Starting phenix.real_space_refine on Sun Aug 24 09:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vgk_21197/08_2025/6vgk_21197.map" } resolution = 3.1 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= 0.014 sd= 0.498 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 12089 2.51 5 N 3276 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 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: 19222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Restraints were copied for chains: B, C, D, E, F, G, I, J, K, L, M, N Time building chain proxies: 2.15, per 1000 atoms: 0.11 Number of scatterers: 19222 At special positions: 0 Unit cell: (117.66, 117.66, 104.94, 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 3738 8.00 N 3276 7.00 C 12089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 723.9 milliseconds Enol-peptide restraints added in 238.4 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: 4676 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 28 sheets defined 52.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 4.170A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 173 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 49 through 67 removed outlier: 4.168A pdb=" N ASP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 173 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 33 through 39 Processing helix chain 'D' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 173 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 33 through 39 Processing helix chain 'E' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 173 Processing helix chain 'E' and resid 175 through 184 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 49 through 67 removed outlier: 4.168A pdb=" N ASP F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 111 through 118 removed outlier: 3.565A pdb=" N LEU F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 173 Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 49 through 67 removed outlier: 4.169A pdb=" N ASP G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 111 through 118 removed outlier: 3.564A pdb=" N LEU G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 173 Processing helix chain 'G' and resid 175 through 184 Processing helix chain 'G' and resid 192 through 197 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 removed outlier: 3.991A pdb=" N ILE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 177 through 183 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 removed outlier: 3.991A pdb=" N ILE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 177 through 183 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 removed outlier: 3.992A pdb=" N ILE J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 183 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 removed outlier: 3.991A pdb=" N ILE K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 170 Processing helix chain 'K' and resid 177 through 183 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 removed outlier: 3.990A pdb=" N ILE L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 170 Processing helix chain 'L' and resid 177 through 183 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 removed outlier: 3.991A pdb=" N ILE M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'N' and resid 16 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 removed outlier: 3.991A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 170 Processing helix chain 'N' and resid 177 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 131 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 106 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 133 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET A 125 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR A 102 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG E 131 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY E 106 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU E 133 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA E 108 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.176A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET E 125 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR E 102 