) REVERT: K 138 SER cc_start: 0.8823 (p) cc_final: 0.8589 (m) REVERT: K 158 GLU cc_start: 0.9265 (tp30) cc_final: 0.9010 (tp30) REVERT: L 34 ASN cc_start: 0.8373 (m110) cc_final: 0.7671 (m110) REVERT: L 50 ASP cc_start: 0.8823 (m-30) cc_final: 0.8509 (m-30) REVERT: L 52 SER cc_start: 0.9572 (OUTLIER) cc_final: 0.9342 (p) REVERT: M 54 ASN cc_start: 0.9322 (m-40) cc_final: 0.8969 (m110) REVERT: M 138 SER cc_start: 0.8961 (p) cc_final: 0.8619 (m) REVERT: M 202 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9013 (p) REVERT: M 205 GLU cc_start: 0.7890 (pp20) cc_final: 0.7529 (pp20) REVERT: N 47 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8207 (tp40) REVERT: N 71 ASP cc_start: 0.9041 (m-30) cc_final: 0.8756 (m-30) REVERT: N 151 GLU cc_start: 0.8960 (tt0) cc_final: 0.8259 (tp30) REVERT: N 205 GLU cc_start: 0.8616 (pm20) cc_final: 0.8403 (pp20) outliers start: 62 outliers final: 20 residues processed: 706 average time/residue: 1.6032 time to fit residues: 1270.8931 Evaluate side-chains 654 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 625 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 17 THR 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 F residue 17 THR Chi-restraints excluded: chain F residue 58 LYS 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 H residue 17 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 85 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 L residue 52 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 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 GLN G 54 ASN G 101 GLN G 144 GLN I 54 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 94 GLN J 101 GLN J 144 GLN K 101 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.069493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.061199 restraints weight = 34433.347| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.22 r_work: 0.2544 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19859 Z= 0.244 Angle : 0.638 10.746 26824 Z= 0.298 Chirality : 0.044 0.280 3087 Planarity : 0.003 0.040 3479 Dihedral : 7.973 59.253 2989 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.08 % Allowed : 21.06 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2478 helix: 1.90 (0.13), residues: 1407 sheet: -1.65 (0.35), residues: 182 loop : -0.94 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 174 HIS 0.004 0.001 HIS A 117 PHE 0.008 0.001 PHE H 102 TYR 0.021 0.001 TYR C 113 ARG 0.008 0.001 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 1176) hydrogen bonds : angle 3.84137 ( 3789) covalent geometry : bond 0.00537 (19845) covalent geometry : angle 0.63828 (26824) Misc. bond : bond 0.00189 ( 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 713 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 631 time to evaluate : 2.791 Fit side-chains 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: 0.8566 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 42 ASN cc_start: 0.9355 (m110) cc_final: 0.8863 (m110) REVERT: A 55 ASP cc_start: 0.8284 (t0) cc_final: 0.7655 (t0) REVERT: A 59 ASP cc_start: 0.8958 (m-30) cc_final: 0.8525 (m-30) REVERT: A 170 ASP cc_start: 0.9075 (t70) cc_final: 0.8851 (t70) REVERT: B 22 GLU cc_start: 0.8524 (tt0) cc_final: 0.7633 (tp30) REVERT: B 38 ASP cc_start: 0.8939 (m-30) cc_final: 0.8353 (m-30) REVERT: B 42 ASN cc_start: 0.9450 (m110) cc_final: 0.8868 (m110) REVERT: B 43 ARG cc_start: 0.8766 (tmm-80) cc_final: 0.8449 (ttp-110) REVERT: B 55 ASP cc_start: 0.8363 (t70) cc_final: 0.7780 (t0) REVERT: B 58 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8373 (ttmm) REVERT: B 170 ASP cc_start: 0.9102 (t70) cc_final: 0.8765 (t70) REVERT: C 38 ASP cc_start: 0.9043 (m-30) cc_final: 0.8652 (m-30) REVERT: C 42 ASN cc_start: 0.9354 (m110) cc_final: 0.8996 (m110) REVERT: C 55 ASP cc_start: 0.8212 (t70) cc_final: 0.7732 (t0) REVERT: C 59 ASP cc_start: 0.8949 (m-30) cc_final: 0.8602 (m-30) REVERT: C 139 GLN cc_start: 0.9134 (mt0) cc_final: 0.8893 (mt0) REVERT: D 18 ASP cc_start: 0.8935 (m-30) cc_final: 0.8721 (m-30) REVERT: D 38 ASP cc_start: 0.9043 (m-30) cc_final: 0.8712 (m-30) REVERT: D 42 ASN cc_start: 0.9425 (m110) cc_final: 0.9010 (m110) REVERT: D 55 ASP cc_start: 0.8364 (t70) cc_final: 0.7983 (t0) REVERT: D 59 ASP cc_start: 0.8997 (m-30) cc_final: 0.8685 (m-30) REVERT: E 17 THR cc_start: 0.8748 (p) cc_final: 0.8467 (t) REVERT: E 22 GLU cc_start: 0.8879 (tt0) cc_final: 0.8071 (tm-30) REVERT: E 42 ASN cc_start: 0.9177 (m110) cc_final: 0.8804 (m110) REVERT: E 55 ASP cc_start: 0.8389 (t70) cc_final: 0.7747 (t0) REVERT: E 58 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8631 (mtpp) REVERT: E 59 ASP cc_start: 0.8944 (m-30) cc_final: 0.8371 (m-30) REVERT: E 111 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8895 (mtmt) REVERT: E 135 ASP cc_start: 0.8964 (m-30) cc_final: 0.8492 (m-30) REVERT: E 170 ASP cc_start: 0.8926 (t70) cc_final: 0.8556 (t0) REVERT: F 38 ASP cc_start: 0.8854 (m-30) cc_final: 0.8615 (m-30) REVERT: F 42 ASN cc_start: 0.9395 (m110) cc_final: 0.9136 (m110) REVERT: F 55 ASP cc_start: 0.8082 (t0) cc_final: 0.7810 (t0) REVERT: F 58 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8742 (mtmm) REVERT: F 59 ASP cc_start: 0.9088 (m-30) cc_final: 0.8622 (m-30) REVERT: F 111 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8937 (mttt) REVERT: G 42 ILE cc_start: 0.9407 (mt) cc_final: 0.9203 (mm) REVERT: G 50 ASP cc_start: 0.8834 (m-30) cc_final: 0.8501 (m-30) REVERT: G 71 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8725 (m-30) REVERT: G 192 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8746 (mm-30) REVERT: H 23 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8867 (mtp85) REVERT: H 38 ASP cc_start: 0.8922 (m-30) cc_final: 0.8505 (m-30) REVERT: H 42 ASN cc_start: 0.9380 (m110) cc_final: 0.8959 (m110) REVERT: H 55 ASP cc_start: 0.8217 (t70) cc_final: 0.7654 (t0) REVERT: H 58 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8743 (mtpp) REVERT: H 59 ASP cc_start: 0.8990 (m-30) cc_final: 0.8466 (m-30) REVERT: H 135 ASP cc_start: 0.8895 (m-30) cc_final: 0.8476 (m-30) REVERT: H 152 ARG cc_start: 0.9208 (ttp80) cc_final: 0.8768 (ttp80) REVERT: H 170 ASP cc_start: 0.9118 (t70) cc_final: 0.8803 (t0) REVERT: H 182 GLU cc_start: 0.9137 (tp30) cc_final: 0.8906 (tp30) REVERT: I 31 ASN cc_start: 0.8556 (t0) cc_final: 0.8321 (t160) REVERT: I 34 ASN cc_start: 0.8438 (m110) cc_final: 0.7943 (m110) REVERT: I 50 ASP cc_start: 0.9021 (m-30) cc_final: 0.8612 (m-30) REVERT: I 59 GLN cc_start: 0.9178 (mt0) cc_final: 0.8814 (mt0) REVERT: I 205 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: J 34 ASN cc_start: 0.8469 (m110) cc_final: 0.8195 (m110) REVERT: K 34 ASN cc_start: 0.8339 (m110) cc_final: 0.7785 (m110) REVERT: K 38 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8274 (mm-30) REVERT: K 47 GLN cc_start: 0.8666 (tp40) cc_final: 0.8383 (tp40) REVERT: K 50 ASP cc_start: 0.8965 (m-30) cc_final: 0.8538 (m-30) REVERT: K 52 SER cc_start: 0.9491 (OUTLIER) cc_final: 0.9244 (p) REVERT: K 54 ASN cc_start: 0.9134 (m-40) cc_final: 0.8933 (m110) REVERT: K 158 GLU cc_start: 0.9215 (tp30) cc_final: 0.9004 (tp30) REVERT: L 34 ASN cc_start: 0.8449 (m110) cc_final: 0.8140 (m110) REVERT: L 50 ASP cc_start: 0.8899 (m-30) cc_final: 0.8623 (m-30) REVERT: M 54 ASN cc_start: 0.9351 (m-40) cc_final: 0.9033 (m110) REVERT: M 101 GLN cc_start: 0.8804 (tt0) cc_final: 0.8450 (tt0) REVERT: M 202 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9093 (p) REVERT: M 205 GLU cc_start: 0.7828 (pp20) cc_final: 0.7568 (pp20) REVERT: N 47 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8352 (tp40) REVERT: N 71 ASP cc_start: 0.9102 (m-30) cc_final: 0.8807 (m-30) REVERT: N 151 GLU cc_start: 0.8973 (tt0) cc_final: 0.8325 (tp30) outliers start: 82 outliers final: 34 residues processed: 663 average time/residue: 1.4480 time to fit residues: 1076.4586 Evaluate side-chains 650 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 609 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 B residue 126 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 86 CYS 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 58 LYS 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 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 85 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 K residue 138 SER Chi-restraints excluded: chain K residue 153 GLN 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 143 ILE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain N residue 47 GLN Chi-restraints excluded: chain N residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 8.9990 chunk 215 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN G 54 ASN G 101 GLN G 144 GLN I 54 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN J 94 GLN J 144 GLN K 101 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 31 ASN N 54 ASN N 107 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.062895 restraints weight = 34265.957| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.22 r_work: 0.2585 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19859 Z= 0.169 Angle : 0.603 12.486 26824 Z= 0.281 Chirality : 0.043 0.264 3087 Planarity : 0.003 0.037 3479 Dihedral : 7.997 59.123 2989 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.63 % Allowed : 21.35 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2478 helix: 1.99 (0.13), residues: 1407 sheet: -1.58 (0.35), residues: 182 loop : -0.86 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.004 0.001 HIS D 117 PHE 0.007 0.001 PHE A 185 TYR 0.016 0.001 TYR C 113 ARG 0.009 0.001 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1176) hydrogen bonds : angle 3.78483 ( 3789) covalent geometry : bond 0.00375 (19845) covalent geometry : angle 0.60337 (26824) Misc. bond : bond 0.00143 ( 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 711 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 638 time to evaluate : 2.094 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: 0.8538 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 39 GLU cc_start: 0.9082 (tt0) cc_final: 0.8853 (tt0) REVERT: A 42 ASN cc_start: 0.9371 (m110) cc_final: 0.8797 (m110) REVERT: A 43 ARG cc_start: 0.8693 (tmm-80) cc_final: 0.8394 (ttp80) REVERT: A 55 ASP cc_start: 0.8262 (t0) cc_final: 0.7836 (t0) REVERT: A 59 ASP cc_start: 0.8920 (m-30) cc_final: 0.8458 (m-30) REVERT: A 152 ARG cc_start: 0.9171 (ttp80) cc_final: 0.8790 (ttp80) REVERT: A 164 ARG cc_start: 0.8989 (tpt-90) cc_final: 0.8717 (tpt-90) REVERT: A 170 ASP cc_start: 0.9016 (t70) cc_final: 0.8768 (t70) REVERT: B 22 GLU cc_start: 0.8486 (tt0) cc_final: 0.7532 (tp30) REVERT: B 38 ASP cc_start: 0.8897 (m-30) cc_final: 0.8316 (m-30) REVERT: B 42 ASN cc_start: 0.9440 (m110) cc_final: 0.8831 (m110) REVERT: B 43 ARG cc_start: 0.8738 (tmm-80) cc_final: 0.8276 (ttp-110) REVERT: B 47 GLN cc_start: 0.9468 (mt0) cc_final: 0.9250 (mt0) REVERT: B 55 ASP cc_start: 0.8308 (t70) cc_final: 0.7661 (t0) REVERT: B 58 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8245 (ttmm) REVERT: B 170 ASP cc_start: 0.9074 (t70) cc_final: 0.8717 (t70) REVERT: C 38 ASP cc_start: 0.9009 (m-30) cc_final: 0.8600 (m-30) REVERT: C 42 ASN cc_start: 0.9357 (m110) cc_final: 0.8976 (m110) REVERT: C 55 ASP cc_start: 0.8169 (t70) cc_final: 0.7671 (t0) REVERT: C 139 GLN cc_start: 0.9073 (mt0) cc_final: 0.8764 (mt0) REVERT: D 18 ASP cc_start: 0.8907 (m-30) cc_final: 0.8682 (m-30) REVERT: D 38 ASP cc_start: 0.9016 (m-30) cc_final: 0.8648 (m-30) REVERT: D 42 ASN cc_start: 0.9420 (m110) cc_final: 0.8988 (m110) REVERT: D 55 ASP cc_start: 0.8322 (t70) cc_final: 0.7977 (t0) REVERT: D 59 ASP cc_start: 0.8942 (m-30) cc_final: 0.8583 (m-30) REVERT: E 17 THR cc_start: 0.8683 (p) cc_final: 0.8425 (t) REVERT: E 