Starting phenix.real_space_refine on Fri May 16 22:48:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.map" model { file = "/net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m66_30114/05_2025/6m66_30114.cif" } resolution = 4.1 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= 0.015 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 5.06, per 1000 atoms: 0.34 Number of scatterers: 14938 At special positions: 0 Unit cell: (113.94, 113.94, 113.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.02 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.02 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.02 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.02 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.02 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.02 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: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 5.032A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.698A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'B' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.698A pdb=" N GLN B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 157 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 310' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'C' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.698A pdb=" N GLN C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.595A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 157 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 310' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'D' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.698A pdb=" N GLN D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 157 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 removed outlier: 4.443A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 310' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.749A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'E' and resid 36 through 59 removed outlier: 5.031A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.697A pdb=" N GLN E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 157 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 310' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL E 317 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'F' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.697A pdb=" N GLN F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 removed outlier: 4.107A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 157 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 Processing helix chain 'F' and resid 209 through 238 removed outlier: 3.771A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.139A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.121A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'G' and resid 36 through 59 removed outlier: 5.032A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.697A pdb=" N GLN G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.596A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 removed outlier: 4.106A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 157 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 209 through 238 removed outlier: 3.770A pdb=" N TYR G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.138A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 275 removed outlier: 3.769A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.564A pdb=" N LEU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 removed outlier: 4.120A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 310 removed outlier: 4.442A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 310' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.750A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL G 317 " --> pdb=" O PRO G 313 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.910A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.911A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 3.77 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: 4322 1.34 - 1.46: 3089 1.46 - 1.57: 7814 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C VAL C 297 " pdb=" N PRO C 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" C VAL A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.83e+00 bond pdb=" C VAL G 297 " pdb=" N PRO G 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.82e+00 bond pdb=" C VAL E 297 " pdb=" N PRO E 298 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C VAL D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.75e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19352 1.74 - 