Starting phenix.real_space_refine on Thu Mar 5 07:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.map" model { file = "/net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw3_47234/03_2026/9dw3_47234.cif" } resolution = 2.4 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= -0.000 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 182 5.16 5 B 14 2.79 5 C 12698 2.51 5 N 3416 2.21 5 O 3626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1396 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 1.98, per 1000 atoms: 0.10 Number of scatterers: 19936 At special positions: 0 Unit cell: (113.74, 111.86, 108.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 182 16.00 O 3626 8.00 N 3416 7.00 C 12698 6.00 B 14 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 871.1 milliseconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 53.6% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 125 through 139 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 188 through 214 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 92 through 110 Processing helix chain 'B' and resid 125 through 139 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 188 through 214 Processing helix chain 'B' and resid 216 through 225 Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 92 through 110 Processing helix chain 'C' and resid 125 through 139 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 188 through 214 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 92 through 110 Processing helix chain 'D' and resid 125 through 139 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 188 through 214 Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'E' and resid 74 through 81 Processing helix chain 'E' and resid 92 through 110 Processing helix chain 'E' and resid 125 through 139 Processing helix chain 'E' and resid 153 through 161 Processing helix chain 'E' and resid 188 through 214 Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'F' and resid 74 through 81 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 125 through 139 Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 188 through 214 Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 125 through 139 Processing helix chain 'G' and resid 153 through 161 Processing helix chain 'G' and resid 188 through 214 Processing helix chain 'G' and resid 216 through 225 Processing helix chain 'G' and resid 231 through 239 Processing helix chain 'H' and resid 74 through 81 Processing helix chain 'H' and resid 92 through 110 Processing helix chain 'H' and resid 125 through 139 Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 188 through 214 Processing helix chain 'H' and resid 216 through 225 Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'I' and resid 74 through 81 Processing helix chain 'I' and resid 92 through 110 Processing helix chain 'I' and resid 125 through 139 Processing helix chain 'I' and resid 153 through 161 Processing helix chain 'I' and resid 188 through 214 Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 231 through 239 Processing helix chain 'J' and resid 74 through 81 Processing helix chain 'J' and resid 92 through 110 Processing helix chain 'J' and resid 125 through 139 Processing helix chain 'J' and resid 153 through 161 Processing helix chain 'J' and resid 188 through 214 Processing helix chain 'J' and resid 216 through 225 Processing helix chain 'J' and resid 231 through 239 Processing helix chain 'K' and resid 74 through 81 Processing helix chain 'K' and resid 92 through 110 Processing helix chain 'K' and resid 125 through 139 Processing helix chain 'K' and resid 153 through 161 Processing helix chain 'K' and resid 188 through 214 Processing helix chain 'K' and resid 216 through 225 Processing helix chain 'K' and resid 231 through 239 Processing helix chain 'L' and resid 74 through 81 Processing helix chain 'L' and resid 92 through 110 Processing helix chain 'L' and resid 125 through 139 Processing helix chain 'L' and resid 153 through 161 Processing helix chain 'L' and resid 188 through 214 Processing helix chain 'L' and resid 216 through 225 Processing helix chain 'L' and resid 231 through 239 Processing helix chain 'M' and resid 74 through 81 Processing helix chain 'M' and resid 92 through 110 Processing helix chain 'M' and resid 125 through 139 Processing helix chain 'M' and resid 153 through 161 Processing helix chain 'M' and resid 188 through 214 Processing helix chain 'M' and resid 216 through 225 Processing helix chain 'M' and resid 231 through 239 Processing helix chain 'N' and resid 74 through 81 Processing helix chain 'N' and resid 92 through 110 Processing helix chain 'N' and resid 125 through 139 Processing helix chain 'N' and resid 153 through 161 Processing helix chain 'N' and resid 188 through 214 Processing helix chain 'N' and resid 216 through 225 Processing helix chain 'N' and resid 231 through 239 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER A 121 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN A 150 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG A 174 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY A 149 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET A 176 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 151 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER A 121 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN A 150 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS A 168 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR A 145 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG A 167 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 187 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER B 121 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN B 150 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG B 174 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY B 149 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET B 176 