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.175A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY H 94 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA H 96 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET H 122 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG H 173 " --> pdb=" O MET H 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG I 119 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY I 94 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU I 121 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET I 122 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG I 173 " --> pdb=" O MET I 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG J 119 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY J 94 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA J 96 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET J 122 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG J 173 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR J 90 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG K 119 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY K 94 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU K 121 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET K 122 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG K 173 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG L 119 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY L 94 " --> pdb=" O ARG L 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU L 121 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA L 96 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET L 122 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG L 173 " --> pdb=" O MET L 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR L 113 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR L 90 " --> pdb=" O TYR L 113 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG M 119 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY M 94 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU M 121 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA M 96 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET M 122 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG M 173 " --> pdb=" O MET M 122 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 29 through 32 removed outlier: 7.971A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG N 119 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY N 94 " --> pdb=" O ARG N 119 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU N 121 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET N 122 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG N 173 " --> pdb=" O MET N 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 29 through 32 removed outlier: 7.970A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4094 1.32 - 1.45: 5222 1.45 - 1.58: 9934 1.58 - 1.71: 28 1.71 - 1.84: 217 Bond restraints: 19495 Sorted by residual: bond pdb=" CB LEU F 86 " pdb=" CG LEU F 86 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CB LEU C 86 " pdb=" CG LEU C 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CB LEU B 86 " pdb=" CG LEU B 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CB LEU A 86 " pdb=" CG LEU A 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU D 86 " pdb=" CG LEU D 86 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 19490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 26062 5.65 - 11.29: 286 11.29 - 16.93: 7 16.93 - 22.58: 0 22.58 - 28.22: 7 Bond angle restraints: 26362 Sorted by residual: angle pdb=" C MET H 93 " pdb=" N GLY H 94 " pdb=" CA GLY H 94 " ideal model delta sigma weight residual 121.41 149.63 -28.22 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET K 93 " pdb=" N GLY K 94 " pdb=" CA GLY K 94 " ideal model delta sigma weight residual 121.41 149.62 -28.21 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET M 93 " pdb=" N GLY M 94 " pdb=" CA GLY M 94 " ideal model delta sigma weight residual 121.41 149.61 -28.20 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET J 93 " pdb=" N GLY J 94 " pdb=" CA GLY J 94 " ideal model delta sigma weight residual 121.41 149.60 -28.19 1.96e+00 2.60e-01 2.07e+02 angle pdb=" C MET L 93 " pdb=" N GLY L 94 " pdb=" CA GLY L 94 " ideal model delta sigma weight residual 121.41 149.59 -28.18 1.96e+00 2.60e-01 2.07e+02 ... (remaining 26357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.31: 11156 13.31 - 26.63: 541 26.63 - 39.94: 140 39.94 - 53.25: 28 53.25 - 66.56: 42 Dihedral angle restraints: 11907 sinusoidal: 4648 harmonic: 7259 Sorted by residual: dihedral pdb=" CA PRO D 32 " pdb=" C PRO D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -149.78 -30.22 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA PRO E 32 " pdb=" C PRO E 32 " pdb=" N TYR E 33 " pdb=" CA TYR E 33 " ideal model delta harmonic sigma weight residual -180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA PRO G 32 " pdb=" C PRO G 32 " pdb=" N TYR G 33 " pdb=" CA TYR G 33 " ideal model delta harmonic sigma weight residual 180.00 -149.81 -30.19 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 11904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1881 0.068 - 0.136: 830 0.136 - 0.204: 264 0.204 - 0.272: 74 0.272 - 0.341: 17 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CA GLU K 35 " pdb=" N GLU K 35 " pdb=" C GLU K 35 " pdb=" CB GLU K 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU L 35 " pdb=" N GLU L 35 " pdb=" C GLU L 35 " pdb=" CB GLU L 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA GLU I 35 " pdb=" N GLU I 35 " pdb=" C GLU I 35 " pdb=" CB GLU I 35 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3063 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.068 2.00e-02 2.50e+03 1.42e-01 2.02e+02 pdb=" C SER A 110 " -0.246 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.094 2.00e-02 2.50e+03 pdb=" N ALA A 111 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 110 " 0.068 2.00e-02 2.50e+03 1.42e-01 2.01e+02 pdb=" C SER G 110 " -0.245 2.00e-02 2.50e+03 pdb=" O SER G 110 " 0.094 2.00e-02 2.50e+03 pdb=" N ALA G 111 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 110 " -0.068 2.00e-02 2.50e+03 1.42e-01 2.01e+02 pdb=" C SER C 110 " 0.245 2.00e-02 2.50e+03 pdb=" O SER C 110 " -0.094 2.00e-02 2.50e+03 pdb=" N ALA C 111 " -0.083 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7868 2.90 - 3.40: 19209 3.40 - 3.90: 33527 3.90 - 4.40: 40202 4.40 - 4.90: 63297 Nonbonded interactions: 164103 Sorted by model distance: nonbonded pdb=" OE2 GLU E 151 " pdb=" NZ LYS L 147 " model vdw 2.394 3.120 nonbonded pdb=" OE2 GLU F 151 " pdb=" NZ LYS M 147 " model vdw 2.394 3.120 nonbonded pdb=" OE2 GLU B 151 " pdb=" NZ LYS I 147 " model vdw 2.395 3.120 nonbonded pdb=" OE2 GLU D 151 " pdb=" NZ LYS K 147 " model vdw 2.395 3.120 nonbonded pdb=" OE2 GLU A 151 " pdb=" NZ LYS H 147 " model vdw 2.395 3.120 ... (remaining 164098 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.780 Find NCS groups from input model: 0.170 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 : 0.020 0.137 19495 Z= 1.039 Angle : 1.841 28.225 26362 Z= 1.226 Chirality : 0.088 0.341 3066 Planarity : 0.014 0.142 3430 Dihedral : 9.906 66.564 7231 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.38 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.29 (0.15), residues: 2485 helix: -0.49 (0.11), residues: 1386 sheet: 2.64 (0.30), residues: 231 loop : -0.23 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 124 TYR 0.038 0.008 TYR K 183 PHE 0.019 0.004 PHE E 43 TRP 0.017 0.007 TRP J 174 HIS 0.010 0.003 HIS L 123 Details of bonding type rmsd covalent geometry : bond 0.01987 (19495) covalent geometry : angle 1.84060 (26362) hydrogen bonds : bond 0.16645 ( 1092) hydrogen bonds : angle 6.87494 ( 3612) *********************** 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 400 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.6697 (mmmt) cc_final: 0.6487 (tptp) REVERT: B 35 LYS cc_start: 0.6843 (mmmt) cc_final: 0.6364 (tptp) REVERT: C 35 LYS cc_start: 0.6600 (mmmt) cc_final: 0.5992 (tptp) REVERT: C 164 MET cc_start: 0.6174 (ttm) cc_final: 0.5938 (ttt) REVERT: D 35 LYS cc_start: 0.6727 (mmmt) cc_final: 0.5974 (tptp) REVERT: D 136 GLN cc_start: 0.8155 (mt0) cc_final: 0.7822 (mt0) REVERT: E 35 LYS cc_start: 0.6755 (mmmt) cc_final: 0.6157 (tptp) REVERT: F 125 MET cc_start: 0.7738 (mtm) cc_final: 0.7528 (mtt) REVERT: H 70 SER cc_start: 0.8558 (m) cc_final: 0.8156 (p) REVERT: H 75 MET cc_start: 0.7948 (mmt) cc_final: 0.7536 (mmm) REVERT: J 70 SER cc_start: 0.8532 (m) cc_final: 0.8249 (p) REVERT: J 75 MET cc_start: 0.8130 (mmt) cc_final: 0.7766 (mmm) REVERT: K 70 SER cc_start: 0.8507 (m) cc_final: 0.8195 (p) REVERT: K 75 MET cc_start: 0.8010 (mmt) cc_final: 0.7639 (mmt) REVERT: L 70 SER cc_start: 0.8265 (m) cc_final: 0.8003 (p) REVERT: L 75 MET cc_start: 0.8105 (mmt) cc_final: 0.7779 (mmt) REVERT: M 70 SER cc_start: 0.8367 (m) cc_final: 0.8030 (p) REVERT: M 75 MET cc_start: 0.8001 (mmt) cc_final: 0.7600 (mmm) REVERT: N 70 SER cc_start: 0.8468 (m) cc_final: 0.8129 (p) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.1175 time to fit residues: 72.9449 Evaluate side-chains 277 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN D 77 ASN H 123 HIS I 123 HIS J 123 HIS K 123 HIS L 123 HIS M 123 HIS N 123 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.164216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131801 restraints weight = 19785.084| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.02 r_work: 0.3282 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19495 Z= 0.144 Angle : 0.605 7.429 26362 Z= 0.321 Chirality : 0.043 0.139 3066 Planarity : 0.005 0.056 3430 Dihedral : 4.823 26.464 2730 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.79 % Allowed : 4.71 % Favored : 94.49 % 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: 1.11 (0.16), residues: 2485 helix: 1.43 (0.14), residues: 1358 sheet: 1.94 (0.33), residues: 231 loop : -0.64 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 207 TYR 0.014 0.002 TYR C 197 PHE 0.015 0.002 PHE L 185 TRP 0.007 0.001 TRP K 174 HIS 0.004 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00332 (19495) covalent geometry : angle 0.60488 (26362) hydrogen bonds : bond 0.03987 ( 1092) hydrogen bonds : angle 4.72557 ( 3612) *********************** 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 316 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLN cc_start: 0.8414 (mt0) cc_final: 0.7849 (mm-40) REVERT: C 123 LYS cc_start: 0.8242 (mttt) cc_final: 0.7970 (mttp) REVERT: C 160 MET cc_start: 0.6678 (mtt) cc_final: 0.6436 (mtp) REVERT: D 110 SER cc_start: 0.8082 (t) cc_final: 0.7842 (p) REVERT: D 125 MET cc_start: 0.8421 (mtt) cc_final: 0.8209 (mtt) REVERT: D 160 MET cc_start: 0.6655 (mtt) cc_final: 0.6402 (mtp) REVERT: E 123 LYS cc_start: 0.8153 (mttt) cc_final: 0.7812 (mttp) REVERT: E 160 MET cc_start: 0.6606 (mtt) cc_final: 0.6364 (mtp) REVERT: F 110 SER cc_start: 0.7894 (t) cc_final: 0.7512 (m) REVERT: F 160 MET cc_start: 0.6743 (mtt) cc_final: 0.6497 (mtp) REVERT: G 110 SER cc_start: 0.8187 (t) cc_final: 0.7832 (m) REVERT: H 75 MET cc_start: 0.8589 (mmt) cc_final: 0.8274 (tpp) REVERT: I 75 MET cc_start: 0.8254 (mmm) cc_final: 0.7729 (mmm) REVERT: J 75 MET cc_start: 0.8790 (mmt) cc_final: 0.8394 (mmm) REVERT: J 82 VAL cc_start: 0.8419 (t) cc_final: 0.8160 (t) REVERT: K 75 MET cc_start: 0.8442 (mmt) cc_final: 0.8123 (tpp) REVERT: L 75 MET cc_start: 0.8549 (mmt) cc_final: 0.8153 (mmt) REVERT: L 150 MET cc_start: 0.7298 (ttt) cc_final: 0.7085 (ttt) REVERT: M 75 MET cc_start: 0.8580 (mmt) cc_final: 0.8312 (mmm) outliers start: 16 outliers final: 9 residues processed: 309 average time/residue: 0.1283 time to fit residues: 59.8683 Evaluate side-chains 279 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain N residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 30 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 GLN E 136 GLN F 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121124 restraints weight = 20056.581| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.03 r_work: 0.3157 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19495 Z= 0.213 Angle : 0.643 7.263 26362 Z= 0.333 Chirality : 0.045 0.154 3066 Planarity : 0.005 0.052 3430 Dihedral : 5.061 28.528 2730 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.74 % Allowed : 5.90 % Favored : 92.36 % 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: 1.32 (0.16), residues: 2485 helix: 1.81 (0.14), residues: 1351 sheet: 1.61 (0.34), residues: 196 loop : -0.68 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 131 TYR 0.016 0.002 TYR B 206 PHE 0.016 0.002 PHE J 102 TRP 