Starting phenix.real_space_refine on Sat Sep 12 22:27:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.map" model { file = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vgq_21199/09_2026/6vgq_21199.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.336 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: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 12194 2.51 5 N 3290 2.21 5 O 3745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19348 Number of models: 1 Model: "" Number of chains: 4 Chain: "N" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "A" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1383 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "U" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'0QE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Restraints were copied for chains: H, I, J, K, L, M, B, C, D, E, F, G, O, P, Q, R, S, T Time building chain proxies: 2.44, per 1000 atoms: 0.13 Number of scatterers: 19348 At special positions: 0 Unit cell: (112.36, 114.48, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 3745 8.00 N 3290 7.00 C 12194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 657.3 milliseconds 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4690 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 53.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'N' and resid 15 through 26 Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 132 through 159 Processing helix chain 'N' and resid 161 through 169 Processing helix chain 'N' and resid 177 through 184 Processing helix chain 'H' and resid 16 through 26 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 177 through 184 Processing helix chain 'I' and resid 16 through 26 Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 132 through 159 Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 177 through 184 Processing helix chain 'J' and resid 16 through 26 Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 132 through 159 Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 177 through 184 Processing helix chain 'K' and resid 16 through 26 Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 132 through 159 Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 177 through 184 Processing helix chain 'L' and resid 16 through 26 Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 132 through 159 Processing helix chain 'L' and resid 161 through 169 Processing helix chain 'L' and resid 177 through 184 Processing helix chain 'M' and resid 16 through 26 Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 132 through 159 Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 177 through 184 Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 147 through 173 removed outlier: 3.677A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 49 through 67 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 147 through 173 removed outlier: 3.677A pdb=" N ILE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 49 through 67 Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 147 through 173 removed outlier: 3.678A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 49 through 67 Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 147 through 173 removed outlier: 3.677A pdb=" N ILE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 183 Processing helix chain 'D' and resid 191 through 197 Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 49 through 67 Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 147 through 173 removed outlier: 3.678A pdb=" N ILE E 152 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 191 through 197 Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 49 through 67 Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 147 through 173 removed outlier: 3.677A pdb=" N ILE F 152 " --> pdb=" O SER F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 183 Processing helix chain 'F' and resid 191 through 197 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 Processing helix chain 'G' and resid 147 through 173 removed outlier: 3.678A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 191 through 197 Processing sheet with id=AA1, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.321A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.321A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 126 through 129 Processing sheet with id=AA4, first strand: chain 'H' and resid 29 through 32 removed outlier: 5.323A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 32 removed outlier: 5.323A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 126 through 129 Processing sheet with id=AA7, first strand: chain 'I' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 126 through 129 Processing sheet with id=AB1, first strand: chain 'J' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR J 90 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 126 through 129 Processing sheet with id=AB4, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 126 through 129 Processing sheet with id=AB7, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.321A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 29 through 32 removed outlier: 5.321A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TYR L 113 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR L 90 " --> pdb=" O TYR L 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 126 through 129 Processing sheet with id=AC1, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 