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA B 151 " --> pdb=" O MET B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER B 121 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN B 150 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS B 168 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 145 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 167 " --> pdb=" O LYS B 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 187 Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER C 121 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 150 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG C 174 " --> pdb=" O CYS C 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY C 149 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET C 176 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA C 151 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER C 121 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 150 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS C 168 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 145 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG C 167 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 187 Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER D 121 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN D 150 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG D 174 " --> pdb=" O CYS D 147 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY D 149 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET D 176 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA D 151 " --> pdb=" O MET D 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER D 121 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN D 150 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS D 168 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR D 145 " --> pdb=" O HIS D 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG D 167 " --> pdb=" O LYS D 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 181 through 187 Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER E 121 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN E 150 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 174 " --> pdb=" O CYS E 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY E 149 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET E 176 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA E 151 " --> pdb=" O MET E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER E 121 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN E 150 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS E 168 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR E 145 " --> pdb=" O HIS E 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG E 167 " --> pdb=" O LYS E 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 181 through 187 Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER F 121 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN F 150 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG F 174 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY F 149 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET F 176 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA F 151 " --> pdb=" O MET F 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER F 121 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN F 150 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS F 168 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR F 145 " --> pdb=" O HIS F 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG F 167 " --> pdb=" O LYS F 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 181 through 187 Processing sheet with id=AC1, first strand: chain 'G' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER G 121 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN G 150 " --> pdb=" O SER G 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG G 174 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY G 149 " --> pdb=" O ARG G 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET G 176 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA G 151 " --> pdb=" O MET G 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER G 121 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN G 150 " --> pdb=" O SER G 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS G 168 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR G 145 " --> pdb=" O HIS G 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG G 167 " --> pdb=" O LYS G 243 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 181 through 187 Processing sheet with id=AC4, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG H 174 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY H 149 " --> pdb=" O ARG H 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET H 176 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA H 151 " --> pdb=" O MET H 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS H 168 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR H 145 " --> pdb=" O HIS H 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG H 167 " --> pdb=" O LYS H 243 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER I 121 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN I 150 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG I 174 " --> pdb=" O CYS I 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY I 149 " --> pdb=" O ARG I 174 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET I 176 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA I 151 " --> pdb=" O MET I 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER I 121 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN I 150 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N HIS I 168 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR I 145 " --> pdb=" O HIS I 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG I 167 " --> pdb=" O LYS I 243 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.293A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG J 174 " --> pdb=" O CYS J 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY J 149 " --> pdb=" O ARG J 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET J 176 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA J 151 " --> pdb=" O MET J 176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.293A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS J 168 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR J 145 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG J 167 " --> pdb=" O LYS J 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 84 through 88 removed outlier: 5.293A pdb=" N SER K 121 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN K 150 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG K 174 " --> pdb=" O CYS K 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY K 149 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET K 176 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA K 151 " --> pdb=" O MET K 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 84 through 88 removed outlier: 5.293A pdb=" N SER K 121 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN K 150 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS K 168 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR K 145 " --> pdb=" O HIS K 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG K 167 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER L 121 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN L 150 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG L 174 " --> pdb=" O CYS L 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY L 149 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET L 176 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA L 151 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER L 121 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN L 150 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS L 168 " --> pdb=" O ILE L 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR L 145 " --> pdb=" O HIS L 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG L 167 " --> pdb=" O LYS L 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER M 121 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN M 150 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG M 174 " --> pdb=" O CYS M 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY M 149 " --> pdb=" O ARG M 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET M 176 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA M 151 " --> pdb=" O MET M 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER M 121 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN M 150 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS M 168 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR M 145 " --> pdb=" O HIS M 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG M 167 " --> pdb=" O LYS M 243 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER N 121 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN N 150 " --> pdb=" O SER N 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG N 174 " --> pdb=" O CYS N 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY N 149 " --> pdb=" O ARG N 174 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N MET N 176 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA N 151 " --> pdb=" O MET N 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 84 through 88 removed outlier: 5.294A pdb=" N SER N 121 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLN N 150 " --> pdb=" O SER N 121 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS N 168 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR N 145 " --> pdb=" O HIS N 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG N 167 " --> pdb=" O LYS N 243 " (cutoff:3.500A) 1316 hydrogen bonds defined for protein. 3906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3234 1.30 - 1.43: 4863 1.43 - 1.56: 11867 1.56 - 1.69: 14 1.69 - 1.81: 322 Bond restraints: 20300 Sorted by residual: bond pdb=" C18 BO2 J1001 " pdb=" N20 BO2 J1001 " ideal model delta sigma weight residual 1.342 1.477 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C18 BO2 G1001 " pdb=" N20 BO2 G1001 " ideal model delta sigma weight residual 1.342 1.477 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C18 BO2 K1001 " pdb=" N20 BO2 K1001 " ideal model delta sigma weight residual 1.342 1.477 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C18 BO2 M1001 " pdb=" N20 BO2 M1001 " ideal model delta sigma weight residual 1.342 1.477 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C18 BO2 B1001 " pdb=" N20 BO2 B1001 " ideal model delta sigma weight residual 1.342 1.477 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 20295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 24662 1.42 - 2.84: 2227 2.84 - 4.25: 393 4.25 - 5.67: 88 5.67 - 7.09: 70 Bond angle restraints: 27440 Sorted by residual: angle pdb=" N ILE C 75 " pdb=" CA ILE C 75 " pdb=" C ILE C 75 " ideal model delta sigma weight residual 110.62 114.56 -3.94 1.02e+00 9.61e-01 1.49e+01 angle pdb=" N ILE E 75 " pdb=" CA ILE E 75 " pdb=" C ILE E 75 " ideal model delta sigma weight residual 110.62 114.55 -3.93 1.02e+00 9.61e-01 1.49e+01 angle pdb=" N ILE D 75 " pdb=" CA ILE D 75 " pdb=" C ILE D 75 " ideal model delta sigma weight residual 110.62 114.55 -3.93 1.02e+00 9.61e-01 1.48e+01 angle pdb=" N ILE K 75 " pdb=" CA ILE K 75 " pdb=" C ILE K 75 " ideal model delta sigma weight residual 110.62 114.52 -3.90 1.02e+00 9.61e-01 1.46e+01 angle pdb=" N ILE L 75 " pdb=" CA ILE L 75 " pdb=" C ILE L 75 " ideal model delta sigma weight residual 110.62 114.51 -3.89 1.02e+00 9.61e-01 1.46e+01 ... (remaining 27435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11606 17.30 - 34.61: 644 34.61 - 51.91: 126 51.91 - 69.21: 98 69.21 - 86.52: 56 Dihedral angle restraints: 12530 sinusoidal: 5180 harmonic: 7350 Sorted by residual: dihedral