0.011 0.002 TRP M 174 HIS 0.006 0.002 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.00522 (19495) covalent geometry : angle 0.64333 (26362) hydrogen bonds : bond 0.04463 ( 1092) hydrogen bonds : angle 4.45762 ( 3612) *********************** 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 316 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.632 Fit side-chains REVERT: C 123 LYS cc_start: 0.8614 (mttt) cc_final: 0.8362 (mttp) REVERT: D 110 SER cc_start: 0.8153 (t) cc_final: 0.7868 (m) REVERT: E 37 PHE cc_start: 0.8401 (t80) cc_final: 0.8100 (t80) REVERT: E 123 LYS cc_start: 0.8573 (mttt) cc_final: 0.8305 (mttp) REVERT: F 101 GLN cc_start: 0.8033 (pt0) cc_final: 0.7789 (pt0) REVERT: F 160 MET cc_start: 0.7269 (mtt) cc_final: 0.7046 (mtp) REVERT: H 75 MET cc_start: 0.8631 (mmt) cc_final: 0.8252 (tpp) REVERT: I 95 MET cc_start: 0.8388 (ttm) cc_final: 0.8142 (ttt) outliers start: 35 outliers final: 21 residues processed: 295 average time/residue: 0.1275 time to fit residues: 57.3043 Evaluate side-chains 275 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 101 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 181 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 177 optimal weight: 0.0980 chunk 31 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.162777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129715 restraints weight = 19627.659| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.02 r_work: 0.3241 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19495 Z= 0.091 Angle : 0.492 6.547 26362 Z= 0.258 Chirality : 0.040 0.130 3066 Planarity : 0.004 0.046 3430 Dihedral : 4.538 29.375 2730 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.14 % Allowed : 7.84 % Favored : 91.02 % 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: 1.62 (0.17), residues: 2485 helix: 2.17 (0.14), residues: 1365 sheet: 0.85 (0.34), residues: 231 loop : -0.61 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 131 TYR 0.010 0.001 TYR A 95 PHE 0.010 0.001 PHE I 185 TRP 0.010 0.001 TRP M 174 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00193 (19495) covalent geometry : angle 0.49186 (26362) hydrogen bonds : bond 0.02943 ( 1092) hydrogen bonds : angle 4.09265 ( 3612) *********************** 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 281 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.519 Fit side-chains REVERT: C 123 LYS cc_start: 0.8485 (mttt) cc_final: 0.8223 (mttp) REVERT: D 125 MET cc_start: 0.8620 (mtt) cc_final: 0.8284 (mtt) REVERT: D 179 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7128 (mm) REVERT: E 37 PHE cc_start: 0.8225 (t80) cc_final: 0.7794 (t80) REVERT: F 74 MET cc_start: 0.8581 (ttm) cc_final: 0.8052 (ttt) REVERT: G 202 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8243 (t) REVERT: I 75 MET cc_start: 0.7992 (mmm) cc_final: 0.7676 (mmm) REVERT: J 75 MET cc_start: 0.8496 (mmm) cc_final: 0.8270 (mmm) REVERT: L 36 VAL cc_start: 0.8514 (t) cc_final: 0.8290 (t) REVERT: L 162 ILE cc_start: 0.7039 (mp) cc_final: 0.6795 (mp) REVERT: M 166 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6933 (mt-10) REVERT: N 79 ASP cc_start: 0.8306 (m-30) cc_final: 0.7800 (m-30) REVERT: N 166 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6945 (mt-10) outliers start: 23 outliers final: 9 residues processed: 266 average time/residue: 0.1295 time to fit residues: 52.5551 Evaluate side-chains 252 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 129 ASN E 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.155885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.122951 restraints weight = 19871.428| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.02 r_work: 0.3149 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19495 Z= 0.159 Angle : 0.546 6.139 26362 Z= 0.281 Chirality : 0.042 0.141 3066 Planarity : 0.004 0.046 3430 Dihedral : 4.657 27.745 2730 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.19 % Allowed : 8.18 % Favored : 90.62 % 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: 1.65 (0.17), residues: 2485 helix: 2.22 (0.14), residues: 1365 sheet: 1.21 (0.35), residues: 196 loop : -0.68 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 119 TYR 0.013 0.002 TYR L 91 PHE 