29 through 32 removed outlier: 5.322A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 126 through 129 Processing sheet with id=AC4, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 131 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 106 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU A 133 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET A 125 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR A 102 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.226A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.226A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.226A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG E 131 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY E 106 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU E 133 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA E 108 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.226A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET E 125 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR E 102 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.227A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) 1338 hydrogen bonds defined for protein. 3888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6538 1.34 - 1.46: 3863 1.46 - 1.58: 8996 1.58 - 1.70: 0 1.70 - 1.81: 217 Bond restraints: 19614 Sorted by residual: bond pdb=" C PHE O 3 " pdb=" O PHE O 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C PHE P 3 " pdb=" O PHE P 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C PHE U 3 " pdb=" O PHE U 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" C PHE T 3 " pdb=" O PHE T 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C PHE Q 3 " pdb=" O PHE Q 3 " ideal model delta sigma weight residual 1.231 1.429 -0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 19609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 26280 3.22 - 6.43: 180 6.43 - 9.65: 35 9.65 - 12.87: 6 12.87 - 16.08: 8 Bond angle restraints: 26509 Sorted by residual: angle pdb=" CA PHE S 3 " pdb=" C PHE S 3 " pdb=" O PHE S 3 " ideal model delta sigma weight residual 120.80 104.72 16.08 1.70e+00 3.46e-01 8.95e+01 angle pdb=" CA PHE O 3 " pdb=" C PHE O 3 " pdb=" O PHE O 3 " ideal model delta sigma weight residual 120.80 104.72 16.08 1.70e+00 3.46e-01 8.94e+01 angle pdb=" CA PHE P 3 " pdb=" C PHE P 3 " pdb=" O PHE P 3 " ideal model delta sigma weight residual 120.80 104.73 16.07 1.70e+00 3.46e-01 8.93e+01 angle pdb=" CA PHE Q 3 " pdb=" C PHE Q 3 " pdb=" O PHE Q 3 " ideal model delta sigma weight residual 120.80 104.74 16.06 1.70e+00 3.46e-01 8.93e+01 angle pdb=" CA PHE T 3 " pdb=" C PHE T 3 " pdb=" O PHE T 3 " ideal model delta sigma weight residual 120.80 104.75 16.05 1.70e+00 3.46e-01 8.92e+01 ... (remaining 26504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 11361 14.28 - 28.57: 448 28.57 - 42.85: 77 42.85 - 57.13: 35 57.13 - 71.41: 28 Dihedral angle restraints: 11949 sinusoidal: 4669 harmonic: 7280 Sorted by residual: dihedral pdb=" CA MET J 99 " pdb=" C MET J 99 " pdb=" N GLY J 100 " pdb=" CA GLY J 100 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA MET I 99 " pdb=" C MET I 99 " pdb=" N GLY I 100 " pdb=" CA GLY I 100 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA MET N 99 " pdb=" C MET N 99 " pdb=" N GLY N 100 " pdb=" CA GLY N 100 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 11946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1869 0.033 - 0.066: 792 0.066 - 0.099: 323 0.099 - 0.132: 62 0.132 - 0.165: 34 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA ILE G 72 " pdb=" N ILE G 72 " pdb=" C ILE G 72 " pdb=" CB ILE G 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ILE E 72 " pdb=" N ILE E 72 " pdb=" C ILE E 72 " pdb=" CB ILE E 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 3077 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 110 " -0.032 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C SER B 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER B 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA B 111 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 110 " -0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C SER C 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER C 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA C 111 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 110 " -0.032 2.00e-02 2.50e+03 6.33e-02 4.00e+01 pdb=" C SER F 110 " 0.110 2.00e-02 2.50e+03 pdb=" O SER F 110 " -0.040 2.00e-02 2.50e+03 pdb=" N ALA F 111 " -0.038 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 14 2.05 - 2.76: 3103 2.76 - 3.47: 27706 3.47 - 4.19: 47873 4.19 - 4.90: 85892 Nonbonded interactions: 164588 Sorted by model distance: nonbonded pdb=" OG SER N 98 " pdb=" C PHE U 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER I 98 " pdb=" C PHE P 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER H 98 " pdb=" C PHE O 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER K 98 " pdb=" C PHE R 3 " model vdw 1.335 3.270 nonbonded pdb=" OG SER M 98 " pdb=" C PHE T 3 " model vdw 1.335 3.270 ... (remaining 164583 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: 0.06 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'U' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.198 19621 Z= 0.294 Angle : 0.882 16.082 26509 Z= 0.526 Chirality : 0.044 0.165 3080 Planarity : 0.005 0.064 3444 Dihedral : 9.856 71.415 7259 