pdb=" CA SER I 169 " pdb=" C SER I 169 " pdb=" N LEU I 170 " pdb=" CA LEU I 170 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER B 169 " pdb=" C SER B 169 " pdb=" N LEU B 170 " pdb=" CA LEU B 170 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA SER H 169 " pdb=" C SER H 169 " pdb=" N LEU H 170 " pdb=" CA LEU H 170 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 12527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2526 0.072 - 0.143: 560 0.143 - 0.215: 36 0.215 - 0.286: 0 0.286 - 0.358: 14 Chirality restraints: 3136 Sorted by residual: chirality pdb=" C21 BO2 I1001 " pdb=" B26 BO2 I1001 " pdb=" C22 BO2 I1001 " pdb=" N20 BO2 I1001 " both_signs ideal model delta sigma weight residual False 2.49 2.85 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C21 BO2 J1001 " pdb=" B26 BO2 J1001 " pdb=" C22 BO2 J1001 " pdb=" N20 BO2 J1001 " both_signs ideal model delta sigma weight residual False 2.49 2.85 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C21 BO2 E1001 " pdb=" B26 BO2 E1001 " pdb=" C22 BO2 E1001 " pdb=" N20 BO2 E1001 " both_signs ideal model delta sigma weight residual False 2.49 2.85 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 3133 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.043 2.00e-02 2.50e+03 2.35e-02 1.11e+01 pdb=" CG TYR B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 73 " -0.043 2.00e-02 2.50e+03 2.35e-02 1.10e+01 pdb=" CG TYR G 73 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR G 73 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 73 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR G 73 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 73 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR G 73 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 73 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 73 " -0.043 2.00e-02 2.50e+03 2.35e-02 1.10e+01 pdb=" CG TYR A 73 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 73 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 73 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 73 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 73 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 73 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 73 " -0.034 2.00e-02 2.50e+03 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 28 1.97 - 2.70: 294 2.70 - 3.44: 28298 3.44 - 4.17: 50790 4.17 - 4.90: 89324 Nonbonded interactions: 168734 Sorted by model distance: nonbonded pdb=" OG SER B 153 " pdb=" O27 BO2 B1001 " model vdw 1.238 3.040 nonbonded pdb=" OG SER L 153 " pdb=" O27 BO2 L1001 " model vdw 1.238 3.040 nonbonded pdb=" OG SER A 153 " pdb=" O27 BO2 A1001 " model vdw 1.238 3.040 nonbonded pdb=" OG SER N 153 " pdb=" O27 BO2 N1001 " model vdw 1.238 3.040 nonbonded pdb=" OG SER F 153 " pdb=" O27 BO2 F1001 " model vdw 1.238 3.040 ... (remaining 168729 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' selection = 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.290 Find NCS groups from input model: 0.190 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.008 0.135 20300 Z= 0.388 Angle : 0.945 7.089 27440 Z= 0.555 Chirality : 0.060 0.358 3136 Planarity : 0.009 0.097 3472 Dihedral : 14.764 86.518 7798 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 2478 helix: -0.23 (0.12), residues: 1372 sheet: -0.19 (0.28), residues: 266 loop : -1.17 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG I 167 TYR 0.043 0.008 TYR G 73 PHE 0.009 0.002 PHE N 105 TRP 0.007 0.002 TRP N 146 HIS 0.005 0.002 HIS F 178 Details of bonding type rmsd covalent geometry : bond 0.00764 (20300) covalent geometry : angle 0.94502 (27440) hydrogen bonds : bond 0.15180 ( 1190) hydrogen bonds : angle 6.46357 ( 3906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 0.634 Fit side-chains REVERT: A 176 MET cc_start: 0.9130 (tmm) cc_final: 0.8696 (tmm) REVERT: A 218 GLN cc_start: 0.8107 (mp10) cc_final: 0.7846 (mp-120) REVERT: A 230 MET cc_start: 0.9261 (mtt) cc_final: 0.9035 (mtt) REVERT: B 166 MET cc_start: 0.9184 (mtt) cc_final: 0.8894 (mtp) REVERT: B 218 GLN cc_start: 0.8233 (mp10) cc_final: 0.7424 (tm130) REVERT: C 136 MET cc_start: 0.9196 (mtp) cc_final: 0.8937 (mtp) REVERT: C 154 MET cc_start: 0.8740 (tpp) cc_final: 0.8522 (tpp) REVERT: C 218 GLN cc_start: 0.8279 (mp10) cc_final: 0.8057 (mp-120) REVERT: D 185 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8253 (mmt180) REVERT: D 218 GLN cc_start: 0.8060 (mp10) cc_final: 0.7315 (tm130) REVERT: E 136 MET cc_start: 0.9181 (mtp) cc_final: 0.8782 (mtp) REVERT: E 218 GLN cc_start: 0.8287 (mp10) cc_final: 0.8058 (mp-120) REVERT: E 230 MET cc_start: 0.9277 (mtt) cc_final: 0.9021 (mtt) REVERT: F 176 MET cc_start: 0.9113 (tmm) cc_final: 0.8851 (tmm) REVERT: F 185 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8230 (mmt180) REVERT: F 218 GLN cc_start: 0.8211 (mp10) cc_final: 0.7950 (mp-120) REVERT: G 218 GLN cc_start: 0.8210 (mp10) cc_final: 0.7365 (tm130) REVERT: H 136 MET cc_start: 0.9197 (mtp) cc_final: 0.8939 (mtp) REVERT: H 154 MET cc_start: 0.8742 (tpp) cc_final: 0.8523 (tpp) REVERT: H 218 GLN cc_start: 0.8279 (mp10) cc_final: 0.8057 (mp-120) REVERT: I 185 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8253 (mmt180) REVERT: I 218 GLN cc_start: 0.8060 (mp10) cc_final: 0.7314 (tm130) REVERT: J 136 MET cc_start: 0.9186 (mtp) cc_final: 0.8790 (mtp) REVERT: J 218 GLN cc_start: 0.8287 (mp10) cc_final: 0.8059 (mp-120) REVERT: J 230 MET cc_start: 0.9277 (mtt) cc_final: 0.9018 (mtt) REVERT: K 218 GLN cc_start: 0.8207 (mp10) cc_final: 0.7363 (tm130) REVERT: L 176 MET cc_start: 0.9130 (tmm) cc_final: 0.8695 (tmm) REVERT: L 218 GLN cc_start: 0.8135 (mp10) cc_final: 0.7878 (mp-120) REVERT: L 230 MET cc_start: 0.9261 (mtt) cc_final: 0.9035 (mtt) REVERT: M 166 MET cc_start: 0.9177 (mtt) cc_final: 0.8885 (mtp) REVERT: M 218 GLN cc_start: 0.8233 (mp10) cc_final: 0.7423 (tm130) REVERT: N 176 MET cc_start: 0.9114 (tmm) cc_final: 0.8851 (tmm) REVERT: N 218 GLN cc_start: 