0.012 0.001 PHE G 83 TRP 0.012 0.002 TRP M 174 HIS 0.003 0.001 HIS K 117 Details of bonding type rmsd covalent geometry : bond 0.00382 (19495) covalent geometry : angle 0.54576 (26362) hydrogen bonds : bond 0.03589 ( 1092) hydrogen bonds : angle 4.15287 ( 3612) *********************** 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 281 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.715 Fit side-chains REVERT: B 207 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7397 (mtm-85) REVERT: C 101 GLN cc_start: 0.8122 (pt0) cc_final: 0.7880 (pt0) REVERT: C 123 LYS cc_start: 0.8535 (mttt) cc_final: 0.8290 (mttp) REVERT: D 101 GLN cc_start: 0.8059 (tt0) cc_final: 0.7650 (tt0) REVERT: D 179 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7023 (mm) REVERT: E 37 PHE cc_start: 0.8346 (t80) cc_final: 0.7987 (t80) REVERT: G 202 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8160 (t) REVERT: H 156 GLU cc_start: 0.7858 (tt0) cc_final: 0.7607 (tt0) REVERT: I 95 MET cc_start: 0.8360 (ttt) cc_final: 0.8121 (ttp) REVERT: J 75 MET cc_start: 0.8456 (mmm) cc_final: 0.8169 (mmm) REVERT: M 187 ASP cc_start: 0.8548 (m-30) cc_final: 0.8304 (m-30) REVERT: N 79 ASP cc_start: 0.8344 (m-30) cc_final: 0.7851 (m-30) REVERT: N 166 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6835 (mt-10) outliers start: 24 outliers final: 16 residues processed: 267 average time/residue: 0.1310 time to fit residues: 53.6069 Evaluate side-chains 266 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 244 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.162166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130363 restraints weight = 19693.548| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.93 r_work: 0.3178 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19495 Z= 0.127 Angle : 0.514 6.861 26362 Z= 0.266 Chirality : 0.041 0.138 3066 Planarity : 0.004 0.047 3430 Dihedral : 4.583 29.177 2730 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.98 % Rotamer: Outliers : 1.24 % Allowed : 8.43 % Favored : 90.33 % 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: 1.74 (0.17), residues: 2485 helix: 2.34 (0.14), residues: 1365 sheet: 1.14 (0.35), residues: 196 loop : -0.69 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 131 TYR 0.011 0.001 TYR L 91 PHE 0.011 0.001 PHE F 83 TRP 0.012 0.001 TRP M 174 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00299 (19495) covalent geometry : angle 0.51379 (26362) hydrogen bonds : bond 0.03239 ( 1092) hydrogen bonds : angle 4.07172 ( 3612) *********************** 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 263 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.724 Fit side-chains REVERT: B 207 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7361 (mtm-85) REVERT: C 101 GLN cc_start: 0.8222 (pt0) cc_final: 0.8009 (pt0) REVERT: C 105 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7459 (mt) REVERT: D 101 GLN cc_start: 0.8294 (tt0) cc_final: 0.7870 (tt0) REVERT: D 179 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7070 (mm) REVERT: E 37 PHE cc_start: 0.8372 (t80) cc_final: 0.7950 (t80) REVERT: F 74 MET cc_start: 0.8654 (ttm) cc_final: 0.8149 (ttt) REVERT: F 125 MET cc_start: 0.8912 (mtt) cc_final: 0.8556 (mtt) REVERT: H 156 GLU cc_start: 0.7993 (tt0) cc_final: 0.7741 (tt0) REVERT: I 95 MET cc_start: 0.8525 (ttt) cc_final: 0.8295 (ttp) REVERT: J 75 MET cc_start: 0.8491 (mmm) cc_final: 0.7936 (mmm) REVERT: M 187 ASP cc_start: 0.8669 (m-30) cc_final: 0.8449 (m-30) REVERT: N 79 ASP cc_start: 0.8438 (m-30) cc_final: 0.7949 (m-30) REVERT: N 166 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6864 (mt-10) outliers start: 25 outliers final: 18 residues processed: 249 average time/residue: 0.1335 time to fit residues: 50.4021 Evaluate side-chains 252 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 133 optimal weight: 0.3980 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131050 restraints weight = 19848.054| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.94 r_work: 0.3179 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19495 Z= 0.132 Angle : 0.516 7.132 26362 Z= 0.267 Chirality : 0.041 0.136 3066 Planarity : 0.004 0.046 3430 Dihedral : 4.526 29.568 2730 