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 2485 helix: 0.66 (0.12), residues: 1407 sheet: 2.31 (0.32), residues: 168 loop : -0.04 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.011 0.001 TYR B 33 PHE 0.021 0.002 PHE C 83 TRP 0.002 0.001 TRP N 174 HIS 0.008 0.003 HIS I 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.29 (19614) covalent geometry : angle 0.88243 / 0.53 (26509) hydrogen bonds : bond 0.13384 / 9.05 ( 1212) hydrogen bonds : angle 6.39293 / 4.57 ( 3888) Misc. bond : bond 0.03235 / 1.94 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 70 SER cc_start: 0.9120 (t) cc_final: 0.8886 (m) REVERT: H 55 ASP cc_start: 0.8491 (t0) cc_final: 0.8266 (t0) REVERT: H 70 SER cc_start: 0.8855 (t) cc_final: 0.8587 (m) REVERT: H 168 ASP cc_start: 0.8655 (m-30) cc_final: 0.8429 (m-30) REVERT: I 55 ASP cc_start: 0.8386 (t0) cc_final: 0.8110 (t0) REVERT: I 179 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6597 (mt-10) REVERT: J 55 ASP cc_start: 0.8333 (t0) cc_final: 0.7691 (t0) REVERT: J 75 MET cc_start: 0.9101 (mmp) cc_final: 0.8728 (mmt) REVERT: L 183 TYR cc_start: 0.8778 (t80) cc_final: 0.8318 (t80) REVERT: M 35 GLU cc_start: 0.7897 (tt0) cc_final: 0.7675 (tt0) REVERT: B 184 ASP cc_start: 0.7264 (t70) cc_final: 0.6933 (t0) REVERT: C 184 ASP cc_start: 0.7380 (t70) cc_final: 0.7147 (t0) REVERT: C 206 TYR cc_start: 0.6915 (m-80) cc_final: 0.6597 (m-10) REVERT: D 69 ASP cc_start: 0.7621 (m-30) cc_final: 0.7367 (m-30) REVERT: D 74 MET cc_start: 0.8421 (ttm) cc_final: 0.8201 (ttt) REVERT: D 129 ASN cc_start: 0.8555 (m-40) cc_final: 0.8229 (m110) REVERT: D 184 ASP cc_start: 0.7929 (t70) cc_final: 0.7663 (t0) REVERT: E 87 MET cc_start: 0.8314 (mmm) cc_final: 0.7924 (mmt) REVERT: F 34 ASN cc_start: 0.7889 (m-40) cc_final: 0.7576 (m110) REVERT: F 87 MET cc_start: 0.8493 (mmm) cc_final: 0.7994 (mmt) outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.1198 time to fit residues: 107.1082 Evaluate side-chains 405 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 124 GLN H 160 GLN J 124 GLN J 160 GLN K 160 GLN M 160 GLN A 171 HIS C 101 GLN C 136 GLN D 77 ASN D 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124346 restraints weight = 24049.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128861 restraints weight = 11909.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131831 restraints weight = 7012.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133791 restraints weight = 4568.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135149 restraints weight = 3200.379| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19621 Z= 0.265 Angle : 0.703 9.382 26509 Z= 0.363 Chirality : 0.046 0.180 3080 Planarity : 0.005 0.060 3444 Dihedral : 4.967 25.788 2737 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.37 % Allowed : 8.16 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2485 helix: 1.59 (0.13), residues: 1393 sheet: 2.44 (0.39), residues: 168 loop : -0.59 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 97 TYR 0.018 0.002 TYR G 197 PHE 0.025 0.002 PHE R 3 TRP 0.016 0.002 TRP H 174 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.26 (19614) covalent geometry : angle 0.70332 / 0.36 (26509) hydrogen bonds : bond 0.04349 / 2.95 ( 1212) hydrogen bonds : angle 4.74322 / 3.44 ( 3888) Misc. bond : bond 0.00013 / 0.01 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 445 time to evaluate : 0.655 Fit side-chains REVERT: N 150 MET cc_start: 0.8939 (mmm) cc_final: 0.8724 (mmm) REVERT: N 168 ASP cc_start: 0.8591 (m-30) cc_final: 0.8251 (m-30) REVERT: H 168 ASP cc_start: 0.8650 (m-30) cc_final: 0.8095 (m-30) REVERT: H 182 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8166 (tm-30) REVERT: I 55 ASP cc_start: 0.8325 (t0) cc_final: 0.8055 (t0) REVERT: I 164 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.7629 (mmm-85) REVERT: I 168 ASP cc_start: 0.8680 (m-30) cc_final: 0.7743 (m-30) REVERT: I 179 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7266 (mt-10) REVERT: J 26 SER cc_start: 0.8579 (m) cc_final: 0.8255 (t) REVERT: K 58 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8504 (mtpp) REVERT: K 150 MET cc_start: 0.8728 (mmp) cc_final: 0.8437 (mmt) REVERT: K 169 SER cc_start: 0.9262 (p) cc_final: 0.9009 (t) REVERT: L 113 TYR cc_start: 0.8745 (m-80) cc_final: 0.8503 (m-80) REVERT: L 183 TYR cc_start: 0.9010 (t80) cc_final: 0.8692 (t80) REVERT: M 23 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8107 (mtp180) REVERT: M 183 TYR cc_start: 0.9007 (t80) cc_final: 0.8757 (t80) REVERT: A 38 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7158 (mt-10) REVERT: A 55 ASP cc_start: 0.7974 (m-30) cc_final: 0.7713 (m-30) REVERT: A 60 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 164 MET cc_start: 0.7533 (ttp) cc_final: 0.7171 (ttt) REVERT: A 197 TYR cc_start: 0.8589 (t80) cc_final: 0.8329 (t80) REVERT: B 38 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7193 (mt-10) REVERT: C 146 GLN cc_start: 0.8241 (mt0) cc_final: 0.7852 (mt0) REVERT: F 74 MET cc_start: 0.8245 (ttm) cc_final: 0.8007 (ttp) REVERT: G 37 PHE cc_start: 0.8367 (t80) cc_final: 0.8109 (t80) REVERT: G 209 LEU cc_start: 0.7815 (mt) cc_final: 0.6916 (mp) outliers start: 48 outliers final: 29 residues processed: 477 average time/residue: 0.1280 time to fit residues: 95.1308 Evaluate side-chains 411 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 124 GLN A 171 HIS C 129 ASN G 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127369 restraints weight = 24030.