Starting phenix.real_space_refine on Sun Dec 29 11:21:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214.map" model { file = "/net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mrw_9214/12_2024/6mrw_9214_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 31304 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 20006 2.51 5 N 5040 2.21 5 O 6230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 31346 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2239 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 3, 'TRANS': 281} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 5.88, per 1000 atoms: 0.19 Number of scatterers: 31346 At special positions: 0 Unit cell: (146.59, 144.45, 156.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 6230 8.00 N 5040 7.00 C 20006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 3.1 seconds 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7644 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.560A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 291 Processing helix chain 'B' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.605A pdb=" N LEU B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 265 removed outlier: 3.561A pdb=" N ILE B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 291 Processing helix chain 'C' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 171 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 291 Processing helix chain 'D' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.605A pdb=" N LEU D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 291 Processing helix chain 'E' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU E 192 " --> pdb=" O GLY E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP E 265 " --> pdb=" O ARG E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 291 Processing helix chain 'F' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR F 125 " --> pdb=" O ASP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP F 171 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU F 192 " --> pdb=" O GLY F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP F 265 " --> pdb=" O ARG F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 291 Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS G 51 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP G 171 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU G 192 " --> pdb=" O GLY G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP G 265 " --> pdb=" O ARG G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 291 Processing helix chain 'H' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS H 51 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL H 60 " --> pdb=" O GLN H 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR H 125 " --> pdb=" O ASP H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 160 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP H 171 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 291 Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL I 60 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR I 125 " --> pdb=" O ASP I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP I 171 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS I 172 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU I 192 " --> pdb=" O GLY I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU I 256 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP I 265 " --> pdb=" O ARG I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 291 Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.559A pdb=" N GLU J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS J 51 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL J 60 " --> pdb=" O GLN J 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP J 114 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP J 171 " --> pdb=" O GLN J 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS J 172 " --> pdb=" O SER J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU J 192 " --> pdb=" O GLY J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP J 265 " --> pdb=" O ARG J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 291 Processing helix chain 'K' and resid 9 through 35 removed outlier: 3.560A pdb=" N GLU K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL K 60 " --> pdb=" O GLN K 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU K 61 " --> pdb=" O ALA K 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN K 92 " --> pdb=" O GLY K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU K 149 " --> pdb=" O SER K 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU K 192 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 265 removed outlier: 3.559A pdb=" N ILE K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP K 265 " --> pdb=" O ARG K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 291 Processing helix chain 'L' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 101 removed outlier: 3.630A pdb=" N LYS L 51 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL L 60 " --> pdb=" O GLN L 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN L 92 " --> pdb=" O GLY L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 125 " --> pdb=" O ASP L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 181 removed outlier: 3.924A pdb=" N LEU L 149 " --> pdb=" O SER L 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER L 160 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP L 171 " --> pdb=" O GLN L 167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU L 192 " --> pdb=" O GLY L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP L 265 " --> pdb=" O ARG L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 291 Processing helix chain 'M' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN M 33 " --> pdb=" O LYS M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 101 removed outlier: 3.632A pdb=" N LYS M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL M 60 " --> pdb=" O GLN M 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 61 " --> pdb=" O ALA M 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL M 89 " --> pdb=" O GLU M 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN M 92 " --> pdb=" O GLY M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 140 removed outlier: 3.563A pdb=" N ASP M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR M 125 " --> pdb=" O ASP M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU M 149 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER M 160 " --> pdb=" O THR M 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP M 171 " --> pdb=" O GLN M 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 202 removed outlier: 3.603A pdb=" N LEU M 192 " --> pdb=" O GLY M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU M 256 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP M 265 " --> pdb=" O ARG M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 291 Processing helix chain 'N' and resid 9 through 35 removed outlier: 3.561A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 101 removed outlier: 3.631A pdb=" N LYS N 51 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL N 60 " --> pdb=" O GLN N 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN N 92 " --> pdb=" O GLY N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 140 removed outlier: 3.562A pdb=" N ASP N 114 " --> pdb=" O SER N 110 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR N 125 " --> pdb=" O ASP N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 181 removed outlier: 3.925A pdb=" N LEU N 149 " --> pdb=" O SER N 145 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER N 160 " --> pdb=" O THR N 156 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP N 171 " --> pdb=" O GLN N 167 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 202 removed outlier: 3.604A pdb=" N LEU N 192 " --> pdb=" O GLY N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 265 removed outlier: 3.560A pdb=" N ILE N 253 " --> pdb=" O ALA N 249 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP N 265 " --> pdb=" O ARG N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 291 3053 hydrogen bonds defined for protein. 9159 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: 8.70 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9848 1.34 - 1.45: 4378 1.45 - 1.57: 17442 1.57 - 1.69: 0 1.69 - 1.80: 112 Bond restraints: 31780 Sorted by residual: bond pdb=" CA ILE H 208 " pdb=" C ILE H 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.02e+00 bond pdb=" CA ILE D 208 " pdb=" C ILE D 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 3.00e+00 bond pdb=" CA ILE N 208 " pdb=" C ILE N 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.98e+00 bond pdb=" CA ILE G 208 " pdb=" C ILE G 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.91e+00 bond pdb=" CA ILE I 208 " pdb=" C ILE I 208 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.90e+00 ... (remaining 31775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 39458 1.64 - 3.28: 3058 3.28 - 4.92: 268 