3.47: 1098 3.47 - 5.21: 222 5.21 - 6.95: 91 6.95 - 8.68: 62 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU G 122 " pdb=" CA LEU G 122 " pdb=" C LEU G 122 " ideal model delta sigma weight residual 109.81 117.98 -8.17 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N LEU D 122 " pdb=" CA LEU D 122 " pdb=" C LEU D 122 " ideal model delta sigma weight residual 109.81 117.97 -8.16 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU F 122 " pdb=" CA LEU F 122 " pdb=" C LEU F 122 " ideal model delta sigma weight residual 109.81 117.96 -8.15 2.21e+00 2.05e-01 1.36e+01 angle pdb=" N LEU A 122 " pdb=" CA LEU A 122 " pdb=" C LEU A 122 " ideal model delta sigma weight residual 109.81 117.95 -8.14 2.21e+00 2.05e-01 1.36e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.27: 7305 14.27 - 28.53: 1291 28.53 - 42.80: 420 42.80 - 57.07: 84 57.07 - 71.33: 14 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA PRO C 260 " pdb=" C PRO C 260 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 260 " pdb=" C PRO A 260 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO D 260 " pdb=" C PRO D 260 " pdb=" N ASP D 261 " pdb=" CA ASP D 261 " ideal model delta harmonic sigma weight residual -180.00 -155.98 -24.02 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1431 0.045 - 0.091: 758 0.091 - 0.136: 183 0.136 - 0.181: 85 0.181 - 0.226: 14 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE C 109 " pdb=" N PHE C 109 " pdb=" C PHE C 109 " pdb=" CB PHE C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE A 109 " pdb=" N PHE A 109 " pdb=" C PHE A 109 " pdb=" CB PHE A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " -0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 124 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 123 " 0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO G 124 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 124 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.054 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 124 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.045 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2999 2.76 - 3.30: 14723 3.30 - 3.83: 25889 3.83 - 4.37: 28545 4.37 - 4.90: 46095 Nonbonded interactions: 118251 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 275 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 275 " model vdw 2.257 3.040 nonbonded pdb=" O ARG G 217 " pdb=" OG1 THR G 220 " model vdw 2.279 3.040 nonbonded pdb=" O ARG C 217 " pdb=" OG1 THR C 220 " model vdw 2.280 3.040 nonbonded pdb=" O ARG F 217 " pdb=" OG1 THR F 220 " model vdw 2.280 3.040 ... (remaining 118246 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 27.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.005 0.054 15323 Z= 0.263 Angle : 1.076 8.681 20853 Z= 0.566 Chirality : 0.060 0.226 2471 Planarity : 0.010 0.080 2520 Dihedral : 16.352 71.333 5460 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % 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: -5.00 (0.14), residues: 1827 helix: -3.08 (0.11), residues: 1008 sheet: -4.52 (0.40), residues: 70 loop : -3.38 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 127 HIS 0.004 0.001 HIS A 106 PHE 0.028 0.002 PHE E 109 TYR 0.017 0.002 TYR F 309 ARG 0.002 0.001 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.22734 ( 736) hydrogen bonds : angle 8.24486 ( 2187) SS BOND : bond 0.00522 ( 14) SS BOND : angle 1.14911 ( 28) covalent geometry : bond 0.00544 (15309) covalent geometry : angle 1.07623 (20825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.632 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 38 VAL cc_start: 0.9217 (t) cc_final: 0.8970 (p) REVERT: A 144 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 38 VAL cc_start: 0.9216 (t) cc_final: 0.8999 (p) REVERT: B 128 ARG cc_start: 0.9427 (tmm-80) cc_final: 0.9216 (ttp-110) REVERT: B 141 PHE cc_start: 0.7595 (m-10) cc_final: 0.7358 (m-80) REVERT: B 144 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9194 (tm-30) REVERT: C 141 PHE cc_start: 0.7613 (m-10) cc_final: 0.7411 (m-80) REVERT: C 144 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9219 (tm-30) REVERT: C 152 ARG cc_start: 0.5779 (ttt180) cc_final: 0.5517 (ptt90) REVERT: D 128 ARG cc_start: 0.9498 (tmm-80) cc_final: 0.9250 (ttp-110) REVERT: D 141 PHE cc_start: 0.7765 (m-10) cc_final: 0.7422 (m-80) REVERT: D 144 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9154 (tm-30) REVERT: D 152 ARG cc_start: 0.5509 (ttt180) cc_final: 0.5176 (ptt90) REVERT: E 128 ARG cc_start: 0.9452 (tmm-80) cc_final: 0.9141 (ttp-110) REVERT: F 38 VAL cc_start: 0.9311 (t) cc_final: 