0.8214 (mp10) cc_final: 0.7956 (mp-120) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.8213 time to fit residues: 468.0108 Evaluate side-chains 456 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.128672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.114591 restraints weight = 14763.604| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.56 r_work: 0.2998 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20300 Z= 0.191 Angle : 0.656 4.642 27440 Z= 0.355 Chirality : 0.050 0.155 3136 Planarity : 0.005 0.052 3472 Dihedral : 7.437 51.424 2996 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.49 % Allowed : 6.86 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2478 helix: 2.16 (0.14), residues: 1372 sheet: 0.78 (0.32), residues: 238 loop : -0.86 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 226 TYR 0.014 0.002 TYR K 209 PHE 0.009 0.001 PHE D 105 TRP 0.008 0.003 TRP D 146 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00414 (20300) covalent geometry : angle 0.65579 (27440) hydrogen bonds : bond 0.06271 ( 1190) hydrogen bonds : angle 4.54805 ( 3906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 474 time to evaluate : 0.787 Fit side-chains REVERT: A 136 MET cc_start: 0.9212 (mtp) cc_final: 0.8856 (mtp) REVERT: B 185 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7771 (mmt180) REVERT: B 218 GLN cc_start: 0.8150 (mp10) cc_final: 0.7894 (mp10) REVERT: B 230 MET cc_start: 0.9235 (mtt) cc_final: 0.9009 (mtt) REVERT: D 154 MET cc_start: 0.8851 (tpp) cc_final: 0.8548 (tpp) REVERT: D 199 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8155 (tpp) REVERT: D 218 GLN cc_start: 0.7953 (mp10) cc_final: 0.7653 (tm130) REVERT: E 136 MET cc_start: 0.9079 (mtp) cc_final: 0.8767 (mtp) REVERT: F 176 MET cc_start: 0.8901 (tmm) cc_final: 0.8654 (tmm) REVERT: I 154 MET cc_start: 0.8850 (tpp) cc_final: 0.8545 (tpp) REVERT: I 199 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8150 (tpp) REVERT: I 218 GLN cc_start: 0.7957 (mp10) cc_final: 0.7661 (tm130) REVERT: J 136 MET cc_start: 0.9084 (mtp) cc_final: 0.8779 (mtp) REVERT: L 136 MET cc_start: 0.9213 (mtp) cc_final: 0.8862 (mtp) REVERT: M 185 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7773 (mmt180) REVERT: M 218 GLN cc_start: 0.8149 (mp10) cc_final: 0.7893 (mp10) REVERT: M 230 MET cc_start: 0.9238 (mtt) cc_final: 0.9015 (mtt) REVERT: N 176 MET cc_start: 0.8892 (tmm) cc_final: 0.8644 (tmm) outliers start: 32 outliers final: 2 residues processed: 474 average time/residue: 0.8177 time to fit residues: 424.8376 Evaluate side-chains 487 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 481 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.130648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.116937 restraints weight = 14937.627| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.55 r_work: 0.3041 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20300 Z= 0.161 Angle : 0.594 4.270 27440 Z= 0.318 Chirality : 0.047 0.148 3136 Planarity : 0.005 0.036 3472 Dihedral : 7.260 51.335 2996 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.59 % Allowed : 9.24 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.17), residues: 2478 helix: 2.58 (0.14), residues: 1372 sheet: 0.88 (0.34), residues: 238 loop : -0.87 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 226 TYR 0.012 0.002 TYR K 209 PHE 0.009 0.001 PHE D 105 TRP 0.006 0.002 TRP D 146 HIS 0.005 0.001 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00344 (20300) covalent geometry : angle 0.59399 (27440) hydrogen bonds : bond 0.05698 ( 1190) hydrogen bonds : angle 4.26643 ( 3906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 491 time to evaluate : 0.492 Fit side-chains REVERT: A 218 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7880 (mp-120) REVERT: B 185 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7759 (mmt180) REVERT: B 218 GLN cc_start: 0.8086 (mp10) cc_final: 0.7853 (mp10) REVERT: C 230 MET cc_start: 0.9204 (mtt) cc_final: 0.8992 (mtt) REVERT: D 154 MET cc_start: 0.8834 (tpp) cc_final: 0.8463 (tpp) REVERT: D 199 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8232 (tpp) REVERT: D 214 LYS cc_start: 0.8752 (mptt) cc_final: 0.8493 (mptt) REVERT: D 218 GLN cc_start: 0.7920 (mp10) cc_final: 0.7685 (tm130) REVERT: E 234 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8596 (mt-10) REVERT: F 176 MET cc_start: 0.8814 (tmm) cc_final: 0.8557 (tmm) REVERT: H 230 MET cc_start: 0.9210 (mtt) cc_final: 0.8999 (mtt) REVERT: I 154 MET cc_start: 0.8838 (tpp) cc_final: 0.8464 (tpp) REVERT: I 199 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: I 214 LYS cc_start: 0.8749 (mptt) cc_final: 0.8488 (mptt) REVERT: I 218 GLN cc_start: 0.7923 (mp10) cc_final: 0.7688 (tm130) REVERT: J 98 LEU cc_start: 0.8696 (mt) cc_final: 0.8449 (tp) REVERT: L 218 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7879 (mp-120) REVERT: M 185 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7777 (mmt180) REVERT: M 218 GLN cc_start: 0.8090 (mp10) cc_final: 0.7853 (mp10) REVERT: N 176 MET cc_start: 0.8822 (tmm) cc_final: 0.8565 (tmm) outliers start: 34 outliers final: 2 residues processed: 491 average time/residue: 0.8471 time to fit residues: 454.6023 Evaluate side-chains 496 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 488 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 194 GLN F 236 GLN N 194 GLN N 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.129087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.115460 restraints weight = 14910.602| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 0.54 r_work: 0.3025 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20300 Z= 0.212 Angle : 0.666 4.473 27440 Z= 0.359 Chirality : 0.050 0.151 3136 Planarity : 0.006 0.039 3472 Dihedral : 7.474 52.424 2996 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.59 % Allowed : 9.99 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.16), residues: 2478 helix: 