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131785 restraints weight = 12131.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134691 restraints weight = 7186.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136584 restraints weight = 4679.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137912 restraints weight = 3265.563| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19621 Z= 0.145 Angle : 0.546 8.411 26509 Z= 0.280 Chirality : 0.041 0.154 3080 Planarity : 0.004 0.050 3444 Dihedral : 4.492 24.635 2737 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.37 % Favored : 98.35 % Rotamer: Outliers : 1.98 % Allowed : 11.72 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.16), residues: 2485 helix: 2.13 (0.13), residues: 1400 sheet: 2.18 (0.40), residues: 168 loop : -0.51 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 70 TYR 0.011 0.001 TYR H 91 PHE 0.021 0.002 PHE A 83 TRP 0.006 0.001 TRP H 174 HIS 0.002 0.001 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19614) covalent geometry : angle 0.54602 / 0.28 (26509) hydrogen bonds : bond 0.03634 / 2.47 ( 1212) hydrogen bonds : angle 4.28594 / 3.11 ( 3888) Misc. bond : bond 0.00034 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 393 time to evaluate : 0.592 Fit side-chains REVERT: N 168 ASP cc_start: 0.8481 (m-30) cc_final: 0.8224 (m-30) REVERT: H 150 MET cc_start: 0.8967 (mmm) cc_final: 0.8611 (mmt) REVERT: H 168 ASP cc_start: 0.8536 (m-30) cc_final: 0.8286 (m-30) REVERT: I 93 MET cc_start: 0.8425 (ptt) cc_final: 0.8176 (ptm) REVERT: I 164 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.7680 (mmm-85) REVERT: I 168 ASP cc_start: 0.8676 (m-30) cc_final: 0.7933 (m-30) REVERT: J 26 SER cc_start: 0.8481 (m) cc_final: 0.8192 (t) REVERT: K 169 SER cc_start: 0.9174 (p) cc_final: 0.8946 (t) REVERT: L 183 TYR cc_start: 0.8998 (t80) cc_final: 0.8747 (t80) REVERT: A 38 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 57 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: A 60 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8284 (mt) REVERT: A 171 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6869 (m90) REVERT: A 183 THR cc_start: 0.8952 (p) cc_final: 0.8724 (t) REVERT: A 197 TYR cc_start: 0.8614 (t80) cc_final: 0.8390 (t80) REVERT: B 38 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 171 HIS cc_start: 0.7802 (m-70) cc_final: 0.7501 (m-70) REVERT: C 146 GLN cc_start: 0.8407 (mt0) cc_final: 0.8183 (mt0) REVERT: D 164 MET cc_start: 0.7676 (ttp) cc_final: 0.7409 (ttp) REVERT: E 95 TYR cc_start: 0.8769 (t80) cc_final: 0.8556 (t80) REVERT: E 197 TYR cc_start: 0.8832 (t80) cc_final: 0.8551 (t80) REVERT: F 74 MET cc_start: 0.8246 (ttm) cc_final: 0.8006 (ttp) REVERT: F 115 LEU cc_start: 0.8247 (mt) cc_final: 0.7918 (mt) REVERT: G 37 PHE cc_start: 0.8462 (t80) cc_final: 0.8165 (t80) REVERT: G 57 MET cc_start: 0.8629 (mtm) cc_final: 0.8346 (mtm) outliers start: 40 outliers final: 21 residues processed: 417 average time/residue: 0.1215 time to fit residues: 81.1106 Evaluate side-chains 394 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 370 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain G residue 77 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 61 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.1134 > 50:) overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 124 GLN J 124 GLN M 124 GLN B 129 ASN D 129 ASN E 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124832 restraints weight = 24269.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129218 restraints weight = 12222.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132131 restraints weight = 7234.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134060 restraints weight = 4681.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135344 restraints weight = 3257.071| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19621 Z= 0.166 Angle : 0.550 6.966 26509 Z= 0.282 Chirality : 0.042 0.195 3080 Planarity : 0.004 0.052 3444 Dihedral : 4.416 23.122 2737 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.33 % Favored : 98.39 % Rotamer: Outliers : 2.62 % Allowed : 11.62 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.16), residues: 2485 helix: 2.21 (0.13), residues: 1400 sheet: 1.93 (0.40), residues: 168 loop : -0.59 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 70 TYR 0.020 0.001 TYR K 91 PHE 0.021 0.002 PHE F 83 TRP 0.007 0.001 TRP H 174 HIS 0.011 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (19614) covalent geometry : angle 0.55048 / 0.28 (26509) hydrogen bonds : bond 0.03682 / 2.50 ( 1212) hydrogen bonds : angle 4.24095 / 3.08 ( 3888) Misc. bond : bond 0.00035 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 0.631 Fit side-chains REVERT: N 168 ASP cc_start: 0.8521 (m-30) cc_final: 0.8273 (m-30) REVERT: H 168 ASP cc_start: 0.8501 (m-30) cc_final: 0.7975 (m-30) REVERT: H 182 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7962 (tm-30) REVERT: I 168 ASP cc_start: 0.8674 (m-30) cc_final: 0.8435 (m-30) REVERT: J 26 SER cc_start: 0.8532 (m) cc_final: 0.8186 (t) REVERT: K 160 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8281 (mm-40) REVERT: K 169 SER cc_start: 0.9179 (p) cc_final: 0.8975 (t) REVERT: L 182 GLU cc_start: 0.8023 (tp30) cc_final: 0.7723 (tm-30) REVERT: L 183 TYR cc_start: 0.9008 (t80) cc_final: 0.8553 (t80) REVERT: M 156 GLU cc_start: 0.7877 (tt0) cc_final: 0.7627 (tt0) REVERT: A 57 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7736 (mtp) REVERT: A 60 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 38 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 129 ASN cc_start: 0.8811 (m-40) cc_final: 0.8540 (m110) REVERT: E 197 TYR cc_start: 0.8863 (t80) cc_final: 0.8602 (t80) REVERT: F 74 MET cc_start: 0.8326 (ttm) cc_final: 0.8112 (ttp) outliers start: 53 outliers final: 32 residues processed: 415 average time/residue: 0.1219 time to fit residues: 80.4334 Evaluate side-chains 403 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 369 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 10 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 124 GLN M 124 GLN F 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.122490 restraints weight = 24193.