0.9097 (p) REVERT: F 152 ARG cc_start: 0.5709 (ttt180) cc_final: 0.5467 (ptt90) REVERT: G 38 VAL cc_start: 0.9324 (t) cc_final: 0.9100 (p) REVERT: G 144 GLU cc_start: 0.9419 (tm-30) cc_final: 0.9180 (tm-30) REVERT: G 152 ARG cc_start: 0.5803 (ttt180) cc_final: 0.5523 (ptt90) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3020 time to fit residues: 106.7154 Evaluate side-chains 130 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 207 ASN A 319 HIS B 134 HIS B 319 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 207 ASN C 319 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 207 ASN D 319 HIS E 134 HIS E 207 ASN E 319 HIS F 134 HIS F 207 ASN F 319 HIS G 134 HIS G 207 ASN G 319 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.092761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071805 restraints weight = 67491.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073354 restraints weight = 43905.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.074391 restraints weight = 32669.184| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15323 Z= 0.229 Angle : 0.888 8.507 20853 Z= 0.437 Chirality : 0.052 0.229 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.779 22.799 1981 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % 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: -3.58 (0.17), residues: 1827 helix: -1.70 (0.13), residues: 1155 sheet: -5.02 (0.37), residues: 84 loop : -3.06 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 127 HIS 0.003 0.001 HIS B 134 PHE 0.019 0.001 PHE B 109 TYR 0.032 0.002 TYR E 234 ARG 0.005 0.000 ARG C 128 Details of bonding type rmsd hydrogen bonds : bond 0.05209 ( 736) hydrogen bonds : angle 5.74490 ( 2187) SS BOND : bond 0.00504 ( 14) SS BOND : angle 1.35863 ( 28) covalent geometry : bond 0.00488 (15309) covalent geometry : angle 0.88673 (20825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.614 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 56 GLN cc_start: 0.8104 (mm110) cc_final: 0.7768 (mm110) REVERT: A 128 ARG cc_start: 0.9410 (ttp-110) cc_final: 0.9206 (ttp-110) REVERT: A 141 PHE cc_start: 0.7774 (m-10) cc_final: 0.7559 (m-80) REVERT: A 272 ILE cc_start: 0.9329 (pt) cc_final: 0.8918 (tt) REVERT: B 56 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7716 (mm110) REVERT: B 128 ARG cc_start: 0.9567 (tmm-80) cc_final: 0.9278 (ttp-110) REVERT: B 141 PHE cc_start: 0.7548 (m-10) cc_final: 0.7347 (m-80) REVERT: B 272 ILE cc_start: 0.9292 (pt) cc_final: 0.8994 (tt) REVERT: C 36 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8563 (tptt) REVERT: C 56 GLN cc_start: 0.7894 (mm110) cc_final: 0.7268 (mm110) REVERT: C 152 ARG cc_start: 0.5833 (ttt180) cc_final: 0.5508 (ptt90) REVERT: D 37 MET cc_start: 0.7888 (ttp) cc_final: 0.7687 (mtp) REVERT: D 128 ARG cc_start: 0.9527 (tmm-80) cc_final: 0.9324 (ttp-110) REVERT: D 141 PHE cc_start: 0.7717 (m-10) cc_final: 0.7442 (m-80) REVERT: D 152 ARG cc_start: 0.5333 (ttt180) cc_final: 0.5046 (ptt90) REVERT: E 56 GLN cc_start: 0.8025 (mm110) cc_final: 0.7678 (mm110) REVERT: E 128 ARG cc_start: 0.9514 (tmm-80) cc_final: 0.9159 (ttp-110) REVERT: E 272 ILE cc_start: 0.9360 (pt) cc_final: 0.9111 (tt) REVERT: F 128 ARG cc_start: 0.9427 (ttp-110) cc_final: 0.9212 (ttp-110) REVERT: F 141 PHE cc_start: 0.7783 (m-10) cc_final: 0.7564 (m-80) REVERT: F 152 ARG cc_start: 0.5630 (ttt180) cc_final: 0.5412 (ptt90) REVERT: G 128 ARG cc_start: 0.9445 (ttp-110) cc_final: 0.9230 (ttp-110) REVERT: G 152 ARG cc_start: 0.5683 (ttt180) cc_final: 0.5422 (ptt90) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3029 time to fit residues: 78.3687 Evaluate side-chains 104 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 74 optimal weight: 0.0170 chunk 170 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.095064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074999 restraints weight = 65760.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.075477 restraints weight = 46113.