2.32 (0.14), residues: 1372 sheet: 0.37 (0.31), residues: 266 loop : -1.05 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 226 TYR 0.014 0.003 TYR M 118 PHE 0.012 0.002 PHE I 105 TRP 0.005 0.002 TRP D 146 HIS 0.005 0.001 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00470 (20300) covalent geometry : angle 0.66638 (27440) hydrogen bonds : bond 0.06630 ( 1190) hydrogen bonds : angle 4.45119 ( 3906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 486 time to evaluate : 0.817 Fit side-chains REVERT: A 136 MET cc_start: 0.9190 (mtp) cc_final: 0.8872 (mtp) REVERT: A 218 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7906 (mp-120) REVERT: B 98 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8612 (mp) REVERT: B 185 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7790 (mmt180) REVERT: B 218 GLN cc_start: 0.8150 (mp10) cc_final: 0.7907 (mp10) REVERT: D 154 MET cc_start: 0.8871 (tpp) cc_final: 0.8670 (tpt) REVERT: D 199 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8249 (tpp) REVERT: D 218 GLN cc_start: 0.7947 (mp10) cc_final: 0.7721 (tm130) REVERT: E 154 MET cc_start: 0.8825 (tpp) cc_final: 0.8620 (tpp) REVERT: F 199 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: F 218 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7964 (mp-120) REVERT: I 154 MET cc_start: 0.8875 (tpp) cc_final: 0.8673 (tpt) REVERT: I 199 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8244 (tpp) REVERT: I 218 GLN cc_start: 0.7952 (mp10) cc_final: 0.7725 (tm130) REVERT: J 154 MET cc_start: 0.8834 (tpp) cc_final: 0.8628 (tpp) REVERT: L 136 MET cc_start: 0.9194 (mtp) cc_final: 0.8881 (mtp) REVERT: L 218 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7905 (mp-120) REVERT: M 98 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8608 (mp) REVERT: M 185 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7806 (mmt180) REVERT: M 218 GLN cc_start: 0.8156 (mp10) cc_final: 0.7907 (mp10) REVERT: N 199 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8194 (tpp) REVERT: N 218 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7968 (mp-120) outliers start: 34 outliers final: 4 residues processed: 488 average time/residue: 0.8621 time to fit residues: 459.5094 Evaluate side-chains 500 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 484 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 199 MET Chi-restraints excluded: chain N residue 218 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 120 optimal weight: 0.0040 chunk 219 optimal weight: 3.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 GLN N 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.132106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118575 restraints weight = 15032.318| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.54 r_work: 0.3058 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20300 Z= 0.130 Angle : 0.540 4.081 27440 Z= 0.285 Chirality : 0.044 0.145 3136 Planarity : 0.004 0.034 3472 Dihedral : 7.130 50.997 2996 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.40 % Allowed : 10.88 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.17), residues: 2478 helix: 2.72 (0.14), residues: 1372 sheet: 0.65 (0.35), residues: 238 loop : -0.90 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 226 TYR 0.010 0.001 TYR J 209 PHE 0.009 0.001 PHE L 105 TRP 0.007 0.001 TRP B 146 HIS 0.005 0.001 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00270 (20300) covalent geometry : angle 0.53968 (27440) hydrogen bonds : bond 0.04903 ( 1190) hydrogen bonds : angle 4.01390 ( 3906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 500 time to evaluate : 0.607 Fit side-chains REVERT: A 218 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7852 (mp-120) REVERT: B 185 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7723 (mmt180) REVERT: D 154 MET cc_start: 0.8801 (tpp) cc_final: 0.8480 (tpp) REVERT: D 199 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8205 (tpp) REVERT: D 218 GLN cc_start: 0.7860 (mp10) cc_final: 0.7655 (tm130) REVERT: E 211 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8723 (tttt) REVERT: I 154 MET cc_start: 0.8804 (tpp) cc_final: 0.8480 (tpp) REVERT: I 199 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: I 218 GLN cc_start: 0.7861 (mp10) cc_final: 0.7653 (tm130) REVERT: J 211 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8734 (tttt) REVERT: L 218 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7884 (mp-120) REVERT: M 185 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7733 (mmt180) outliers start: 30 outliers final: 4 residues processed: 502 average time/residue: 0.8080 time to fit residues: 444.5180 Evaluate side-chains 504 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 492 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 211 LYS Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 176 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 107 optimal weight: 0.0980 chunk 228 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 194 GLN J 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.129937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116417 restraints weight = 14893.100| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 0.54 r_work: 0.3029 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20300 Z= 0.188 Angle : 0.628 4.242 27440 Z= 0.336 Chirality : 0.048 0.149 3136 Planarity : 0.005 0.036 3472 Dihedral : 7.417 52.402 2996 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.12 % Allowed : 12.84 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.16), residues: 2478 helix: 2.48 (0.14), residues: 1372 sheet: 0.50 (0.34), residues: 238 loop : -1.02 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 226 TYR 0.015 0.002 TYR G 76 PHE 0.012 0.002 PHE D 105 TRP 0.005 0.002 TRP I 146 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00411 (20300) covalent geometry : angle 0.62758 (27440) hydrogen bonds : bond 0.06189 ( 1190) hydrogen bonds : angle 4.28837 ( 3906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 481 time to evaluate : 0.599 Fit side-chains REVERT: A 218 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7887 (mp-120) REVERT: B 185 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7758 (mmt180) REVERT: D 199 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: F 112 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8013 (mptm) REVERT: I 199 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8229 (tpp) REVERT: L 218 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7882 (mp-120) REVERT: M 185 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7765 (mmt180) REVERT: N 112 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8014 (mptm) outliers start: 24 outliers final: 4 residues processed: 483 average time/residue: 0.8412 time to fit residues: 443.7192 Evaluate side-chains 497 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 485 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 112 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 245 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 221 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN E 194 GLN J 194 GLN M 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.118345 restraints weight = 14996.992| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 0.54 r_work: 0.3056 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20300 Z= 0.140 Angle : 0.556 4.063 27440 Z= 0.294 Chirality : 0.045 0.144 3136 Planarity : 0.005 0.035 3472 Dihedral : 7.221 51.622 2996 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.40 % Allowed : 13.26 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2478 helix: 2.70 (0.14), residues: 1372 sheet: 0.55 (0.35), residues: 238 loop : -0.93 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 226 TYR 0.011 0.002 TYR M 118 PHE 0.010 0.001 PHE A 105 TRP 0.006 0.002 TRP M 146 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00296 (20300) covalent geometry : angle 0.55596 (27440) hydrogen bonds : bond 0.05091 ( 1190) hydrogen bonds : angle 4.02576 ( 3906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 500 time to evaluate : 0.802 Fit side-chains REVERT: A 218 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7864 (mp-120) REVERT: B 185 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7731 (mmt180) REVERT: D 199 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: D 218 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7838 (tm130) REVERT: E 211 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8763 (tttt) REVERT: I 199 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8186 (tpp) REVERT: I 218 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7839 (tm130) REVERT: J 211 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (tttt) REVERT: L 218 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7865 (mp-120) REVERT: M 185 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7737 (mmt180) outliers start: 30 outliers final: 4 residues processed: 502 average time/residue: 0.8411 time to fit residues: 462.0730 Evaluate side-chains 512 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 498 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 218 GLN Chi-restraints excluded: chain J residue 211 LYS Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 215 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN E 194 GLN I 194 GLN J 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.126291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.113575 restraints weight = 15228.253| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 0.51 r_work: 0.2977 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20300 Z= 0.272 Angle : 0.742 4.820 27440 Z= 0.400 Chirality : 0.053 0.167 3136 Planarity : 0.006 0.037 3472 Dihedral : 7.709 54.024 2996 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.07 % Allowed : 14.05 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2478 helix: 2.10 (0.13), residues: 1372 sheet: 0.12 (0.31), residues: 266 loop : -1.27 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 226 TYR 0.021 0.003 TYR G 76 PHE 0.017 0.002 PHE L 105 TRP 0.008 0.003 TRP N 146 HIS 0.005 0.002 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00616 (20300) covalent geometry : angle 0.74188 (27440) hydrogen bonds : bond 0.07315 ( 1190) hydrogen bonds : angle 4.55992 ( 3906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 478 time to evaluate : 0.833 Fit side-chains REVERT: A 218 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7900 (mp-120) REVERT: B 98 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 185 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7730 (mmt180) REVERT: B 218 GLN cc_start: 0.8382 (mp10) cc_final: 0.8143 (tm130) REVERT: D 199 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8228 (tpp) REVERT: D 218 GLN cc_start: 0.8189 (mp-120) cc_final: 0.7950 (tm130) REVERT: F 199 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: F 218 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8015 (mp-120) REVERT: I 199 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8225 (tpp) REVERT: I 218 GLN cc_start: 0.8188 (mp-120) cc_final: 0.7958 (tm130) REVERT: L 218 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7877 (mp-120) REVERT: M 98 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8634 (mp) REVERT: M 185 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7730 (mmt180) REVERT: M 218 GLN cc_start: 0.8378 (mp10) cc_final: 0.8145 (tm130) REVERT: N 199 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8218 (tpp) REVERT: N 218 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8015 (mp-120) outliers start: 23 outliers final: 4 residues processed: 480 average time/residue: 0.9086 time to fit residues: 475.3957 Evaluate side-chains 486 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 470 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain F residue 218 