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126950 restraints weight = 12070.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129959 restraints weight = 7127.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131909 restraints weight = 4594.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133229 restraints weight = 3192.347| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19621 Z= 0.181 Angle : 0.554 7.022 26509 Z= 0.284 Chirality : 0.042 0.151 3080 Planarity : 0.004 0.045 3444 Dihedral : 4.423 22.446 2737 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.73 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 13.00 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.16), residues: 2485 helix: 2.27 (0.13), residues: 1400 sheet: 1.65 (0.39), residues: 168 loop : -0.71 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 192 TYR 0.017 0.001 TYR K 91 PHE 0.021 0.002 PHE F 83 TRP 0.007 0.001 TRP M 174 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (19614) covalent geometry : angle 0.55398 / 0.28 (26509) hydrogen bonds : bond 0.03718 / 2.51 ( 1212) hydrogen bonds : angle 4.25307 / 3.09 ( 3888) Misc. bond : bond 0.00048 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 386 time to evaluate : 0.728 Fit side-chains REVERT: N 57 SER cc_start: 0.8804 (m) cc_final: 0.8557 (m) REVERT: N 168 ASP cc_start: 0.8526 (m-30) cc_final: 0.8200 (m-30) REVERT: N 179 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7119 (mt-10) REVERT: H 168 ASP cc_start: 0.8535 (m-30) cc_final: 0.7995 (m-30) REVERT: H 182 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7823 (tm-30) REVERT: I 168 ASP cc_start: 0.8691 (m-30) cc_final: 0.8389 (m-30) REVERT: J 26 SER cc_start: 0.8374 (m) cc_final: 0.8092 (t) REVERT: K 160 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8279 (mm-40) REVERT: K 169 SER cc_start: 0.9328 (p) cc_final: 0.9081 (t) REVERT: L 182 GLU cc_start: 0.8074 (tp30) cc_final: 0.7745 (tm-30) REVERT: L 183 TYR cc_start: 0.9001 (t80) cc_final: 0.8491 (t80) REVERT: M 156 GLU cc_start: 0.7972 (tt0) cc_final: 0.7734 (tt0) REVERT: A 57 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: A 125 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7377 (mtt) REVERT: B 164 MET cc_start: 0.7688 (ttp) cc_final: 0.7433 (ttp) REVERT: B 171 HIS cc_start: 0.7861 (m-70) cc_final: 0.7543 (m-70) REVERT: C 38 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 164 MET cc_start: 0.7743 (ttp) cc_final: 0.7435 (ttp) REVERT: E 99 ASP cc_start: 0.7835 (m-30) cc_final: 0.7544 (t70) REVERT: F 74 MET cc_start: 0.8323 (ttm) cc_final: 0.8094 (ttp) REVERT: G 57 MET cc_start: 0.8682 (mtm) cc_final: 0.8333 (mtm) outliers start: 53 outliers final: 34 residues processed: 420 average time/residue: 0.1257 time to fit residues: 83.8681 Evaluate side-chains 410 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 166 GLU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 124 GLN J 124 GLN M 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124382 restraints weight = 24065.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128854 restraints weight = 11948.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131822 restraints weight = 7013.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133721 restraints weight = 4533.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135076 restraints weight = 3147.047| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19621 Z= 0.142 Angle : 0.519 8.698 26509 Z= 0.266 Chirality : 0.041 0.146 3080 Planarity : 0.004 0.041 3444 Dihedral : 4.271 22.139 2737 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.52 % Allowed : 13.64 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2485 helix: 2.40 (0.13), residues: 1400 sheet: 0.64 (0.37), residues: 210 loop : -0.68 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 70 TYR 0.014 0.001 TYR K 91 PHE 0.017 0.001 PHE E 83 TRP 0.005 0.001 TRP L 174 HIS 0.002 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (19614) covalent geometry : angle 0.51855 / 0.27 (26509) hydrogen bonds : bond 0.03423 / 2.32 ( 1212) hydrogen bonds : angle 4.13642 / 3.01 ( 3888) Misc. bond : bond 0.00034 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 405 time to evaluate : 0.742 Fit side-chains REVERT: N 57 SER cc_start: 0.8751 (m) cc_final: 0.8522 (m) REVERT: N 168 ASP cc_start: 0.8519 (m-30) cc_final: 0.8184 (m-30) REVERT: N 179 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7010 (mt-10) REVERT: H 150 MET cc_start: 0.8944 (mmm) cc_final: 0.8690 (mmt) REVERT: H 168 ASP cc_start: 0.8514 (m-30) cc_final: 0.8017 (m-30) REVERT: H 182 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7789 (tm-30) REVERT: I 164 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8393 (mmm-85) REVERT: I 168 ASP cc_start: 0.8762 (m-30) cc_final: 0.8516 (m-30) REVERT: J 23 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8129 (mtp180) REVERT: J 183 TYR cc_start: 0.8828 (t80) cc_final: 0.8436 (t80) REVERT: K 23 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8163 (mtp180) REVERT: K 81 MET cc_start: 0.9092 (mtp) cc_final: 0.8825 (ttm) REVERT: K 160 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8244 (mm-40) REVERT: K 169 SER cc_start: 0.9283 (p) cc_final: 0.9065 (t) REVERT: L 182 GLU cc_start: 0.8073 (tp30) cc_final: 0.7764 (tm-30) REVERT: L 183 TYR cc_start: 0.8988 (t80) cc_final: 0.8464 (t80) REVERT: M 156 GLU cc_start: 0.7994 (tt0) cc_final: 0.7738 (tt0) REVERT: A 57 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: A 125 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7211 (mtt) REVERT: A 160 MET cc_start: 0.6784 (ttt) cc_final: 0.6577 (ttt) REVERT: A 193 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: B 74 MET cc_start: 0.8141 (ttp) cc_final: 0.7892 (ttt) REVERT: B 164 MET cc_start: 0.7554 (ttp) cc_final: 0.7270 (ttp) REVERT: B 171 HIS cc_start: 0.7886 (m-70) cc_final: 0.7568 (m-70) REVERT: C 38 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6926 (mt-10) REVERT: E 99 ASP cc_start: 0.7856 (m-30) cc_final: 0.7543 (t70) REVERT: F 74 MET cc_start: 0.8311 (ttm) cc_final: 0.8060 (ttp) REVERT: F 164 MET cc_start: 0.7796 (ttp) cc_final: 0.7441 (ttp) REVERT: G 164 MET cc_start: 0.7629 (ttp) cc_final: 0.7334 (ttp) outliers start: 51 outliers final: 33 residues processed: 434 average time/residue: 0.1336 time to fit residues: 91.7540 Evaluate side-chains 425 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 389 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 242 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122004 restraints weight = 24364.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126426 restraints weight = 12144.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129341 restraints weight = 7151.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131239 restraints weight = 4649.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.132562 restraints weight = 3240.894| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19621 Z= 0.188 Angle : 0.563 7.938 26509 Z= 0.287 Chirality : 0.042 0.152 3080 Planarity : 0.004 0.043 3444 Dihedral : 4.381 22.453 2737 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.42 % Allowed : 13.94 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.17), residues: 2485 helix: 2.29 (0.13), residues: 1400 sheet: 0.48 (0.36), residues: 210 loop : -0.75 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 164 TYR 0.014 0.001 TYR K 91 PHE 0.018 0.001 PHE D 83 TRP 0.006 0.001 TRP M 174 HIS 0.002 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (19614) covalent geometry : angle 0.56304 / 0.29 (26509) hydrogen bonds : bond 0.03714 / 2.50 ( 1212) hydrogen bonds : angle 4.25401 / 3.10 ( 3888) Misc. bond : bond 0.00049 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 390 time to evaluate : 0.767 Fit side-chains REVERT: N 168 ASP cc_start: 0.8537 (m-30) cc_final: 0.8233 (m-30) REVERT: H 150 MET cc_start: 0.8958 (mmm) cc_final: 0.8607 (mmt) REVERT: H 168 ASP cc_start: 0.8521 (m-30) cc_final: 0.7969 (m-30) REVERT: H 182 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7781 (tm-30) REVERT: I 164 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: I 168 ASP cc_start: 0.8739 (m-30) cc_final: 0.8473 (m-30) REVERT: J 26 SER cc_start: 0.8424 (m) cc_final: 0.8122 (t) REVERT: J 183 TYR cc_start: 0.8862 (t80) cc_final: 0.8560 (t80) REVERT: K 23 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8150 (mtp180) REVERT: K 81 MET cc_start: 0.9102 (mtp) cc_final: 0.8845 (ttm) REVERT: K 169 SER cc_start: 0.9309 (p) cc_final: 0.9076 (t) REVERT: K 187 ASP cc_start: 0.8187 (m-30) cc_final: 0.7938 (m-30) REVERT: L 182 GLU cc_start: 0.8095 (tp30) cc_final: 0.7777 (tm-30) REVERT: L 183 TYR cc_start: 0.9010 (t80) cc_final: 0.8492 (t80) REVERT: M 156 GLU cc_start: 0.7996 (tt0) cc_final: 0.7755 (tt0) REVERT: A 57 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: A 125 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7343 (mtt) REVERT: B 160 MET cc_start: 0.6759 (ttt) cc_final: 0.6439 (ttt) REVERT: B 164 MET cc_start: 0.7693 (ttp) cc_final: 0.7420 (ttp) REVERT: D 164 MET cc_start: 0.7799 (ttp) cc_final: 0.7436 (ttp) REVERT: E 99 ASP cc_start: 0.7830 (m-30) cc_final: 0.7506 (t70) REVERT: F 74 MET cc_start: 0.8366 (ttm) cc_final: 0.8135 (ttp) REVERT: G 57 MET cc_start: 0.8701 (mtm) cc_final: 0.8258 (mtm) outliers start: 49 outliers final: 38 residues processed: 421 average time/residue: 0.1316 time to fit residues: 88.0021 Evaluate side-chains 427 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 102 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 228 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 190 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 124 GLN A 129 ASN E 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128736 restraints weight = 24046.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133163 restraints weight = 12035.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.136083 restraints weight = 7062.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.137963 restraints weight = 4511.