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.076429 restraints weight = 36062.757| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15323 Z= 0.159 Angle : 0.810 9.292 20853 Z= 0.391 Chirality : 0.049 0.201 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.240 21.704 1981 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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: -2.87 (0.18), residues: 1827 helix: -1.10 (0.14), residues: 1148 sheet: -4.40 (0.48), residues: 84 loop : -2.93 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 127 HIS 0.002 0.001 HIS D 106 PHE 0.023 0.001 PHE C 141 TYR 0.030 0.002 TYR D 234 ARG 0.005 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.04642 ( 736) hydrogen bonds : angle 5.21278 ( 2187) SS BOND : bond 0.00643 ( 14) SS BOND : angle 1.22385 ( 28) covalent geometry : bond 0.00340 (15309) covalent geometry : angle 0.80934 (20825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.836 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 56 GLN cc_start: 0.8099 (mm110) cc_final: 0.7702 (mm110) REVERT: A 128 ARG cc_start: 0.9445 (ttp-110) cc_final: 0.9182 (ttp-110) REVERT: A 141 PHE cc_start: 0.7704 (m-10) cc_final: 0.7428 (m-80) REVERT: A 272 ILE cc_start: 0.9340 (pt) cc_final: 0.9051 (tt) REVERT: B 128 ARG cc_start: 0.9595 (tmm-80) cc_final: 0.9319 (ttp-110) REVERT: C 36 LYS cc_start: 0.8956 (tmmt) cc_final: 0.8709 (tptt) REVERT: C 56 GLN cc_start: 0.8108 (mm110) cc_final: 0.7592 (mm-40) REVERT: C 152 ARG cc_start: 0.5857 (ttt180) cc_final: 0.5551 (ptt90) REVERT: D 56 GLN cc_start: 0.8223 (mt0) cc_final: 0.7977 (mm110) REVERT: D 141 PHE cc_start: 0.7664 (m-10) cc_final: 0.7414 (m-80) REVERT: D 152 ARG cc_start: 0.5370 (ttt180) cc_final: 0.5060 (ptt90) REVERT: D 217 ARG cc_start: 0.9107 (mtt180) cc_final: 0.8679 (mpp80) REVERT: D 272 ILE cc_start: 0.9319 (pt) cc_final: 0.9061 (tt) REVERT: E 56 GLN cc_start: 0.8163 (mm110) cc_final: 0.7784 (mm110) REVERT: E 128 ARG cc_start: 0.9571 (tmm-80) cc_final: 0.9244 (ttp-110) REVERT: F 128 ARG cc_start: 0.9452 (ttp-110) cc_final: 0.9190 (ttp-110) REVERT: F 152 ARG cc_start: 0.5472 (ttt180) cc_final: 0.5257 (ptt90) REVERT: G 128 ARG cc_start: 0.9515 (ttp-110) cc_final: 0.9301 (ttp-110) REVERT: G 152 ARG cc_start: 0.5629 (ttt180) cc_final: 0.5389 (ptt90) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3086 time to fit residues: 73.7704 Evaluate side-chains 111 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 121 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 116 optimal weight: 0.0670 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.094717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.074323 restraints weight = 65751.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075148 restraints weight = 45262.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075914 restraints weight = 33293.898| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15323 Z= 0.169 Angle : 0.810 9.544 20853 Z= 0.391 Chirality : 0.050 0.204 2471 Planarity : 0.006 0.065 2520 Dihedral : 6.098 20.666 1981 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -2.43 (0.18), residues: 1827 helix: -0.70 (0.14), residues: 1169 sheet: -4.35 (0.52), residues: 84 loop : -2.93 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 127 HIS 0.001 0.000 HIS E 106 PHE 0.027 0.001 PHE F 141 TYR 0.034 0.001 TYR A 234 ARG 0.002 0.000 ARG E 217 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 736) hydrogen bonds : angle 5.09604 ( 2187) SS BOND : bond 0.00569 ( 14) SS BOND : angle 1.59078 ( 28) covalent geometry : bond 0.00367 (15309) covalent geometry : angle 0.80817 (20825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8116 (mm110) cc_final: 0.7730 (mm110) REVERT: A 128 ARG cc_start: 0.9439 (ttp-110) cc_final: 0.9180 (ttp-110) REVERT: A 217 ARG cc_start: 0.9240 (mtm180) cc_final: 0.8498 (mtm-85) REVERT: B 56 GLN cc_start: 0.8111 (mm110) cc_final: 0.7321 (mm-40) REVERT: B 128 ARG cc_start: 0.9568 (tmm-80) cc_final: 0.9182 (ttp80) REVERT: B 272 ILE cc_start: 0.9269 (pt) cc_final: 0.8954 (pt) REVERT: D 141 PHE cc_start: 0.7641 (m-10) cc_final: 0.7378 (m-80) REVERT: D 152 ARG cc_start: 0.5279 (ttt180) cc_final: 0.4992 (ptt90) REVERT: D 217 ARG cc_start: 0.9239 (mtt180) cc_final: 0.8675 (mpp80) REVERT: E 128 ARG cc_start: 0.9586 (tmm-80) cc_final: 0.9243 (ttp-110) REVERT: F 128 ARG cc_start: 0.9437 (ttp-110) cc_final: 0.9168 (ttp-110) REVERT: F 152 ARG cc_start: 0.5506 (ttt180) cc_final: 0.5302 (ptt90) REVERT: F 217 ARG cc_start: 0.9294 (mtt180) cc_final: 0.9022 (mtm180) REVERT: G 56 GLN cc_start: 0.8443 (mt0) cc_final: 0.8101 (mm110) REVERT: G 122 LEU cc_start: 0.9531 (mt) cc_final: 0.9312 (tt) REVERT: G 128 ARG cc_start: 0.9515 (ttp-110) cc_final: 0.9304 (ttp-110) REVERT: G 152 ARG cc_start: 0.5587 (ttt180) cc_final: 0.5339 (ptt90) REVERT: G 272 ILE cc_start: 0.9349 (pt) cc_final: 0.9116 (tt) REVERT: G 280 ASN cc_start: 0.8768 (t0) cc_final: 0.8332 (t0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2682 time to fit residues: 66.2803 Evaluate side-chains 107 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 15 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 174 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.097291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.075748 restraints weight = 65691.