4.92 - 6.56: 84 6.56 - 8.19: 42 Bond angle restraints: 42910 Sorted by residual: angle pdb=" C LEU K 207 " pdb=" N ILE K 208 " pdb=" CA ILE K 208 " ideal model delta sigma weight residual 120.24 124.34 -4.10 6.30e-01 2.52e+00 4.23e+01 angle pdb=" C LEU N 207 " pdb=" N ILE N 208 " pdb=" CA ILE N 208 " ideal model delta sigma weight residual 120.24 124.32 -4.08 6.30e-01 2.52e+00 4.20e+01 angle pdb=" C LEU B 207 " pdb=" N ILE B 208 " pdb=" CA ILE B 208 " ideal model delta sigma weight residual 120.24 124.31 -4.07 6.30e-01 2.52e+00 4.16e+01 angle pdb=" C LEU A 207 " pdb=" N ILE A 208 " pdb=" CA ILE A 208 " ideal model delta sigma weight residual 120.24 124.30 -4.06 6.30e-01 2.52e+00 4.16e+01 angle pdb=" C LEU D 207 " pdb=" N ILE D 208 " pdb=" CA ILE D 208 " ideal model delta sigma weight residual 120.24 124.30 -4.06 6.30e-01 2.52e+00 4.15e+01 ... (remaining 42905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 18480 15.31 - 30.61: 602 30.61 - 45.92: 294 45.92 - 61.22: 0 61.22 - 76.53: 28 Dihedral angle restraints: 19404 sinusoidal: 7602 harmonic: 11802 Sorted by residual: dihedral pdb=" CA PHE D 141 " pdb=" C PHE D 141 " pdb=" N ASN D 142 " pdb=" CA ASN D 142 " ideal model delta harmonic sigma weight residual 180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PHE G 141 " pdb=" C PHE G 141 " pdb=" N ASN G 142 " pdb=" CA ASN G 142 " ideal model delta harmonic sigma weight residual -180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA PHE M 141 " pdb=" C PHE M 141 " pdb=" N ASN M 142 " pdb=" CA ASN M 142 " ideal model delta harmonic sigma weight residual 180.00 -146.89 -33.11 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 19401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3244 0.035 - 0.070: 1415 0.070 - 0.105: 290 0.105 - 0.140: 71 0.140 - 0.175: 34 Chirality restraints: 5054 Sorted by residual: chirality pdb=" CA TYR B 54 " pdb=" N TYR B 54 " pdb=" C TYR B 54 " pdb=" CB TYR B 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA TYR A 54 " pdb=" N TYR A 54 " pdb=" C TYR A 54 " pdb=" CB TYR A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA TYR F 54 " pdb=" N TYR F 54 " pdb=" C TYR F 54 " pdb=" CB TYR F 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 5051 not shown) Planarity restraints: 5404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 35 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO B 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 35 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO M 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO M 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO M 36 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 35 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO D 36 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.025 5.00e-02 4.00e+02 ... (remaining 5401 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 308 2.64 - 3.21: 30315 3.21 - 3.77: 51717 3.77 - 4.34: 65191 4.34 - 4.90: 107320 Nonbonded interactions: 254851 Sorted by model distance: nonbonded pdb=" OD1 ASP L 21 " pdb=" NZ LYS M 29 " model vdw 2.080 3.120 nonbonded pdb=" OH TYR K 54 " pdb=" OD2 ASP K 158 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR N 54 " pdb=" OD2 ASP N 158 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR F 54 " pdb=" OD2 ASP F 158 " model vdw 2.132 3.040 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP I 158 " model vdw 2.132 3.040 ... (remaining 254846 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: 0.00 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 44.040 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 31780 Z= 0.373 Angle : 0.982 8.194 42910 Z= 0.651 Chirality : 0.042 0.175 5054 Planarity : 0.005 0.044 5404 Dihedral : 10.348 76.525 11760 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.41 % Allowed : 3.67 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 3962 helix: 0.25 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -3.14 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP L 86 HIS 0.005 0.003 HIS F 292 PHE 0.009 0.002 PHE D 40 TYR 0.028 0.002 TYR F 54 ARG 0.002 0.000 ARG D 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 269 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 0 residues processed: 283 average time/residue: 0.3232 time to fit residues: 149.8556 Evaluate side-chains 142 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 40.0000 chunk 307 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 186 optimal weight: 40.0000 chunk 228 optimal weight: 4.9990 chunk 355 