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.09 % Allowed : 8.73 % Favored : 90.18 % 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: 1.76 (0.17), residues: 2485 helix: 2.37 (0.14), residues: 1365 sheet: 1.16 (0.35), residues: 196 loop : -0.72 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 131 TYR 0.011 0.001 TYR L 91 PHE 0.011 0.001 PHE F 83 TRP 0.013 0.002 TRP M 174 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00312 (19495) covalent geometry : angle 0.51607 (26362) hydrogen bonds : bond 0.03278 ( 1092) hydrogen bonds : angle 4.04043 ( 3612) *********************** 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 265 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.640 Fit side-chains REVERT: B 207 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7379 (mtm-85) REVERT: C 105 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7375 (mt) REVERT: D 179 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7085 (mm) REVERT: E 37 PHE cc_start: 0.8373 (t80) cc_final: 0.7962 (t80) REVERT: F 125 MET cc_start: 0.8903 (mtt) cc_final: 0.8317 (mtt) REVERT: I 95 MET cc_start: 0.8528 (ttt) cc_final: 0.8316 (ttp) REVERT: M 187 ASP cc_start: 0.8691 (m-30) cc_final: 0.8475 (m-30) REVERT: N 79 ASP cc_start: 0.8453 (m-30) cc_final: 0.7968 (m-30) REVERT: N 166 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6843 (mt-10) outliers start: 22 outliers final: 19 residues processed: 252 average time/residue: 0.1369 time to fit residues: 52.3750 Evaluate side-chains 260 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127625 restraints weight = 20012.310| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.88 r_work: 0.3128 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19495 Z= 0.212 Angle : 0.598 7.318 26362 Z= 0.308 Chirality : 0.044 0.143 3066 Planarity : 0.004 0.049 3430 Dihedral : 4.898 31.826 2730 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 1.34 % Allowed : 8.68 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 1.52 (0.17), residues: 2485 helix: 2.14 (0.14), residues: 1365 sheet: 1.17 (0.35), residues: 196 loop : -0.81 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 131 TYR 0.014 0.002 TYR N 91 PHE 0.013 0.002 PHE A 83 TRP 0.017 0.002 TRP M 174 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00519 (19495) covalent geometry : angle 0.59836 (26362) hydrogen bonds : bond 0.04008 ( 1092) hydrogen bonds : angle 4.26304 ( 3612) *********************** 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 269 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.570 Fit side-chains REVERT: B 207 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7519 (mtm-85) REVERT: C 105 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7251 (mt) REVERT: D 101 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: D 179 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7370 (mm) REVERT: E 37 PHE cc_start: 0.8457 (t80) cc_final: 0.8112 (t80) REVERT: F 125 MET cc_start: 0.8947 (mtt) cc_final: 0.8561 (mtt) REVERT: F 201 ASP cc_start: 0.8234 (m-30) cc_final: 0.7951 (m-30) REVERT: I 95 MET cc_start: 0.8612 (ttt) cc_final: 0.8378 (ttp) outliers start: 27 outliers final: 20 residues processed: 251 average time/residue: 0.1371 time to fit residues: 52.2018 Evaluate side-chains 261 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 87 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.152748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.120761 restraints weight = 19920.634| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.92 r_work: 0.3127 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19495 Z= 0.191 Angle : 0.573 6.757 26362 Z= 0.295 Chirality : 0.043 0.143 3066 Planarity : 0.004 0.050 3430 Dihedral : 4.835 31.741 2730 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.58 % Favored : 96.18 % Rotamer: Outliers : 1.14 % Allowed : 8.93 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 1.49 (0.17), residues: 2485 helix: 2.14 (0.14), residues: 1365 sheet: 1.16 (0.36), residues: 196 loop : -0.85 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 131 TYR 0.013 0.002 TYR L 91 PHE 0.014 0.001 PHE H 175 TRP 0.017 0.002 TRP M 174 HIS 0.003 0.001 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00465 (19495) covalent geometry : angle 0.57267 (26362) hydrogen bonds : bond 0.03779 ( 1092) hydrogen bonds : angle 4.20604 ( 3612) *********************** 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 261 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.699 Fit side-chains REVERT: C 105 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7254 (mt) REVERT: D 101 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: D 179 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7335 (mm) REVERT: E 37 PHE cc_start: 0.8439 (t80) cc_final: 0.8084 (t80) REVERT: F 125 MET cc_start: 0.8955 (mtt) cc_final: 0.8577 (mtt) REVERT: I 95 MET cc_start: 0.8607 (ttt) cc_final: 0.8372 (ttp) outliers start: 23 outliers final: 19 residues processed: 247 average time/residue: 0.1277 time to fit residues: 48.4782 Evaluate side-chains 258 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 150 MET Chi-restraints excluded: chain M residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 131 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135788 restraints weight = 19630.865| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.91 r_work: 0.3223 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19495 Z= 0.088 Angle : 0.479 6.685 26362 Z= 0.251 Chirality : 0.040 0.130 3066 Planarity : 0.004 0.046 3430 Dihedral : 4.361 30.631 2730 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.54 % Favored : 97.18 % Rotamer: Outliers : 0.79 % Allowed : 9.47 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.73 (0.17), residues: 2485 helix: 2.43 (0.14), residues: 1372 sheet: -0.02 (0.32), residues: 273 loop : -0.63 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 131 TYR 0.014 0.001 TYR G 95 PHE 0.008 0.001 PHE D 83 TRP 0.010 0.001 TRP M 174 HIS 0.002 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00188 (19495) covalent geometry : angle 0.47854 (26362) hydrogen bonds : bond 0.02802 ( 1092) hydrogen bonds : angle 3.94509 ( 3612) ********************** 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 258 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.459 Fit side-chains REVERT: B 207 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7423 (mtm-85) REVERT: D 101 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: D 125 MET cc_start: 0.8564 (mtt) cc_final: 0.8212 (mtt) REVERT: D 179 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7082 (mm) REVERT: E 37 PHE cc_start: 0.8315 (t80) cc_final: 0.7995 (t80) REVERT: F 74 MET cc_start: 0.8724 (ttm) cc_final: 0.8195 (ttt) REVERT: F 125 MET cc_start: 0.8873 (mtt) cc_final: 0.8319 (mtt) REVERT: F 202 THR cc_start: 0.8571 (m) cc_final: 0.8339 (t) REVERT: K 95 MET cc_start: 0.8604 (ttm) cc_final: 0.8237 (ttt) REVERT: L 162 ILE cc_start: 0.7059 (mp) cc_final: 0.6748 (mp) REVERT: N 79 ASP cc_start: 0.8436 (m-30) cc_final: 0.7928 (m-30) outliers start: 16 outliers final: 11 residues processed: 250 average time/residue: 0.1335 time to fit residues: 49.2839 Evaluate side-chains 247 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 150 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 155 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.141096 restraints weight = 19547.031| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.83 r_work: 0.3240 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19495 Z= 0.093 Angle : 0.483 9.552 26362 Z= 0.251 Chirality : 0.040 0.132 3066 Planarity : 0.004 0.044 3430 Dihedral : 4.256 29.269 2730 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.14 % Favored : 96.62 % Rotamer: Outliers : 0.64 % Allowed : 9.82 % Favored : 89.53 % 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: 1.84 (0.17), residues: 2485 helix: 2.52 (0.14), residues: 1372 sheet: 0.03 (0.32), residues: 273 loop : -0.58 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 131 TYR 0.012 0.001 TYR D 95 PHE 0.008 0.001 PHE G 83 TRP 0.013 0.002 TRP H 174 HIS 0.002 0.001 HIS L 117 Details of bonding type rmsd covalent geometry : bond 0.00203 (19495) covalent geometry : angle 0.48264 (26362) hydrogen bonds : bond 0.02834 ( 1092) hydrogen bonds : angle 3.89001 ( 3612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3651.09 seconds wall clock time: 63 minutes 21.60 seconds (3801.60 seconds total)