GLN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 199 MET Chi-restraints excluded: chain N residue 218 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN E 194 GLN I 194 GLN J 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.132340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.118916 restraints weight = 14871.844| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.54 r_work: 0.3065 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20300 Z= 0.128 Angle : 0.547 4.452 27440 Z= 0.288 Chirality : 0.044 0.143 3136 Planarity : 0.004 0.035 3472 Dihedral : 7.186 51.604 2996 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.79 % Allowed : 14.38 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.17), residues: 2478 helix: 2.69 (0.14), residues: 1372 sheet: 0.43 (0.35), residues: 238 loop : -0.99 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 226 TYR 0.013 0.001 TYR M 118 PHE 0.010 0.001 PHE L 105 TRP 0.008 0.002 TRP M 146 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00266 (20300) covalent geometry : angle 0.54690 (27440) hydrogen bonds : bond 0.04859 ( 1190) hydrogen bonds : angle 3.97207 ( 3906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 506 time to evaluate : 0.820 Fit side-chains REVERT: A 176 MET cc_start: 0.8928 (tmm) cc_final: 0.8333 (tmm) REVERT: A 218 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7869 (mp-120) REVERT: B 185 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7695 (mmt180) REVERT: D 154 MET cc_start: 0.8698 (tpp) cc_final: 0.8340 (tpp) REVERT: D 199 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: D 218 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7809 (tm130) REVERT: I 154 MET cc_start: 0.8701 (tpp) cc_final: 0.8337 (tpp) REVERT: I 199 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8199 (tpp) REVERT: I 218 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7813 (tm130) REVERT: L 176 MET cc_start: 0.8924 (tmm) cc_final: 0.8327 (tmm) REVERT: L 218 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7862 (mp-120) REVERT: M 185 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7702 (mmt180) outliers start: 17 outliers final: 3 residues processed: 507 average time/residue: 0.8714 time to fit residues: 482.7193 Evaluate side-chains 512 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 501 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 218 GLN Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN E 194 GLN I 194 GLN J 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.131504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.117908 restraints weight = 14969.576| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 0.55 r_work: 0.3052 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20300 Z= 0.150 Angle : 0.580 4.689 27440 Z= 0.307 Chirality : 0.046 0.143 3136 Planarity : 0.005 0.035 3472 Dihedral : 7.281 52.159 2996 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.65 % Allowed : 14.75 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.17), residues: 2478 helix: 2.63 (0.14), residues: 1372 sheet: 0.45 (0.35), residues: 238 loop : -0.97 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 226 TYR 0.014 0.002 TYR K 76 PHE 0.011 0.001 PHE D 105 TRP 0.007 0.002 TRP B 146 HIS 0.005 0.001 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00321 (20300) covalent geometry : angle 0.57989 (27440) hydrogen bonds : bond 0.05366 ( 1190) hydrogen bonds : angle 4.06502 ( 3906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 496 time to evaluate : 0.800 Fit side-chains REVERT: A 218 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7882 (mp-120) REVERT: B 185 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7753 (mmt180) REVERT: D 154 MET cc_start: 0.8766 (tpp) cc_final: 0.8352 (tpp) REVERT: D 199 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8237 (tpp) REVERT: D 218 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7839 (tm130) REVERT: I 154 MET cc_start: 0.8773 (tpp) cc_final: 0.8354 (tpp) REVERT: I 199 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8234 (tpp) REVERT: I 218 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7845 (tm130) REVERT: L 218 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7874 (mp-120) REVERT: M 185 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7761 (mmt180) outliers start: 14 outliers final: 4 residues processed: 498 average time/residue: 0.8800 time to fit residues: 478.3947 Evaluate side-chains 506 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 494 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 218 GLN Chi-restraints excluded: chain L residue 218 GLN Chi-restraints excluded: chain M residue 185 ARG Chi-restraints excluded: chain M residue 199 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 235 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN E 194 GLN I 194 GLN J 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.132070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.118553 restraints weight = 14960.515| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.54 r_work: 0.3061 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20300 Z= 0.139 Angle : 0.562 4.758 27440 Z= 0.296 Chirality : 0.045 0.143 3136 Planarity : 0.004 0.035 3472 Dihedral : 7.207 51.734 2996 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.65 % Allowed : 15.27 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2478 helix: 2.72 (0.14), residues: 1372 sheet: 0.48 (0.35), residues: 238 loop : -0.94 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 226 TYR 0.013 0.002 TYR G 76 PHE 0.010 0.001 PHE A 105 TRP 0.007 0.002 TRP M 146 HIS 0.005 0.001 HIS M 212 Details of bonding type rmsd covalent geometry : bond 0.00295 (20300) covalent geometry : angle 0.56152 (27440) hydrogen bonds : bond 0.05087 ( 1190) hydrogen bonds : angle 3.99410 ( 3906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8969.87 seconds wall clock time: 153 minutes 6.99 seconds (9186.99 seconds total)