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN B 289 GLN C 289 GLN D 289 GLN E 289 GLN F 289 GLN G 289 GLN H 289 GLN I 289 GLN J 289 GLN K 289 GLN L 289 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 GLN N 289 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31780 Z= 0.176 Angle : 0.510 8.895 42910 Z= 0.279 Chirality : 0.034 0.146 5054 Planarity : 0.003 0.044 5404 Dihedral : 4.237 26.824 4214 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.13), residues: 3962 helix: 2.44 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.58 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP N 86 HIS 0.001 0.001 HIS M 292 PHE 0.010 0.001 PHE L 221 TYR 0.017 0.001 TYR M 54 ARG 0.005 0.000 ARG J 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9159 (mtp) cc_final: 0.8872 (mmm) REVERT: A 285 CYS cc_start: 0.9666 (m) cc_final: 0.9284 (m) REVERT: B 285 CYS cc_start: 0.9734 (m) cc_final: 0.9275 (m) REVERT: C 28 ASN cc_start: 0.9212 (t0) cc_final: 0.8942 (t0) REVERT: C 285 CYS cc_start: 0.9750 (m) cc_final: 0.9311 (m) REVERT: D 285 CYS cc_start: 0.9640 (m) cc_final: 0.9240 (m) REVERT: E 285 CYS cc_start: 0.9605 (m) cc_final: 0.9321 (m) REVERT: F 28 ASN cc_start: 0.9212 (t0) cc_final: 0.8941 (t0) REVERT: G 28 ASN cc_start: 0.9087 (t0) cc_final: 0.8862 (t0) REVERT: H 28 ASN cc_start: 0.9061 (t0) cc_final: 0.8827 (t0) REVERT: H 285 CYS cc_start: 0.9694 (m) cc_final: 0.9291 (m) REVERT: I 28 ASN cc_start: 0.9161 (t0) cc_final: 0.8856 (t0) REVERT: I 285 CYS cc_start: 0.9732 (m) cc_final: 0.9312 (m) REVERT: J 28 ASN cc_start: 0.9150 (t0) cc_final: 0.8884 (t0) REVERT: J 285 CYS cc_start: 0.9752 (m) cc_final: 0.9291 (m) REVERT: K 28 ASN cc_start: 0.9091 (t0) cc_final: 0.8820 (t0) REVERT: K 285 CYS cc_start: 0.9583 (m) cc_final: 0.9249 (m) REVERT: L 28 ASN cc_start: 0.9253 (t0) cc_final: 0.8944 (t0) REVERT: L 285 CYS cc_start: 0.9635 (m) cc_final: 0.9314 (m) REVERT: M 28 ASN cc_start: 0.9136 (t0) cc_final: 0.8909 (t0) REVERT: M 285 CYS cc_start: 0.9708 (m) cc_final: 0.9307 (m) REVERT: N 28 ASN cc_start: 0.9148 (t0) cc_final: 0.8931 (t0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3623 time to fit residues: 136.2500 Evaluate side-chains 145 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 317 optimal weight: 0.9980 chunk 353 optimal weight: 40.0000 chunk 121 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 GLN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN N 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31780 Z= 0.155 Angle : 0.465 6.268 42910 Z= 0.253 Chirality : 0.033 0.153 5054 Planarity : 0.003 0.041 5404 Dihedral : 3.889 24.448 4214 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.13), residues: 3962 helix: 3.29 (0.08), residues: 3640 sheet: None (None), residues: 0 loop : -2.84 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 86 HIS 0.001 0.001 HIS M 292 PHE 0.007 0.001 PHE D 40 TYR 0.012 0.001 TYR L 54 ARG 0.009 0.001 ARG G 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9479 (tpp) cc_final: 0.9116 (mmm) REVERT: A 285 CYS cc_start: 0.9516 (m) cc_final: 0.8784 (t) REVERT: B 285 CYS cc_start: 0.9503 (m) cc_final: 0.8630 (t) REVERT: D 31 LEU cc_start: 0.8256 (tp) cc_final: 0.8039 (pp) REVERT: D 281 MET cc_start: 0.9523 (tpp) cc_final: 0.9274 (tpp) REVERT: D 285 CYS cc_start: 0.9443 (m) cc_final: 0.8590 (t) REVERT: E 281 MET cc_start: 0.9451 (tpp) cc_final: 0.9167 (tpp) REVERT: E 285 CYS cc_start: 0.9411 (m) cc_final: 0.8649 (t) REVERT: F 70 MET cc_start: 0.9455 (mtm) cc_final: 0.9126 (mtm) REVERT: G 70 MET cc_start: 0.9483 (mtm) cc_final: 0.8991 (mmm) REVERT: G 281 MET cc_start: 0.9118 (mmm) cc_final: 0.8762 (mmm) REVERT: J 285 CYS cc_start: 0.9380 (m) cc_final: 0.8519 (t) REVERT: K 281 MET cc_start: 0.9522 (tpp) cc_final: 0.8880 (mmp) REVERT: K 285 CYS cc_start: 0.9377 (m) cc_final: 0.8480 (t) REVERT: L 70 MET cc_start: 0.9140 (mtp) cc_final: 0.8836 (mmm) REVERT: L 281 MET cc_start: 0.9435 (tpp) cc_final: 0.9218 (tpp) REVERT: L 285 CYS cc_start: 0.9418 (m) cc_final: 0.8699 (t) REVERT: N 281 MET cc_start: 0.9009 (mmp) cc_final: 0.8636 (mmm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3807 time to fit residues: 123.8657 Evaluate side-chains 142 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 339 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 169 GLN K 33 GLN L 33 GLN M 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31780 Z= 0.193 Angle : 0.487 6.582 42910 Z= 0.269 Chirality : 0.034 0.150 5054 Planarity : 0.003 0.042 5404 Dihedral : 3.764 24.209 4214 