22 GLU cc_start: 0.8884 (tt0) cc_final: 0.8043 (tm-30) REVERT: E 42 ASN cc_start: 0.9172 (m110) cc_final: 0.8753 (m110) REVERT: E 55 ASP cc_start: 0.8348 (t70) cc_final: 0.7700 (t0) REVERT: E 58 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8586 (mtpp) REVERT: E 59 ASP cc_start: 0.8925 (m-30) cc_final: 0.8392 (m-30) REVERT: E 104 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9087 (tp) REVERT: E 111 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8911 (mttt) REVERT: E 135 ASP cc_start: 0.8947 (m-30) cc_final: 0.8460 (m-30) REVERT: E 152 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8844 (ttp80) REVERT: E 170 ASP cc_start: 0.8923 (t70) cc_final: 0.8528 (t0) REVERT: F 38 ASP cc_start: 0.8832 (m-30) cc_final: 0.8457 (m-30) REVERT: F 42 ASN cc_start: 0.9373 (m110) cc_final: 0.9058 (m110) REVERT: F 58 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8821 (mtmm) REVERT: F 59 ASP cc_start: 0.9081 (m-30) cc_final: 0.8756 (m-30) REVERT: G 42 ILE cc_start: 0.9366 (mt) cc_final: 0.9139 (mm) REVERT: G 50 ASP cc_start: 0.8795 (m-30) cc_final: 0.8416 (m-30) REVERT: G 71 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (m-30) REVERT: G 192 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8702 (mm-30) REVERT: H 23 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8848 (mtp85) REVERT: H 38 ASP cc_start: 0.8874 (m-30) cc_final: 0.8383 (m-30) REVERT: H 42 ASN cc_start: 0.9375 (m110) cc_final: 0.8913 (m110) REVERT: H 55 ASP cc_start: 0.8151 (t70) cc_final: 0.7578 (t0) REVERT: H 58 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8553 (ttmm) REVERT: H 59 ASP cc_start: 0.8953 (m-30) cc_final: 0.8395 (m-30) REVERT: H 135 ASP cc_start: 0.8842 (m-30) cc_final: 0.8417 (m-30) REVERT: H 152 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8657 (ttp80) REVERT: H 170 ASP cc_start: 0.9097 (t70) cc_final: 0.8781 (t0) REVERT: H 182 GLU cc_start: 0.9139 (tp30) cc_final: 0.8916 (tp30) REVERT: I 31 ASN cc_start: 0.8492 (t0) cc_final: 0.8227 (t160) REVERT: I 34 ASN cc_start: 0.8400 (m110) cc_final: 0.7865 (m110) REVERT: I 50 ASP cc_start: 0.8977 (m-30) cc_final: 0.8568 (m-30) REVERT: I 59 GLN cc_start: 0.9077 (mt0) cc_final: 0.8625 (mt0) REVERT: I 160 MET cc_start: 0.9229 (mtt) cc_final: 0.8993 (mtm) REVERT: J 34 ASN cc_start: 0.8412 (m110) cc_final: 0.8136 (m110) REVERT: J 54 ASN cc_start: 0.9052 (m-40) cc_final: 0.8823 (m110) REVERT: J 138 SER cc_start: 0.8948 (p) cc_final: 0.8707 (m) REVERT: K 34 ASN cc_start: 0.8334 (m110) cc_final: 0.7741 (m110) REVERT: K 38 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8246 (mm-30) REVERT: K 47 GLN cc_start: 0.8580 (tp40) cc_final: 0.8277 (tp40) REVERT: K 50 ASP cc_start: 0.8947 (m-30) cc_final: 0.8532 (m-30) REVERT: K 52 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9251 (p) REVERT: K 54 ASN cc_start: 0.9102 (m-40) cc_final: 0.8892 (m110) REVERT: L 34 ASN cc_start: 0.8428 (m110) cc_final: 0.8158 (m110) REVERT: L 50 ASP cc_start: 0.8869 (m-30) cc_final: 0.8584 (m-30) REVERT: M 54 ASN cc_start: 0.9275 (m-40) cc_final: 0.8974 (m110) REVERT: M 138 SER cc_start: 0.8992 (p) cc_final: 0.8596 (m) REVERT: M 202 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9074 (p) REVERT: M 205 GLU cc_start: 0.7818 (pp20) cc_final: 0.7482 (pp20) REVERT: N 71 ASP cc_start: 0.9052 (m-30) cc_final: 0.8754 (m-30) REVERT: N 125 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8893 (mtm) REVERT: N 151 GLU cc_start: 0.8952 (tt0) cc_final: 0.8267 (tp30) outliers start: 73 outliers final: 31 residues processed: 666 average time/residue: 1.4103 time to fit residues: 1048.2565 Evaluate side-chains 660 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 622 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 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 58 LYS Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain G residue 47 GLN 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 143 ILE Chi-restraints excluded: chain G residue 207 ARG 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 85 SER Chi-restraints excluded: chain I residue 86 LEU 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 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 143 ILE Chi-restraints excluded: chain M residue 202 THR 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 227 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN G 54 ASN G 101 GLN G 144 GLN I 54 ASN I 136 GLN J 144 GLN K 101 GLN ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 ASN N 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.060370 restraints weight = 34230.941| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.21 r_work: 0.2524 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 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 : 0.006 0.053 19859 Z= 0.265 Angle : 0.666 10.292 26824 Z= 0.310 Chirality : 0.045 0.275 3087 Planarity : 0.003 0.045 3479 Dihedral : 8.029 59.960 2989 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.19 % Allowed : 21.85 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.17), residues: 2478 helix: 1.88 (0.13), residues: 1407 sheet: -1.59 (0.36), residues: 182 loop : -0.89 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 174 HIS 0.004 0.001 HIS E 117 PHE 0.008 0.001 PHE D 102 TYR 0.019 0.001 TYR C 113 ARG 0.010 0.001 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1176) hydrogen bonds : angle 3.88895 ( 3789) covalent geometry : bond 0.00584 (19845) covalent geometry : angle 0.66588 (26824) Misc. bond : bond 0.00188 ( 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 688 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 624 time to evaluate : 2.189 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: 0.8601 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 42 ASN cc_start: 0.9350 (m110) cc_final: 0.8828 (m110) REVERT: A 55 ASP cc_start: 0.8288 (t0) cc_final: 0.7778 (t0) REVERT: A 59 ASP cc_start: 0.8898 (m-30) cc_final: 0.8440 (m-30) REVERT: A 170 ASP cc_start: 0.9028 (t70) cc_final: 0.8822 (t70) REVERT: B 22 GLU cc_start: 0.8496 (tt0) cc_final: 0.7658 (tp30) REVERT: B 38 ASP cc_start: 0.8953 (m-30) cc_final: 0.8159 (m-30) REVERT: B 42 ASN cc_start: 0.9456 (m110) cc_final: 0.8891 (m110) REVERT: B 43 ARG cc_start: 0.8766 (tmm-80) cc_final: 0.8418 (ttp-110) REVERT: B 55 ASP cc_start: 0.8374 (t70) cc_final: 0.7786 (t0) REVERT: B 58 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8342 (ttmm) REVERT: B 170 ASP cc_start: 0.9065 (t70) cc_final: 0.8753 (t70) REVERT: C 38 ASP cc_start: 0.9054 (m-30) cc_final: 0.8680 (m-30) REVERT: C 42 ASN cc_start: 0.9360 (m110) cc_final: 0.9005 (m110) REVERT: C 55 ASP cc_start: 0.8226 (t70) cc_final: 0.7735 (t0) REVERT: C 139 GLN cc_start: 0.9130 (mt0) cc_final: 0.8894 (mt0) REVERT: C 164 ARG cc_start: 0.9111 (tpt-90) cc_final: 0.8737 (tpt-90) REVERT: C 168 ASP cc_start: 0.9239 (m-30) cc_final: 0.8918 (m-30) REVERT: D 18 ASP cc_start: 0.8956 (m-30) cc_final: 0.8749 (m-30) REVERT: D 38 ASP cc_start: 0.9037 (m-30) cc_final: 0.8724 (m-30) REVERT: D 42 ASN cc_start: 0.9415 (m110) cc_final: 0.8974 (m110) REVERT: D 55 ASP cc_start: 0.8346 (t70) cc_final: 0.7951 (t0) REVERT: E 17 THR cc_start: 0.8788 (p) cc_final: 0.8515 (t) REVERT: E 42 ASN cc_start: 0.9184 (m110) cc_final: 0.8845 (m110) REVERT: E 55 ASP cc_start: 0.8416 (t70) cc_final: 0.7767 (t0) REVERT: E 58 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8617 (mtpp) REVERT: E 59 ASP cc_start: 0.8946 (m-30) cc_final: 0.8374 (m-30) REVERT: E 104 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9011 (tp) REVERT: E 111 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8953 (mttt) REVERT: E 135 ASP cc_start: 0.8958 (m-30) cc_final: 0.8487 (m-30) REVERT: E 170 ASP cc_start: 0.8946 (t70) cc_final: 0.8618 (t0) REVERT: F 38 ASP cc_start: 0.8883 (m-30) cc_final: 0.8524 (m-30) REVERT: F 42 ASN cc_start: 0.9388 (m110) cc_final: 0.9112 (m110) REVERT: F 59 ASP cc_start: 0.9064 (m-30) cc_final: 0.8543 (m-30) REVERT: F 111 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8962 (mttt) REVERT: G 38 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8416 (mm-30) REVERT: G 42 ILE cc_start: 0.9406 (mt) cc_final: 0.9204 (mm) REVERT: G 50 ASP cc_start: 0.8864 (m-30) cc_final: 0.8526 (m-30) REVERT: G 192 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8745 (mm-30) REVERT: H 23 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8848 (mtp85) REVERT: H 38 ASP cc_start: 0.8927 (m-30) cc_final: 0.8487 (m-30) REVERT: H 42 ASN cc_start: 0.9381 (m110) cc_final: 0.8928 (m110) REVERT: H 55 ASP cc_start: 0.8192 (t70) cc_final: 0.7661 (t0) REVERT: H 58 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8543 (ttmm) REVERT: H 59 ASP cc_start: 0.8954 (m-30) cc_final: 0.8398 (m-30) REVERT: H 135 ASP cc_start: 0.8892 (m-30) cc_final: 0.8480 (m-30) REVERT: H 152 ARG cc_start: 0.9215 (ttp80) cc_final: 0.8872 (ttp80) REVERT: H 170 ASP cc_start: 0.9114 (t70) cc_final: 0.8811 (t0) REVERT: H 182 GLU cc_start: 0.9124 (tp30) cc_final: 0.8886 (tp30) REVERT: I 31 ASN cc_start: 0.8525 (t0) cc_final: 0.8314 (t160) REVERT: I 34 ASN cc_start: 0.8444 (m110) cc_final: 0.7963 (m110) REVERT: I 50 ASP cc_start: 0.8982 (m-30) cc_final: 0.8607 (m-30) REVERT: I 105 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8465 (tp) REVERT: J 34 ASN cc_start: 0.8566 (m110) cc_final: 0.8315 (m110) REVERT: J 207 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7759 (ppt-90) REVERT: K 34 ASN cc_start: 0.8373 (m110) cc_final: 0.7733 (m110) REVERT: K 38 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8308 (mm-30) REVERT: K 47 GLN cc_start: 0.8673 (tp40) cc_final: 0.8447 (tp40) REVERT: K 50 ASP cc_start: 0.8976 (m-30) cc_final: 0.8581 (m-30) REVERT: K 52 SER cc_start: 0.9499 (OUTLIER) cc_final: 0.9280 (p) REVERT: K 54 ASN cc_start: 0.9157 (m-40) cc_final: 0.8949 (m110) REVERT: L 34 ASN cc_start: 0.8476 (m110) cc_final: 0.8247 (m110) REVERT: L 50 ASP cc_start: 0.8947 (m-30) cc_final: 0.8702 (m-30) REVERT: M 54 ASN cc_start: 0.9330 (m-40) cc_final: 0.9067 (m110) REVERT: M 202 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9181 (p) REVERT: M 205 GLU cc_start: 0.7887 (pp20) cc_final: 0.7633 (pp20) REVERT: N 125 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8908 (mtm) REVERT: N 151 GLU cc_start: 0.8984 (tt0) cc_final: 0.8320 (tp30) outliers start: 64 outliers final: 36 residues processed: 646 average time/residue: 1.4288 time to fit residues: 1033.5134 Evaluate side-chains 652 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 609 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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 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 G residue 207 ARG 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 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 138 SER 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 J residue 207 ARG 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 85 SER 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 0 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN G 54 ASN G 101 GLN G 144 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN J 94 GLN J 144 GLN K 101 GLN K 153 GLN ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN 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 = 0.2894 r_free = 0.2894 target = 0.071688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063564 restraints weight = 34226.359| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.21 r_work: 0.2594 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19859 Z= 0.153 Angle : 0.618 9.693 26824 Z= 0.288 Chirality : 0.043 0.248 3087 Planarity : 0.003 0.039 3479 Dihedral : 8.025 59.583 2989 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.38 % Allowed : 21.70 