Starting phenix.real_space_refine on Sun Aug 24 09:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_21199.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_21199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_21199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_21199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vgq_21199/08_2025/6vgq_21199.map" } 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-2.0-5787/lib/python3.9/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: 2.43, 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.88 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: 4.12 Time building geometry restraints manager: 2.51 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: 0.07 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: 0.470 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.040 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 aren 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 covalent geometry : bond 0.00549 (19614) covalent geometry : angle 0.88243 (26509) hydrogen bonds : bond 0.13384 ( 1212) hydrogen bonds : angle 6.39293 ( 3888) Misc. bond : bond 0.03235 ( 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 : 0.726 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: 0.7923 (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: 0.1377 time to fit residues: 121.7119 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 : 0.759 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7856 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 aren 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 covalent geometry : bond 0.00645 (19614) covalent geometry : angle 0.70332 (26509) hydrogen bonds : bond 0.04349 ( 1212) hydrogen bonds : angle 4.74322 ( 3888) Misc. bond : bond 0.00013 ( 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 : 0.564 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: 0.1232 time to fit residues: 90.8735 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 : 0.598 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7924 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 aren 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 covalent geometry : bond 0.00340 (19614) covalent geometry : angle 0.54602 (26509) hydrogen bonds : bond 0.03634 ( 1212) hydrogen bonds : angle 4.28594 ( 3888) Misc. bond : bond 0.00034 ( 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 : 0.453 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: 0.8677 (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: 0.8345 (mtm) outliers start: 40 outliers final: 21 residues processed: 417 average time/residue: 0.1122 time to fit residues: 74.4959 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 : 0.766 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1134 > 50: distance: 46 - 50: 3.168 distance: 50 - 51: 7.466 distance: 51 - 52: 6.625 distance: 51 - 54: 5.971 distance: 52 - 53: 29.799 distance: 52 - 55: 31.972 distance: 55 - 56: 22.972 distance: 56 - 57: 6.374 distance: 56 - 59: 9.163 distance: 57 - 58: 4.742 distance: 57 - 63: 5.328 distance: 59 - 60: 12.926 distance: 60 - 61: 4.270 distance: 63 - 64: 6.105 distance: 63 - 69: 9.214 distance: 64 - 65: 7.846 distance: 64 - 67: 12.114 distance: 65 - 66: 12.224 distance: 65 - 70: 14.888 distance: 67 - 68: 6.026 distance: 68 - 69: 8.223 distance: 70 - 71: 3.589 distance: 71 - 72: 5.221 distance: 71 - 74: 3.191 distance: 72 - 73: 5.594 distance: 72 - 80: 5.690 distance: 75 - 76: 4.182 distance: 75 - 77: 3.015 distance: 81 - 84: 3.676 distance: 82 - 83: 4.264 distance: 89 - 90: 3.685 distance: 91 - 92: 3.699 distance: 92 - 93: 4.855 distance: 93 - 94: 5.960 distance: 93 - 95: 3.842 distance: 96 - 195: 3.040 distance: 98 - 99: 3.367 distance: 98 - 104: 3.215 distance: 99 - 192: 5.014 distance: 100 - 102: 6.243 distance: 101 - 103: 5.786 distance: 109 - 110: 6.857 distance: 112 - 176: 4.851 distance: 113 - 116: 3.041 distance: 115 - 173: 5.113 distance: 116 - 117: 3.521 distance: 117 - 118: 5.213 distance: 118 - 119: 5.478 distance: 121 - 124: 3.277 distance: 122 - 130: 3.502 distance: 125 - 126: 3.788 distance: 125 - 127: 3.126 distance: 126 - 128: 3.872 distance: 128 - 129: 3.249