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.13), residues: 3962 helix: 3.47 (0.08), residues: 3626 sheet: None (None), residues: 0 loop : -2.96 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 86 HIS 0.002 0.001 HIS M 292 PHE 0.009 0.001 PHE D 40 TYR 0.023 0.001 TYR C 27 ARG 0.007 0.001 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9454 (tpp) cc_final: 0.9220 (tpp) REVERT: A 285 CYS cc_start: 0.9520 (m) cc_final: 0.8852 (t) REVERT: D 285 CYS cc_start: 0.9440 (m) cc_final: 0.8615 (t) REVERT: E 285 CYS cc_start: 0.9426 (m) cc_final: 0.8685 (t) REVERT: F 281 MET cc_start: 0.9113 (mmt) cc_final: 0.8730 (mmm) REVERT: G 281 MET cc_start: 0.9171 (mmm) cc_final: 0.8770 (mmm) REVERT: H 281 MET cc_start: 0.9591 (tpp) cc_final: 0.9298 (mmm) REVERT: I 281 MET cc_start: 0.9647 (tpp) cc_final: 0.9436 (mmm) REVERT: K 281 MET cc_start: 0.9493 (tpp) cc_final: 0.9084 (mmp) REVERT: L 285 CYS cc_start: 0.9425 (m) cc_final: 0.8724 (t) REVERT: M 281 MET cc_start: 0.9090 (mmp) cc_final: 0.8573 (mmm) REVERT: N 281 MET cc_start: 0.8904 (mmp) cc_final: 0.8467 (mmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3856 time to fit residues: 116.2890 Evaluate side-chains 128 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 0.2980 chunk 323 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN G 169 GLN N 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 31780 Z= 0.121 Angle : 0.418 5.951 42910 Z= 0.229 Chirality : 0.032 0.148 5054 Planarity : 0.003 0.043 5404 Dihedral : 3.638 21.758 4214 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.13 (0.13), residues: 3962 helix: 3.78 (0.08), residues: 3640 sheet: None (None), residues: 0 loop : -2.68 (0.24), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 86 HIS 0.001 0.000 HIS M 292 PHE 0.008 0.001 PHE N 50 TYR 0.024 0.001 TYR H 54 ARG 0.004 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 CYS cc_start: 0.9526 (m) cc_final: 0.8789 (t) REVERT: B 281 MET cc_start: 0.8999 (mmp) cc_final: 0.8625 (mmm) REVERT: C 281 MET cc_start: 0.8948 (mmp) cc_final: 0.8532 (mmm) REVERT: D 281 MET cc_start: 0.9500 (tpp) cc_final: 0.9282 (mmm) REVERT: E 281 MET cc_start: 0.8951 (mmm) cc_final: 0.8367 (mmm) REVERT: E 285 CYS cc_start: 0.9396 (m) cc_final: 0.8613 (t) REVERT: F 70 MET cc_start: 0.9496 (mmp) cc_final: 0.9101 (mmm) REVERT: G 281 MET cc_start: 0.9233 (mmm) cc_final: 0.8898 (mmm) REVERT: H 281 MET cc_start: 0.9616 (tpp) cc_final: 0.9329 (mmm) REVERT: I 281 MET cc_start: 0.9636 (tpp) cc_final: 0.9397 (mmm) REVERT: J 270 MET cc_start: 0.9385 (mmm) cc_final: 0.9131 (mmm) REVERT: J 281 MET cc_start: 0.8851 (mmt) cc_final: 0.8422 (mmm) REVERT: J 285 CYS cc_start: 0.9390 (m) cc_final: 0.8426 (t) REVERT: K 281 MET cc_start: 0.9468 (tpp) cc_final: 0.8919 (mmp) REVERT: K 285 CYS cc_start: 0.9378 (m) cc_final: 0.8470 (t) REVERT: L 281 MET cc_start: 0.9446 (tpp) cc_final: 0.8936 (mmm) REVERT: L 285 CYS cc_start: 0.9375 (m) cc_final: 0.8605 (t) REVERT: M 281 MET cc_start: 0.9026 (mmp) cc_final: 0.8635 (mmm) REVERT: N 281 MET cc_start: 0.8909 (mmp) cc_final: 0.8401 (mmm) REVERT: N 285 CYS cc_start: 0.9479 (m) cc_final: 0.8741 (t) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3826 time to fit residues: 118.4951 Evaluate side-chains 118 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 379 optimal weight: 9.9990 chunk 314 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN C 33 GLN D 33 GLN F 33 GLN H 33 GLN H 142 ASN I 33 GLN I 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31780 Z= 0.155 Angle : 0.443 5.751 42910 Z= 0.244 Chirality : 0.033 0.148 5054 Planarity : 0.003 0.046 5404 Dihedral : 3.574 22.425 4214 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.30 (0.12), residues: 3962 helix: 3.86 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.44 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 86 HIS 0.001 0.001 HIS M 292 PHE 0.008 0.001 PHE A 50 TYR 0.023 0.001 TYR L 54 ARG 0.005 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9475 (tpp) cc_final: 0.9113 (mmm) REVERT: A 285 CYS cc_start: 0.9523 (m) cc_final: 0.8822 (t) REVERT: B 281 MET cc_start: 0.8936 (mmp) cc_final: 0.8619 (mmm) REVERT: C 70 MET cc_start: 0.9380 (mmm) cc_final: 0.9166 (mmm) REVERT: C 281 MET cc_start: 0.8964 (mmp) cc_final: 0.8667 (mmm) REVERT: C 285 CYS cc_start: 0.9431 (m) cc_final: 0.8641 (t) REVERT: D 281 MET cc_start: 0.9485 (tpp) cc_final: 0.9011 (mmm) REVERT: D 285 CYS cc_start: 0.9444 (m) cc_final: 0.8562 (t) REVERT: E 281 MET cc_start: 0.8979 (mmm) cc_final: 0.8249 (mmm) REVERT: E 285 CYS cc_start: 0.9407 (m) cc_final: 