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2478 helix: 1.96 (0.13), residues: 1407 sheet: -1.51 (0.36), residues: 182 loop : -0.83 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 174 HIS 0.004 0.001 HIS D 117 PHE 0.010 0.001 PHE D 102 TYR 0.017 0.001 TYR C 113 ARG 0.009 0.001 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 1176) hydrogen bonds : angle 3.80839 ( 3789) covalent geometry : bond 0.00346 (19845) covalent geometry : angle 0.61785 (26824) Misc. bond : bond 0.00125 ( 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 706 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 638 time to evaluate : 2.295 Fit side-chains 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: 0.8577 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 39 GLU cc_start: 0.9102 (tt0) cc_final: 0.8856 (tt0) REVERT: A 42 ASN cc_start: 0.9355 (m110) cc_final: 0.8701 (m110) REVERT: A 55 ASP cc_start: 0.8345 (t0) cc_final: 0.7914 (t0) REVERT: A 59 ASP cc_start: 0.8909 (m-30) cc_final: 0.8425 (m-30) REVERT: A 152 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8945 (ttp80) REVERT: A 164 ARG cc_start: 0.9009 (tpt-90) cc_final: 0.8665 (tpt-90) REVERT: A 168 ASP cc_start: 0.9009 (m-30) cc_final: 0.8754 (m-30) REVERT: A 170 ASP cc_start: 0.9014 (t70) cc_final: 0.8690 (t70) REVERT: B 22 GLU cc_start: 0.8467 (tt0) cc_final: 0.7619 (tp30) REVERT: B 38 ASP cc_start: 0.8903 (m-30) cc_final: 0.8332 (m-30) REVERT: B 42 ASN cc_start: 0.9451 (m110) cc_final: 0.8852 (m110) REVERT: B 43 ARG cc_start: 0.8788 (tmm-80) cc_final: 0.8314 (ttp-110) REVERT: B 55 ASP cc_start: 0.8391 (t70) cc_final: 0.7753 (t0) REVERT: B 58 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8226 (ttmm) REVERT: B 170 ASP cc_start: 0.9047 (t70) cc_final: 0.8640 (t70) REVERT: C 38 ASP cc_start: 0.9016 (m-30) cc_final: 0.8649 (m-30) REVERT: C 42 ASN cc_start: 0.9350 (m110) cc_final: 0.8975 (m110) REVERT: C 55 ASP cc_start: 0.8282 (t70) cc_final: 0.7731 (t0) REVERT: C 58 LYS cc_start: 0.9095 (mtpt) cc_final: 0.8650 (mtmm) REVERT: C 59 ASP cc_start: 0.9049 (m-30) cc_final: 0.8831 (m-30) REVERT: C 139 GLN cc_start: 0.9112 (mt0) cc_final: 0.8809 (mt0) REVERT: C 152 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8753 (ttp80) REVERT: C 164 ARG cc_start: 0.9139 (tpt-90) cc_final: 0.8708 (tpt-90) REVERT: C 168 ASP cc_start: 0.9257 (m-30) cc_final: 0.8888 (m-30) REVERT: D 18 ASP cc_start: 0.8874 (m-30) cc_final: 0.8618 (m-30) REVERT: D 38 ASP cc_start: 0.8987 (m-30) cc_final: 0.8641 (m-30) REVERT: D 42 ASN cc_start: 0.9425 (m110) cc_final: 0.9005 (m110) REVERT: D 55 ASP cc_start: 0.8393 (t70) cc_final: 0.7939 (t0) REVERT: D 59 ASP cc_start: 0.9088 (m-30) cc_final: 0.8887 (m-30) REVERT: E 17 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8484 (t) REVERT: E 42 ASN cc_start: 0.9183 (m110) cc_final: 0.8784 (m110) REVERT: E 55 ASP cc_start: 0.8441 (t70) cc_final: 0.7798 (t0) REVERT: E 58 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8585 (mtpp) REVERT: E 59 ASP cc_start: 0.8935 (m-30) cc_final: 0.8360 (m-30) REVERT: E 104 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8999 (tp) REVERT: E 109 LYS cc_start: 0.9247 (tppt) cc_final: 0.8954 (mmtp) REVERT: E 111 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8915 (mttt) REVERT: E 135 ASP cc_start: 0.8921 (m-30) cc_final: 0.8453 (m-30) REVERT: E 170 ASP cc_start: 0.8958 (t70) cc_final: 0.8572 (t0) REVERT: F 17 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (t) REVERT: F 38 ASP cc_start: 0.8822 (m-30) cc_final: 0.8491 (m-30) REVERT: F 42 ASN cc_start: 0.9389 (m110) cc_final: 0.9083 (m-40) REVERT: F 59 ASP cc_start: 0.9034 (m-30) cc_final: 0.8494 (m-30) REVERT: F 111 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8894 (mttt) REVERT: G 42 ILE cc_start: 0.9363 (mt) cc_final: 0.9146 (mm) REVERT: G 50 ASP cc_start: 0.8837 (m-30) cc_final: 0.8509 (m-30) REVERT: G 192 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8737 (mm-30) REVERT: H 23 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8836 (mtp85) REVERT: H 38 ASP cc_start: 0.8901 (m-30) cc_final: 0.8408 (m-30) REVERT: H 42 ASN cc_start: 0.9367 (m110) cc_final: 0.8907 (m110) REVERT: H 55 ASP cc_start: 0.8204 (t70) cc_final: 0.7653 (t0) REVERT: H 58 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8523 (ttmm) REVERT: H 59 ASP cc_start: 0.8918 (m-30) cc_final: 0.8534 (m-30) REVERT: H 135 ASP cc_start: 0.8839 (m-30) cc_final: 0.8411 (m-30) REVERT: H 152 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8676 (ttp80) REVERT: H 170 ASP cc_start: 0.9129 (t70) cc_final: 0.8816 (t0) REVERT: H 182 GLU cc_start: 0.9137 (tp30) cc_final: 0.8883 (tp30) REVERT: I 31 ASN cc_start: 0.8531 (t0) cc_final: 0.8289 (t160) REVERT: I 34 ASN cc_start: 0.8446 (m110) cc_final: 0.7942 (m110) REVERT: I 50 ASP cc_start: 0.8950 (m-30) cc_final: 0.8385 (m-30) REVERT: I 59 GLN cc_start: 0.9126 (mt0) cc_final: 0.8666 (mt0) REVERT: I 105 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8601 (tp) REVERT: J 34 ASN cc_start: 0.8501 (m110) cc_final: 0.8215 (m110) REVERT: J 54 ASN cc_start: 0.8945 (m-40) cc_final: 0.8341 (m110) REVERT: J 138 SER cc_start: 0.8987 (p) cc_final: 0.8762 (m) REVERT: K 34 ASN cc_start: 0.8382 (m110) cc_final: 0.7756 (m110) REVERT: K 38 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8276 (mm-30) REVERT: K 47 GLN cc_start: 0.8551 (tp40) cc_final: 0.8301 (tp-100) REVERT: K 50 ASP cc_start: 0.8956 (m-30) cc_final: 0.8543 (m-30) REVERT: K 52 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9303 (p) REVERT: K 54 ASN cc_start: 0.9101 (m-40) cc_final: 0.8882 (m110) REVERT: L 34 ASN cc_start: 0.8480 (m110) cc_final: 0.8220 (m110) REVERT: L 50 ASP cc_start: 0.8894 (m-30) cc_final: 0.8627 (m-30) REVERT: M 47 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: M 54 ASN cc_start: 0.9298 (m-40) cc_final: 0.9047 (m110) REVERT: M 202 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9107 (p) REVERT: M 205 GLU cc_start: 0.7863 (pp20) cc_final: 0.7534 (pp20) REVERT: N 125 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8869 (mtm) REVERT: N 151 GLU cc_start: 0.8965 (tt0) cc_final: 0.8300 (tp30) outliers start: 68 outliers final: 37 residues processed: 670 average time/residue: 1.3879 time to fit residues: 1038.3902 Evaluate side-chains 665 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 619 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 22 GLU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 17 THR 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 G residue 143 ILE Chi-restraints excluded: chain G residue 207 ARG 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 H residue 130 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain J residue 85 SER 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 86 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain M residue 47 GLN 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 52 SER Chi-restraints excluded: chain N residue 85 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 85 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 169 optimal weight: 0.0370 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 47 GLN C 42 ASN G 31 ASN G 34 ASN G 54 ASN G 77 ASN G 101 GLN G 144 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 144 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 136 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.071001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.062824 restraints weight = 34238.879| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.21 r_work: 0.2580 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2448 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19859 Z= 0.190 Angle : 0.649 10.448 26824 Z= 0.303 Chirality : 0.044 0.248 3087 Planarity : 0.003 0.041 3479 Dihedral : 7.914 59.301 2989 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.94 % Allowed : 22.70 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2478 helix: 1.92 (0.13), residues: 1407 sheet: -1.47 (0.37), residues: 182 loop : -0.82 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 174 HIS 0.004 0.001 HIS D 117 PHE 0.011 0.001 PHE D 102 TYR 0.018 0.001 TYR C 113 ARG 0.010 0.001 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 1176) hydrogen bonds : angle 3.83312 ( 3789) covalent geometry : bond 0.00427 (19845) covalent geometry : angle 0.64907 (26824) Misc. bond : bond 0.00144 ( 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 680 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 621 time to evaluate : 3.421 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: symmetry clash REVERT: A 22 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 39 GLU cc_start: 0.9106 (tt0) cc_final: 0.8888 (tt0) REVERT: A 42 ASN cc_start: 0.9347 (m110) cc_final: 0.8796 (m110) REVERT: A 55 ASP cc_start: 0.8367 (t0) cc_final: 0.7921 (t0) REVERT: A 59 ASP cc_start: 0.8892 (m-30) cc_final: 0.8470 (m-30) REVERT: A 152 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8820 (ttp80) REVERT: A 164 ARG cc_start: 0.9003 (tpt-90) cc_final: 0.8752 (tpt-90) REVERT: A 170 ASP cc_start: 0.9009 (t70) cc_final: 0.8787 (t70) REVERT: B 22 GLU cc_start: 0.8447 (tt0) cc_final: 0.7574 (tp30) REVERT: B 38 ASP cc_start: 0.8892 (m-30) cc_final: 0.8312 (m-30) REVERT: B 42 ASN cc_start: 0.9462 (m110) cc_final: 0.8821 (m110) REVERT: B 43 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8323 (ttp-110) REVERT: B 55 ASP cc_start: 0.8415 (t70) cc_final: 0.7748 (t0) REVERT: B 58 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8206 (ttmm) REVERT: B 170 ASP cc_start: 0.8997 (t70) cc_final: 0.8675 (t70) REVERT: C 38 ASP cc_start: 0.9014 (m-30) cc_final: 0.8654 (m-30) REVERT: C 42 ASN cc_start: 0.9379 (m-40) cc_final: 0.9023 (m110) REVERT: C 55 ASP cc_start: 0.8283 (t70) cc_final: 0.7785 (t0) REVERT: C 59 ASP cc_start: 0.9032 (m-30) cc_final: 0.8791 (m-30) REVERT: C 139 GLN cc_start: 0.9130 (mt0) cc_final: 0.8887 (mt0) REVERT: C 152 ARG cc_start: 0.9235 (ttp80) cc_final: 0.8701 (ttp80) REVERT: C 168 ASP cc_start: 0.9250 (m-30) cc_final: 0.8866 (m-30) REVERT: D 18 ASP cc_start: 0.8895 (m-30) cc_final: 0.8641 (m-30) REVERT: D 38 ASP cc_start: 0.8998 (m-30) cc_final: 0.8669 (m-30) REVERT: D 42 ASN cc_start: 0.9427 (m110) cc_final: 0.8990 (m110) REVERT: D 55 ASP cc_start: 0.8413 (t70) cc_final: 0.7965 (t0) REVERT: E 17 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8490 (t) REVERT: E 42 ASN cc_start: 0.9216 (m110) cc_final: 0.8879 (m110) REVERT: E 55 ASP cc_start: 0.8484 (t70) cc_final: 0.7811 (t0) REVERT: E 58 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8579 (mtpp) REVERT: E 59 ASP cc_start: 0.8945 (m-30) cc_final: 0.8368 (m-30) REVERT: E 104 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9014 (tp) REVERT: E 109 LYS cc_start: 0.9257 (tppt) cc_final: 0.8954 (mmtp) REVERT: E 135 ASP cc_start: 0.8954 (m-30) cc_final: 0.8474 (m-30) REVERT: E 170 ASP cc_start: 0.8978 (t70) cc_final: 0.8614 (t0) REVERT: F 17 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8694 (t) REVERT: F 38 ASP cc_start: 0.8830 (m-30) cc_final: 0.8506 (m-30) REVERT: F 42 ASN cc_start: 0.9391 (m110) cc_final: 0.9100 (m-40) REVERT: F 59 ASP cc_start: 0.9034 (m-30) cc_final: 0.8480 (m-30) REVERT: F 111 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8940 (mttt) REVERT: F 135 ASP cc_start: 0.8949 (m-30) cc_final: 0.8425 (m-30) REVERT: G 42 ILE cc_start: 0.9389 (mt) cc_final: 0.9175 (mm) REVERT: G 50 ASP cc_start: 0.8860 (m-30) cc_final: 0.8504 (m-30) REVERT: G 192 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8762 (mm-30) REVERT: H 23 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8831 (mtp85) REVERT: H 35 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: H 38 ASP cc_start: 0.8916 (m-30) cc_final: 0.8435 (m-30) REVERT: H 42 ASN cc_start: 0.9379 (m110) cc_final: 0.8919 (m110) REVERT: H 55 ASP cc_start: 0.8214 (t70) cc_final: 0.7664 (t0) REVERT: H 58 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8496 (ttmm) REVERT: H 59 ASP cc_start: 0.8918 (m-30) cc_final: 0.8576 (m-30) REVERT: H 135 ASP cc_start: 0.8853 (m-30) cc_final: 0.8425 (m-30) REVERT: H 152 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8731 (ttp80) REVERT: H 170 ASP cc_start: 0.9141 (t70) cc_final: 0.8837 (t0) REVERT: H 182 GLU cc_start: 0.9145 (tp30) cc_final: 0.8886 (tp30) REVERT: I 31 ASN cc_start: 0.8551 (t0) cc_final: 0.8315 (t160) REVERT: I 34 ASN cc_start: 0.8469 (m110) cc_final: 0.7968 (m110) REVERT: I 50 ASP cc_start: 0.8903 (m-30) cc_final: 0.8590 (m-30) REVERT: I 59 GLN cc_start: 0.9121 (mt0) cc_final: 0.8723 (mt0) REVERT: I 105 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8652 (tp) REVERT: J 34 ASN cc_start: 0.8460 (m110) cc_final: 0.8197 (m110) REVERT: K 34 ASN cc_start: 0.8379 (m110) cc_final: 0.7713 (m110) REVERT: K 38 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8271 (mm-30) REVERT: K 47 GLN cc_start: 0.8601 (tp40) cc_final: 0.8363 (tp-100) REVERT: K 50 ASP cc_start: 0.8976 (m-30) cc_final: 0.8579 (m-30) REVERT: K 52 SER cc_start: 0.9516 (OUTLIER) cc_final: 0.9303 (p) REVERT: L 34 ASN cc_start: 0.8455 (m110) cc_final: 0.8195 (m110) REVERT: L 50 ASP cc_start: 0.8913 (m-30) cc_final: 0.8660 (m-30) REVERT: M 47 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: M 54 ASN cc_start: 0.9305 (m-40) cc_final: 0.9055 (m110) REVERT: M 123 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8874 (mttt) REVERT: M 202 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9118 (p) REVERT: M 205 GLU cc_start: 0.7858 (pp20) cc_final: 0.7547 (pp20) REVERT: N 125 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8873 (mtm) REVERT: N 151 GLU cc_start: 0.8965 (tt0) cc_final: 0.8305 (tp30) outliers start: 59 outliers final: 42 residues processed: 642 average time/residue: 1.9651 time to fit residues: 1410.3772 Evaluate side-chains 662 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 610 time to evaluate : 3.414 ------------------------------------------------------------------------------- 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 17 THR 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 22 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 129 VAL 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 G residue 143 ILE Chi-restraints excluded: chain G residue 207 ARG Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 86 CYS Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 125 MET Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 85 SER 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 K residue 153 GLN 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 47 GLN 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 52 SER Chi-restraints excluded: chain N residue 85 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 132 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN 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 K 54 ASN K 101 GLN ** K 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 153 GLN ** M 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 54 ASN N 101 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.072986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.064860 restraints weight = 34184.686| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.22 r_work: 0.2620 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 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 : 0.003 0.042 19859 Z= 0.146 Angle : 0.635 15.579 26824 Z= 0.298 Chirality : 0.043 0.240 3087 Planarity : 0.003 0.047 3479 Dihedral : 7.892 59.544 2989 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.79 % Allowed : 23.15 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2478 helix: 1.93 (0.13), residues: 1407 sheet: -1.44 (0.37), residues: 182 loop : -0.81 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 174 HIS 0.004 0.001 HIS D 117 PHE 0.012 0.001 PHE D 102 TYR 0.019 0.001 TYR C 113 ARG 0.011 0.001 ARG E 164 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1176) hydrogen bonds : angle 3.81680 ( 3789) covalent geometry : bond 0.00331 (19845) covalent geometry : angle 0.63526 (26824) Misc. bond : bond 0.00118 ( 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 680 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 624 time to evaluate : 2.091 Fit side-chains 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: symmetry clash REVERT: A 22 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 39 GLU cc_start: 0.9078 (tt0) cc_final: 0.8854 (tt0) REVERT: A 42 ASN cc_start: 0.9365 (m110) cc_final: 0.8863 (m110) REVERT: A 55 ASP cc_start: 0.8320 (t0) cc_final: 0.7916 (t0) REVERT: A 59 ASP cc_start: 0.8887 (m-30) cc_final: 0.8493 (m-30) REVERT: A 152 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8820 (ttp80) REVERT: A 164 ARG cc_start: 0.8981 (tpt-90) cc_final: 0.8743 (tpt-90) REVERT: A 170 ASP cc_start: 0.9049 (t70) cc_final: 0.8754 (t70) REVERT: B 22 GLU cc_start: 0.8427 (tt0) cc_final: 0.7532 (tp30) REVERT: B 38 ASP cc_start: 0.8857 (m-30) cc_final: 0.8197 (m-30) REVERT: B 42 ASN cc_start: 0.9453 (m110) cc_final: 0.8913 (m110) REVERT: B 43 ARG cc_start: 0.8780 (tmm-80) cc_final: 0.8231 (ttp-110) REVERT: B 47 GLN cc_start: 0.9312 (mt0) cc_final: 0.9063 (mt0) REVERT: B 55 ASP cc_start: 0.8437 (t70) cc_final: 0.7791 (t0) REVERT: B 58 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8188 (ttmm) REVERT: B 170 ASP cc_start: 0.9002 (t70) cc_final: 0.8736 (t0) REVERT: C 38 ASP cc_start: 0.9000 (m-30) cc_final: 0.8629 (m-30) REVERT: C 42 ASN cc_start: 0.9394 (m-40) cc_final: 0.9049 (m110) REVERT: C 55 ASP cc_start: 0.8297 (t70) cc_final: 0.7739 (t0) REVERT: C 58 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8620 (mtmm) REVERT: C 59 ASP cc_start: 0.9023 (m-30) cc_final: 0.8763 (m-30) REVERT: C 139 GLN cc_start: 0.9122 (mt0) cc_final: 0.8829 (mt0) REVERT: C 152 ARG cc_start: 0.9239 (ttp80) cc_final: 0.8753 (ttp80) REVERT: C 164 ARG cc_start: 0.9137 (tpt-90) cc_final: 0.8737 (tpt-90) REVERT: C 168 ASP cc_start: 0.9260 (m-30) cc_final: 0.8921 (m-30) REVERT: D 18 ASP cc_start: 0.8863 (m-30) cc_final: 0.8616 (m-30) REVERT: D 38 ASP cc_start: 0.8973 (m-30) cc_final: 0.8613 (m-30) REVERT: D 42 ASN cc_start: 0.9432 (m110) cc_final: 0.9003 (m110) REVERT: D 55 ASP cc_start: 0.8428 (t70) cc_final: 0.7991 (t0) REVERT: E 17 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8480 (t) REVERT: E 42 ASN cc_start: 0.9190 (m110) cc_final: 0.8804 (m110) REVERT: E 55 ASP cc_start: 0.8475 (t70) cc_final: 0.7801 (t0) REVERT: E 58 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8547 (mtpp) REVERT: E 59 ASP cc_start: 0.8824 (m-30) cc_final: 0.8445 (m-30) REVERT: E 104 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9116 (tp) REVERT: E 109 LYS cc_start: 0.9225 (tppt) cc_final: 0.8958 (mmtp) REVERT: E 135 ASP cc_start: 0.8922 (m-30) cc_final: 0.8454 (m-30) REVERT: E 152 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8576 (ttp80) REVERT: E 170 ASP cc_start: 0.8963 (t70) cc_final: 0.8562 (t0) REVERT: F 17 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (t) REVERT: F 38 ASP cc_start: 0.8817 (m-30) cc_final: 0.8505 (m-30) REVERT: F 42 ASN cc_start: 0.9383 (m110) cc_final: 0.9076 (m-40) REVERT: F 43 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8556 (ttp80) REVERT: F 58 LYS cc_start: 0.9057 (mtmm) cc_final: 0.8470 (mttm) REVERT: F 59 ASP cc_start: 0.9017 (m-30) cc_final: 0.8705 (m-30) REVERT: G 42 ILE cc_start: 0.9346 (mt) cc_final: 0.9133 (mm) REVERT: G 50 ASP cc_start: 0.8846 (m-30) cc_final: 0.8500 (m-30) REVERT: G 192 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8745 (mm-30) REVERT: H 23 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8801 (mtp85) REVERT: H 38 ASP cc_start: 0.8888 (m-30) cc_final: 0.8396 (m-30) REVERT: H 42 ASN cc_start: 0.9376 (m110) cc_final: 0.8924 (m110) REVERT: H 55 ASP cc_start: 0.8214 (t70) cc_final: 0.7625 (t0) REVERT: H 58 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8486 (ttmm) REVERT: H 59 ASP cc_start: 0.8898 (m-30) cc_final: 0.8562 (m-30) REVERT: H 135 ASP cc_start: 0.8809 (m-30) cc_final: 0.8399 (m-30) REVERT: H 152 ARG cc_start: 0.9173 (ttp80) cc_final: 0.8802 (ttp80) REVERT: H 170 ASP cc_start: 0.9155 (t70) cc_final: 0.8845 (t0) REVERT: H 182 GLU cc_start: 0.9144 (tp30) cc_final: 0.8881 (tp30) REVERT: I 31 ASN cc_start: 0.8550 (t0) cc_final: 0.8305 (t160) REVERT: I 34 ASN cc_start: 0.8450 (m110) cc_final: 0.7937 (m110) REVERT: J 34 ASN cc_start: 0.8451 (m110) cc_final: 0.8168 (m110) REVERT: J 138 SER cc_start: 0.8988 (p) cc_final: 0.8753 (m) REVERT: J 181 LYS cc_start: 0.9365 (ttmm) cc_final: 0.9058 (mtpt) REVERT: J 195 LYS cc_start: 0.9124 (tttp) cc_final: 0.8884 (tttp) REVERT: K 34 ASN cc_start: 0.8381 (m110) cc_final: 0.7713 (m110) REVERT: K 38 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8274 (mm-30) REVERT: K 47 GLN cc_start: 0.8542 (tp40) cc_final: 0.8308 (tp-100) REVERT: K 50 ASP cc_start: 0.8928 (m-30) cc_final: 0.8576 (m-30) REVERT: K 57 MET cc_start: 0.9036 (mtp) cc_final: 0.8824 (mtt) REVERT: L 34 ASN cc_start: 0.8461 (m110) cc_final: 0.8203 (m110) REVERT: L 50 ASP cc_start: 0.8894 (m-30) cc_final: 0.8645 (m-30) REVERT: M 54 ASN cc_start: 0.9268 (m-40) cc_final: 0.9064 (m110) REVERT: M 202 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9108 (p) REVERT: M 205 GLU cc_start: 0.7800 (pp20) cc_final: 0.7524 (pp20) REVERT: N 151 GLU cc_start: 0.8958 (tt0) cc_final: 0.8289 (tp30) outliers start: 56 outliers final: 39 residues processed: 645 average time/residue: 1.6185 time to fit residues: 1172.0813 Evaluate side-chains 657 residues out of total 2009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 613 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 17 THR 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 C residue 191 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 129 VAL 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 143 ILE Chi-restraints excluded: chain G residue 207 ARG 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 H residue 130 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 85 SER 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 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 202 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 138 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 117 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN J 101 GLN J 144 GLN K 54 ASN ** L 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 = 0.2927 r_free = 0.2927 target = 0.073375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.065213 restraints weight = 34294.340| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.23 r_work: 0.2630 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19859 Z= 0.149 Angle : 0.630 10.955 26824 Z= 0.297 Chirality : 0.043 0.233 3087 Planarity : 0.003 0.042 3479 Dihedral : 7.748 59.675 2989 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.49 % Allowed : 23.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2478 helix: 1.94 (0.13), residues: 1407 sheet: -1.39 (0.37), residues: 182 loop : -0.80 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 174 HIS 0.003 0.001 HIS D 117 PHE 0.012 0.001 PHE D 102 TYR 0.020 0.001 TYR C 113 ARG 0.010 0.001 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 1176) hydrogen bonds : angle 3.80830 ( 3789) covalent geometry : bond 0.00340 (19845) covalent geometry : angle 0.63048 (26824) Misc. bond : bond 0.00125 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19950.66 seconds wall clock time: 350 minutes 58.98 seconds (21058.98 seconds total)