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139233 restraints weight = 3091.656| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19621 Z= 0.100 Angle : 0.491 7.559 26509 Z= 0.251 Chirality : 0.040 0.141 3080 Planarity : 0.004 0.039 3444 Dihedral : 4.084 22.401 2737 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.78 % Allowed : 14.68 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.17), residues: 2485 helix: 2.51 (0.14), residues: 1400 sheet: 0.59 (0.36), residues: 210 loop : -0.71 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 70 TYR 0.009 0.001 TYR K 91 PHE 0.013 0.001 PHE D 83 TRP 0.004 0.001 TRP M 174 HIS 0.001 0.000 HIS I 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (19614) covalent geometry : angle 0.49051 / 0.25 (26509) hydrogen bonds : bond 0.03039 / 2.07 ( 1212) hydrogen bonds : angle 3.98130 / 2.90 ( 3888) Misc. bond : bond 0.00018 / 0.01 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 412 time to evaluate : 0.775 Fit side-chains REVERT: N 57 SER cc_start: 0.8772 (m) cc_final: 0.8557 (m) REVERT: N 168 ASP cc_start: 0.8481 (m-30) cc_final: 0.8171 (m-30) REVERT: H 150 MET cc_start: 0.8954 (mmm) cc_final: 0.8654 (mmt) REVERT: H 168 ASP cc_start: 0.8422 (m-30) cc_final: 0.7992 (m-30) REVERT: H 182 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7648 (tm-30) REVERT: I 168 ASP cc_start: 0.8708 (m-30) cc_final: 0.8489 (m-30) REVERT: J 23 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.8132 (mtm180) REVERT: K 23 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8157 (mtp180) REVERT: K 160 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8209 (mm-40) REVERT: L 182 GLU cc_start: 0.8023 (tp30) cc_final: 0.7765 (tm-30) REVERT: L 183 TYR cc_start: 0.8975 (t80) cc_final: 0.8547 (t80) REVERT: M 156 GLU cc_start: 0.7881 (tt0) cc_final: 0.7638 (tt0) REVERT: A 125 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7295 (mtt) REVERT: A 164 MET cc_start: 0.7675 (ttp) cc_final: 0.7393 (ttp) REVERT: B 37 PHE cc_start: 0.8368 (t80) cc_final: 0.8082 (t80) REVERT: B 129 ASN cc_start: 0.8831 (m-40) cc_final: 0.8540 (m110) REVERT: B 153 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6853 (mp10) REVERT: B 164 MET cc_start: 0.7500 (ttp) cc_final: 0.7260 (ttp) REVERT: B 171 HIS cc_start: 0.7972 (m-70) cc_final: 0.7627 (m-70) REVERT: E 99 ASP cc_start: 0.7802 (m-30) cc_final: 0.7571 (t70) REVERT: E 197 TYR cc_start: 0.8872 (t80) cc_final: 0.8651 (t80) REVERT: F 74 MET cc_start: 0.8296 (ttm) cc_final: 0.8072 (ttp) REVERT: F 164 MET cc_start: 0.7778 (ttp) cc_final: 0.7508 (ttp) REVERT: G 57 MET cc_start: 0.8615 (mtm) cc_final: 0.8054 (mtm) REVERT: G 164 MET cc_start: 0.7601 (ttp) cc_final: 0.7349 (ttp) outliers start: 36 outliers final: 23 residues processed: 430 average time/residue: 0.1332 time to fit residues: 90.0944 Evaluate side-chains 419 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 394 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 168 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 126 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 117 HIS J 124 GLN M 42 ASN D 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129344 restraints weight = 23894.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133788 restraints weight = 11948.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136688 restraints weight = 7001.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138545 restraints weight = 4475.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139810 restraints weight = 3076.530| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19621 Z= 0.105 Angle : 0.512 9.362 26509 Z= 0.258 Chirality : 0.040 0.141 3080 Planarity : 0.004 0.040 3444 Dihedral : 4.010 21.419 2737 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.33 % Allowed : 14.68 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2485 helix: 2.53 (0.14), residues: 1400 sheet: 0.65 (0.36), residues: 210 loop : -0.68 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.011 0.001 TYR J 113 PHE 0.013 0.001 PHE D 83 TRP 0.012 0.001 TRP M 174 HIS 0.002 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (19614) covalent geometry : angle 0.51234 / 0.26 (26509) hydrogen bonds : bond 0.03086 / 2.10 ( 1212) hydrogen bonds : angle 3.98370 / 2.90 ( 3888) Misc. bond : bond 0.00014 / 0.01 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 407 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: N 168 ASP cc_start: 0.8453 (m-30) cc_final: 0.8147 (m-30) REVERT: N 179 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6963 (mt-10) REVERT: H 168 ASP cc_start: 0.8419 (m-30) cc_final: 0.7977 (m-30) REVERT: H 182 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7657 (tm-30) REVERT: I 168 ASP cc_start: 0.8723 (m-30) cc_final: 0.8138 (m-30) REVERT: J 23 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8129 (mtp180) REVERT: J 168 ASP cc_start: 0.8526 (m-30) cc_final: 0.7961 (m-30) REVERT: K 23 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8216 (mtp180) REVERT: K 70 SER cc_start: 0.8686 (m) cc_final: 0.8361 (t) REVERT: K 160 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8218 (mm-40) REVERT: L 182 GLU cc_start: 0.8019 (tp30) cc_final: 0.7767 (tm-30) REVERT: L 183 TYR cc_start: 0.8920 (t80) cc_final: 0.8539 (t80) REVERT: M 156 GLU cc_start: 0.7815 (tt0) cc_final: 0.7576 (tt0) REVERT: A 125 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7362 (mtt) REVERT: A 164 MET cc_start: 0.7696 (ttp) cc_final: 0.7436 (ttp) REVERT: A 183 THR cc_start: 0.8834 (t) cc_final: 0.8527 (p) REVERT: B 129 ASN cc_start: 0.8836 (m-40) cc_final: 0.8502 (m110) REVERT: B 153 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: B 164 MET cc_start: 0.7474 (ttp) cc_final: 0.7229 (ttp) REVERT: B 171 HIS cc_start: 0.8018 (m-70) cc_final: 0.7522 (m-70) REVERT: E 37 PHE cc_start: 0.8660 (t80) cc_final: 0.8363 (t80) REVERT: E 197 TYR cc_start: 0.8834 (t80) cc_final: 0.8598 (t80) REVERT: F 87 MET cc_start: 0.8121 (mmm) cc_final: 0.7845 (mmm) REVERT: F 164 MET cc_start: 0.7809 (ttp) cc_final: 0.7478 (ttp) REVERT: G 57 MET cc_start: 0.8633 (mtm) cc_final: 0.8093 (mtm) REVERT: G 164 MET cc_start: 0.7591 (ttp) cc_final: 0.7365 (ttp) outliers start: 27 outliers final: 18 residues processed: 424 average time/residue: 0.1353 time to fit residues: 90.9933 Evaluate side-chains 411 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 391 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 222 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 117 HIS J 124 GLN L 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121395 restraints weight = 24461.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125805 restraints weight = 12138.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128722 restraints weight = 7142.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130614 restraints weight = 4621.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131887 restraints weight = 3213.589| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19621 Z= 0.219 Angle : 0.625 9.768 26509 Z= 0.311 Chirality : 0.043 0.154 3080 Planarity : 0.004 0.045 3444 Dihedral : 4.403 22.455 2737 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.29 % Allowed : 14.88 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.17), residues: 2485 helix: 2.36 (0.13), residues: 1386 sheet: 0.18 (0.36), residues: 217 loop : -0.83 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 70 TYR 0.022 0.002 TYR J 113 PHE 0.023 0.002 PHE F 83 TRP 0.016 0.002 TRP K 174 HIS 0.006 0.001 HIS K 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (19614) covalent geometry : angle 0.62509 / 0.31 (26509) hydrogen bonds : bond 0.03884 / 2.61 ( 1212) hydrogen bonds : angle 4.31189 / 3.13 ( 3888) Misc. bond : bond 0.00061 / 0.04 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 388 time to evaluate : 0.812 Fit side-chains REVERT: N 168 ASP cc_start: 0.8549 (m-30) cc_final: 0.8261 (m-30) REVERT: N 179 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6923 (mt-10) REVERT: H 168 ASP cc_start: 0.8515 (m-30) cc_final: 0.7963 (m-30) REVERT: H 182 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7788 (tm-30) REVERT: I 168 ASP cc_start: 0.8778 (m-30) cc_final: 0.8069 (m-30) REVERT: J 23 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8080 (mtp180) REVERT: J 26 SER cc_start: 0.8440 (m) cc_final: 0.8150 (t) REVERT: J 168 ASP cc_start: 0.8600 (m-30) cc_final: 0.7952 (m-30) REVERT: J 182 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7927 (tm-30) REVERT: K 23 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8075 (mtp180) REVERT: K 160 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8209 (mm-40) REVERT: K 187 ASP cc_start: 0.8205 (m-30) cc_final: 0.7938 (m-30) REVERT: L 182 GLU cc_start: 0.8096 (tp30) cc_final: 0.7796 (tm-30) REVERT: L 183 TYR cc_start: 0.9000 (t80) cc_final: 0.8515 (t80) REVERT: M 156 GLU cc_start: 0.8002 (tt0) cc_final: 0.7751 (tt0) REVERT: A 125 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7314 (mtt) REVERT: B 153 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: B 160 MET cc_start: 0.7185 (tpp) cc_final: 0.6702 (ttt) REVERT: C 70 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7010 (ttt180) REVERT: G 102 THR cc_start: 0.9202 (t) cc_final: 0.8963 (p) outliers start: 26 outliers final: 22 residues processed: 407 average time/residue: 0.1324 time to fit residues: 85.8427 Evaluate side-chains 402 residues out of total 2023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 193 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 36 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 234 optimal weight: 0.0970 chunk 136 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128108 restraints weight = 24048.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132527 restraints weight = 12080.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135432 restraints weight = 7092.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137311 restraints weight = 4538.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138552 restraints weight = 3112.194| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19621 Z= 0.113 Angle : 0.546 10.479 26509 Z= 0.270 Chirality : 0.041 0.164 3080 Planarity : 0.004 0.039 3444 Dihedral : 4.157 22.676 2737 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.29 % Allowed : 15.47 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2485 helix: 2.37 (0.13), residues: 1400 sheet: 0.57 (0.36), residues: 210 loop : -0.79 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 70 TYR 0.012 0.001 TYR J 113 PHE 0.023 0.001 PHE F 83 TRP 0.010 0.001 TRP M 174 HIS 0.004 0.001 HIS K 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (19614) covalent geometry : angle 0.54570 / 0.27 (26509) hydrogen bonds : bond 0.03169 / 2.15 ( 1212) hydrogen bonds : angle 4.06723 / 2.96 ( 3888) Misc. bond : bond 0.00019 / 0.01 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.73 seconds wall clock time: 47 minutes 51.83 seconds (2871.83 seconds total)