0.8633 (t) REVERT: F 70 MET cc_start: 0.9493 (mmp) cc_final: 0.9076 (mmm) REVERT: F 281 MET cc_start: 0.9035 (mmp) cc_final: 0.8685 (mmm) REVERT: G 70 MET cc_start: 0.9537 (mmm) cc_final: 0.9099 (mmm) REVERT: G 281 MET cc_start: 0.9281 (mmm) cc_final: 0.8877 (mmm) REVERT: J 281 MET cc_start: 0.8850 (mmt) cc_final: 0.8452 (mmm) REVERT: J 285 CYS cc_start: 0.9428 (m) cc_final: 0.8551 (t) REVERT: K 49 ARG cc_start: 0.9298 (pmt-80) cc_final: 0.9093 (pmt-80) REVERT: K 281 MET cc_start: 0.9459 (tpp) cc_final: 0.8859 (mmm) REVERT: K 285 CYS cc_start: 0.9376 (m) cc_final: 0.8500 (t) REVERT: L 281 MET cc_start: 0.9402 (tpp) cc_final: 0.8796 (mmm) REVERT: L 285 CYS cc_start: 0.9405 (m) cc_final: 0.8691 (t) REVERT: M 281 MET cc_start: 0.9011 (mmp) cc_final: 0.8686 (mmm) REVERT: N 281 MET cc_start: 0.8882 (mmp) cc_final: 0.8272 (mmm) REVERT: N 285 CYS cc_start: 0.9499 (m) cc_final: 0.8794 (t) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3487 time to fit residues: 98.1687 Evaluate side-chains 108 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 377 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 33 GLN H 169 GLN L 169 GLN M 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31780 Z= 0.135 Angle : 0.422 8.709 42910 Z= 0.230 Chirality : 0.032 0.148 5054 Planarity : 0.003 0.072 5404 Dihedral : 3.507 21.582 4214 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.53 (0.12), residues: 3962 helix: 4.01 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 86 HIS 0.001 0.000 HIS B 292 PHE 0.010 0.001 PHE C 50 TYR 0.033 0.001 TYR E 54 ARG 0.011 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9472 (tpp) cc_final: 0.9142 (mmm) REVERT: A 285 CYS cc_start: 0.9528 (m) cc_final: 0.8786 (t) REVERT: B 281 MET cc_start: 0.8921 (mmp) cc_final: 0.8342 (mmm) REVERT: B 285 CYS cc_start: 0.9473 (m) cc_final: 0.8630 (t) REVERT: C 70 MET cc_start: 0.9425 (mmm) cc_final: 0.9090 (mmm) REVERT: C 281 MET cc_start: 0.8923 (mmp) cc_final: 0.8348 (mmm) REVERT: C 285 CYS cc_start: 0.9425 (m) cc_final: 0.8636 (t) REVERT: D 70 MET cc_start: 0.9221 (mtp) cc_final: 0.8918 (mmm) REVERT: D 281 MET cc_start: 0.9491 (tpp) cc_final: 0.9052 (mmm) REVERT: D 285 CYS cc_start: 0.9424 (m) cc_final: 0.8537 (t) REVERT: E 281 MET cc_start: 0.9072 (mmm) cc_final: 0.8340 (mmm) REVERT: E 285 CYS cc_start: 0.9382 (m) cc_final: 0.8598 (t) REVERT: F 70 MET cc_start: 0.9482 (mmp) cc_final: 0.9036 (mmm) REVERT: F 281 MET cc_start: 0.8959 (mmp) cc_final: 0.8626 (mmm) REVERT: G 70 MET cc_start: 0.9543 (mmm) cc_final: 0.9048 (mmm) REVERT: G 281 MET cc_start: 0.9332 (mmm) cc_final: 0.8624 (mmm) REVERT: G 285 CYS cc_start: 0.9480 (m) cc_final: 0.8576 (t) REVERT: H 70 MET cc_start: 0.9506 (mmm) cc_final: 0.9023 (mmm) REVERT: H 281 MET cc_start: 0.9484 (mmm) cc_final: 0.9146 (mmm) REVERT: I 281 MET cc_start: 0.9168 (mmm) cc_final: 0.8929 (mmm) REVERT: J 270 MET cc_start: 0.9421 (mmm) cc_final: 0.9156 (mmm) REVERT: J 281 MET cc_start: 0.8796 (mmt) cc_final: 0.8428 (mmm) REVERT: J 285 CYS cc_start: 0.9396 (m) cc_final: 0.8505 (t) REVERT: K 70 MET cc_start: 0.9528 (mmm) cc_final: 0.9107 (mmm) REVERT: K 281 MET cc_start: 0.9444 (tpp) cc_final: 0.8849 (mmm) REVERT: K 285 CYS cc_start: 0.9365 (m) cc_final: 0.8479 (t) REVERT: L 70 MET cc_start: 0.9569 (mmm) cc_final: 0.9279 (mmm) REVERT: L 281 MET cc_start: 0.9402 (tpp) cc_final: 0.8866 (mmm) REVERT: L 285 CYS cc_start: 0.9404 (m) cc_final: 0.8651 (t) REVERT: M 281 MET cc_start: 0.8994 (mmp) cc_final: 0.8661 (mmm) REVERT: N 70 MET cc_start: 0.9513 (mmm) cc_final: 0.9055 (mmm) REVERT: N 281 MET cc_start: 0.8870 (mmp) cc_final: 0.8276 (mmm) REVERT: N 285 CYS cc_start: 0.9484 (m) cc_final: 0.8753 (t) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3712 time to fit residues: 101.0488 Evaluate side-chains 113 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 240 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 296 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 169 GLN J 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31780 Z= 0.132 Angle : 0.423 7.153 42910 Z= 0.231 Chirality : 0.032 0.148 5054 Planarity : 0.004 0.107 5404 Dihedral : 3.479 21.418 4214 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.64 (0.12), residues: 3962 helix: 4.09 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 86 HIS 0.001 0.000 HIS B 292 PHE 0.010 0.001 PHE L 101 TYR 0.029 0.001 TYR D 54 ARG 0.008 0.001 ARG J 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9473 (tpp) cc_final: 0.8937 (mmm) REVERT: A 285 CYS cc_start: 0.9519 (m) cc_final: 0.8780 (t) REVERT: B 70 MET cc_start: 0.9549 (mmm) cc_final: 0.9139 (mmm) REVERT: B 281 MET cc_start: 0.8923 (mmp) cc_final: 0.8350 (mmm) REVERT: B 285 CYS cc_start: 0.9465 (m) cc_final: 0.8622 (t) REVERT: C 70 MET cc_start: 0.9443 (mmm) cc_final: 0.9074 (mmm) REVERT: C 270 MET cc_start: 0.9371 (mmm) cc_final: 0.9098 (mmm) REVERT: C 281 MET cc_start: 0.8908 (mmp) cc_final: 0.8318 (mmm) REVERT: C 285 CYS cc_start: 0.9429 (m) cc_final: 0.8529 (t) REVERT: D 70 MET cc_start: 0.9238 (mtp) cc_final: 0.8931 (mmm) REVERT: E 70 MET cc_start: 0.9543 (mmp) cc_final: 0.9137 (mmm) REVERT: E 281 MET cc_start: 0.9117 (mmm) cc_final: 0.8378 (mmm) REVERT: E 285 CYS cc_start: 0.9370 (m) cc_final: 0.8596 (t) REVERT: F 70 MET cc_start: 0.9476 (mmp) cc_final: 0.9033 (mmm) REVERT: F 281 MET cc_start: 0.8926 (mmp) cc_final: 0.8625 (mmm) REVERT: G 70 MET cc_start: 0.9543 (mmm) cc_final: 0.9048 (mmm) REVERT: G 281 MET cc_start: 0.9357 (mmm) cc_final: 0.8662 (mmm) REVERT: G 285 CYS cc_start: 0.9473 (m) cc_final: 0.8571 (t) REVERT: H 70 MET cc_start: 0.9488 (mmm) cc_final: 0.9003 (mmm) REVERT: H 281 MET cc_start: 0.9494 (mmm) cc_final: 0.9125 (mmm) REVERT: I 70 MET cc_start: 0.9566 (mmm) cc_final: 0.9191 (mmm) REVERT: I 281 MET cc_start: 0.9190 (mmm) cc_final: 0.8970 (mmm) REVERT: J 70 MET cc_start: 0.9485 (mmm) cc_final: 0.9007 (mmm) REVERT: J 270 MET cc_start: 0.9413 (mmm) cc_final: 0.9160 (mmm) REVERT: J 281 MET cc_start: 0.8783 (mmt) cc_final: 0.8522 (mmm) REVERT: J 285 CYS cc_start: 0.9401 (m) cc_final: 0.8506 (t) REVERT: K 70 MET cc_start: 0.9523 (mmm) cc_final: 0.9094 (mmm) REVERT: K 281 MET cc_start: 0.9436 (tpp) cc_final: 0.8859 (mmm) REVERT: K 285 CYS cc_start: 0.9362 (m) cc_final: 0.8474 (t) REVERT: L 70 MET cc_start: 0.9571 (mmm) cc_final: 0.9308 (mmm) REVERT: L 281 MET cc_start: 0.9378 (tpp) cc_final: 0.8934 (mmt) REVERT: L 285 CYS cc_start: 0.9399 (m) cc_final: 0.8638 (t) REVERT: M 281 MET cc_start: 0.9003 (mmp) cc_final: 0.8664 (mmm) REVERT: N 70 MET cc_start: 0.9551 (mmm) cc_final: 0.9030 (mmm) REVERT: N 281 MET cc_start: 0.8863 (mmp) cc_final: 0.8307 (mmm) REVERT: N 285 CYS cc_start: 0.9481 (m) cc_final: 0.8752 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3240 time to fit residues: 89.1808 Evaluate side-chains 111 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9990 chunk 361 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31780 Z= 0.145 Angle : 0.431 6.884 42910 Z= 0.234 Chirality : 0.032 0.145 5054 Planarity : 0.004 0.085 5404 Dihedral : 3.453 21.807 4214 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.68 (0.12), residues: 3962 helix: 4.11 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.41 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 86 HIS 0.001 0.001 HIS B 292 PHE 0.011 0.001 PHE L 101 TYR 0.025 0.001 TYR E 54 ARG 0.010 0.001 ARG M 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9467 (tpp) cc_final: 0.8977 (mmm) REVERT: A 285 CYS cc_start: 0.9516 (m) cc_final: 0.8779 (t) REVERT: B 70 MET cc_start: 0.9529 (mmm) cc_final: 0.9116 (mmm) REVERT: B 285 CYS cc_start: 0.9468 (m) cc_final: 0.8632 (t) REVERT: C 70 MET cc_start: 0.9462 (mmm) cc_final: 0.9073 (mmm) REVERT: C 270 MET cc_start: 0.9385 (mmm) cc_final: 0.9146 (mmm) REVERT: C 281 MET cc_start: 0.8903 (mmp) cc_final: 0.8325 (mmm) REVERT: C 285 CYS cc_start: 0.9442 (m) cc_final: 0.8556 (t) REVERT: D 70 MET cc_start: 0.9230 (mtp) cc_final: 0.8937 (mmm) REVERT: D 281 MET cc_start: 0.9511 (tpp) cc_final: 0.9195 (mmm) REVERT: E 281 MET cc_start: 0.9095 (mmm) cc_final: 0.8331 (mmm) REVERT: E 285 CYS cc_start: 0.9371 (m) cc_final: 0.8606 (t) REVERT: F 70 MET cc_start: 0.9459 (mmp) cc_final: 0.9028 (mmm) REVERT: G 70 MET cc_start: 0.9548 (mmm) cc_final: 0.9050 (mmm) REVERT: G 281 MET cc_start: 0.9399 (mmm) cc_final: 0.8730 (mmm) REVERT: G 285 CYS cc_start: 0.9477 (m) cc_final: 0.8588 (t) REVERT: H 70 MET cc_start: 0.9484 (mmm) cc_final: 0.8986 (mmm) REVERT: H 281 MET cc_start: 0.9486 (mmm) cc_final: 0.9254 (mmm) REVERT: I 70 MET cc_start: 0.9544 (mmm) cc_final: 0.9165 (mmm) REVERT: I 281 MET cc_start: 0.9231 (mmm) cc_final: 0.8989 (mmm) REVERT: J 70 MET cc_start: 0.9482 (mmm) cc_final: 0.9014 (mmm) REVERT: J 270 MET cc_start: 0.9428 (mmm) cc_final: 0.9172 (mmm) REVERT: J 281 MET cc_start: 0.8742 (mmt) cc_final: 0.8473 (mmm) REVERT: J 285 CYS cc_start: 0.9407 (m) cc_final: 0.8522 (t) REVERT: K 70 MET cc_start: 0.9502 (mmm) cc_final: 0.9086 (mmm) REVERT: K 281 MET cc_start: 0.9438 (tpp) cc_final: 0.8969 (mmm) REVERT: L 70 MET cc_start: 0.9561 (mmm) cc_final: 0.9330 (mmm) REVERT: L 281 MET cc_start: 0.9375 (tpp) cc_final: 0.9038 (mmt) REVERT: L 285 CYS cc_start: 0.9398 (m) cc_final: 0.8654 (t) REVERT: M 281 MET cc_start: 0.8993 (mmp) cc_final: 0.8658 (mmm) REVERT: N 70 MET cc_start: 0.9564 (mmm) cc_final: 0.9011 (mmm) REVERT: N 281 MET cc_start: 0.8868 (mmp) cc_final: 0.8311 (mmm) REVERT: N 285 CYS cc_start: 0.9478 (m) cc_final: 0.8746 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2995 time to fit residues: 81.9813 Evaluate side-chains 108 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.5980 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31780 Z= 0.114 Angle : 0.416 10.119 42910 Z= 0.222 Chirality : 0.032 0.140 5054 Planarity : 0.004 0.103 5404 Dihedral : 3.402 20.656 4214 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.87 (0.12), residues: 3962 helix: 4.24 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 86 HIS 0.000 0.000 HIS F 292 PHE 0.013 0.001 PHE C 50 TYR 0.024 0.001 TYR E 54 ARG 0.011 0.001 ARG L 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7924 Ramachandran restraints generated. 3962 Oldfield, 0 Emsley, 3962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.9457 (tpp) cc_final: 0.9124 (mmm) REVERT: A 285 CYS cc_start: 0.9497 (m) cc_final: 0.8764 (t) REVERT: B 70 MET cc_start: 0.9522 (mmm) cc_final: 0.9101 (mmm) REVERT: B 281 MET cc_start: 0.8920 (mmp) cc_final: 0.8346 (mmm) REVERT: B 285 CYS cc_start: 0.9432 (m) cc_final: 0.8560 (t) REVERT: C 70 MET cc_start: 0.9453 (mmm) cc_final: 0.9060 (mmm) REVERT: C 270 MET cc_start: 0.9376 (mmm) cc_final: 0.9099 (mmm) REVERT: C 281 MET cc_start: 0.8894 (mmp) cc_final: 0.8301 (mmm) REVERT: C 285 CYS cc_start: 0.9423 (m) cc_final: 0.8529 (t) REVERT: D 70 MET cc_start: 0.9191 (mtp) cc_final: 0.8911 (mmm) REVERT: D 281 MET cc_start: 0.9509 (tpp) cc_final: 0.9261 (mmm) REVERT: E 70 MET cc_start: 0.9493 (mmm) cc_final: 0.9120 (mmm) REVERT: E 281 MET cc_start: 0.9084 (mmm) cc_final: 0.8446 (mmm) REVERT: E 285 CYS cc_start: 0.9354 (m) cc_final: 0.8584 (t) REVERT: F 70 MET cc_start: 0.9427 (mmp) cc_final: 0.8974 (mmm) REVERT: F 281 MET cc_start: 0.9129 (mmp) cc_final: 0.8768 (mmp) REVERT: G 70 MET cc_start: 0.9539 (mmm) cc_final: 0.9026 (mmm) REVERT: G 281 MET cc_start: 0.9420 (mmm) cc_final: 0.8796 (mmm) REVERT: G 285 CYS cc_start: 0.9462 (m) cc_final: 0.8566 (t) REVERT: H 70 MET cc_start: 0.9471 (mmm) cc_final: 0.8973 (mmm) REVERT: H 281 MET cc_start: 0.9502 (mmm) cc_final: 0.9211 (mmm) REVERT: I 70 MET cc_start: 0.9541 (mmm) cc_final: 0.9159 (mmm) REVERT: J 70 MET cc_start: 0.9471 (mmm) cc_final: 0.9023 (mmm) REVERT: J 270 MET cc_start: 0.9406 (mmm) cc_final: 0.9160 (mmm) REVERT: J 281 MET cc_start: 0.8728 (mmt) cc_final: 0.8429 (mmm) REVERT: J 285 CYS cc_start: 0.9432 (m) cc_final: 0.8531 (t) REVERT: K 70 MET cc_start: 0.9514 (mmm) cc_final: 0.9059 (mmm) REVERT: K 281 MET cc_start: 0.9445 (tpp) cc_final: 0.8909 (mmm) REVERT: K 285 CYS cc_start: 0.9405 (m) cc_final: 0.8490 (t) REVERT: L 70 MET cc_start: 0.9544 (mmm) cc_final: 0.9319 (mmm) REVERT: L 281 MET cc_start: 0.9362 (tpp) cc_final: 0.8998 (mmm) REVERT: L 285 CYS cc_start: 0.9380 (m) cc_final: 0.8619 (t) REVERT: M 281 MET cc_start: 0.8972 (mmp) cc_final: 0.8629 (mmm) REVERT: N 70 MET cc_start: 0.9549 (mmm) cc_final: 0.8980 (mmm) REVERT: N 281 MET cc_start: 0.8864 (mmp) cc_final: 0.8302 (mmm) REVERT: N 285 CYS cc_start: 0.9454 (m) cc_final: 0.8696 (t) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3358 time to fit residues: 101.0983 Evaluate side-chains 122 residues out of total 3430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 319 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.048004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.031333 restraints weight = 230588.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.031944 restraints weight = 168477.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.032359 restraints weight = 131162.207| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31780 Z= 0.176 Angle : 0.463 7.462 42910 Z= 0.248 Chirality : 0.033 0.143 5054 Planarity : 0.004 0.083 5404 Dihedral : 3.423 22.005 4214 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.72 (0.12), residues: 3962 helix: 4.14 (0.08), residues: 3654 sheet: None (None), residues: 0 loop : -2.39 (0.26), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 86 HIS 0.002 0.001 HIS I 292 PHE 0.009 0.001 PHE L 101 TYR 0.025 0.001 TYR D 54 ARG 0.011 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.27 seconds wall clock time: 65 minutes 15.53 seconds (3915.53 seconds total)