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077511 restraints weight = 42454.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.078781 restraints weight = 31297.846| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15323 Z= 0.138 Angle : 0.773 9.450 20853 Z= 0.379 Chirality : 0.047 0.207 2471 Planarity : 0.006 0.055 2520 Dihedral : 5.717 19.131 1981 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -2.05 (0.19), residues: 1827 helix: -0.41 (0.15), residues: 1155 sheet: -4.08 (0.54), residues: 84 loop : -2.75 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 127 HIS 0.001 0.000 HIS E 106 PHE 0.031 0.001 PHE G 334 TYR 0.031 0.002 TYR G 234 ARG 0.007 0.000 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 736) hydrogen bonds : angle 4.95321 ( 2187) SS BOND : bond 0.00290 ( 14) SS BOND : angle 1.06382 ( 28) covalent geometry : bond 0.00287 (15309) covalent geometry : angle 0.77252 (20825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9197 (ttp-110) REVERT: B 56 GLN cc_start: 0.8049 (mm110) cc_final: 0.7233 (mm-40) REVERT: B 128 ARG cc_start: 0.9402 (tmm-80) cc_final: 0.9195 (ttp-110) REVERT: B 272 ILE cc_start: 0.9158 (pt) cc_final: 0.8784 (pt) REVERT: D 56 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7765 (mm-40) REVERT: D 141 PHE cc_start: 0.7722 (m-10) cc_final: 0.7341 (m-80) REVERT: D 152 ARG cc_start: 0.5338 (ttt180) cc_final: 0.5034 (ptt90) REVERT: D 217 ARG cc_start: 0.9194 (mtt180) cc_final: 0.8690 (mpp80) REVERT: E 56 GLN cc_start: 0.8227 (mm110) cc_final: 0.7689 (mm-40) REVERT: E 128 ARG cc_start: 0.9607 (tmm-80) cc_final: 0.9263 (ttp-110) REVERT: F 56 GLN cc_start: 0.8261 (mm110) cc_final: 0.7882 (mm-40) REVERT: F 128 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.9126 (ttp-110) REVERT: G 122 LEU cc_start: 0.9520 (mt) cc_final: 0.9316 (tt) REVERT: G 152 ARG cc_start: 0.5493 (ttt180) cc_final: 0.5273 (ptt90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2725 time to fit residues: 70.8542 Evaluate side-chains 114 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 150 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.095167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074853 restraints weight = 66217.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.076607 restraints weight = 41744.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.078044 restraints weight = 29553.818| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15323 Z= 0.141 Angle : 0.756 9.586 20853 Z= 0.370 Chirality : 0.047 0.195 2471 Planarity : 0.006 0.081 2520 Dihedral : 5.607 18.720 1981 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -1.88 (0.19), residues: 1827 helix: -0.20 (0.15), residues: 1155 sheet: -4.20 (0.55), residues: 84 loop : -2.80 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 127 HIS 0.001 0.000 HIS C 106 PHE 0.032 0.001 PHE E 334 TYR 0.026 0.002 TYR G 234 ARG 0.010 0.001 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 736) hydrogen bonds : angle 4.88470 ( 2187) SS BOND : bond 0.00320 ( 14) SS BOND : angle 0.84672 ( 28) covalent geometry : bond 0.00302 (15309) covalent geometry : angle 0.75619 (20825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9435 (ttp-110) cc_final: 0.9181 (ttp-110) REVERT: A 217 ARG cc_start: 0.9112 (mtm180) cc_final: 0.8732 (mtp-110) REVERT: B 56 GLN cc_start: 0.7928 (mm110) cc_final: 0.7161 (mm-40) REVERT: B 272 ILE cc_start: 0.9227 (pt) cc_final: 0.8786 (pt) REVERT: C 128 ARG cc_start: 0.9330 (ttp-110) cc_final: 0.9049 (ttp-110) REVERT: D 152 ARG cc_start: 0.5335 (ttt180) cc_final: 0.5028 (ptt90) REVERT: D 217 ARG cc_start: 0.9162 (mtt180) cc_final: 0.8611 (mpp80) REVERT: E 40 CYS cc_start: 0.8976 (t) cc_final: 0.8767 (t) REVERT: E 56 GLN cc_start: 0.8089 (mm110) cc_final: 0.7593 (mm-40) REVERT: F 56 GLN cc_start: 0.8008 (mm110) cc_final: 0.7660 (mm-40) REVERT: F 128 ARG cc_start: 0.9392 (ttp-110) cc_final: 0.9123 (ttp-110) REVERT: G 122 LEU cc_start: 0.9516 (mt) cc_final: 0.9304 (tt) REVERT: G 152 ARG cc_start: 0.5562 (ttt180) cc_final: 0.5339 (ptt90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2530 time to fit residues: 62.7896 Evaluate side-chains 111 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.092930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071696 restraints weight = 66598.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073252 restraints weight = 43486.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.074324 restraints weight = 32400.431| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15323 Z= 0.202 Angle : 0.823 10.001 20853 Z= 0.404 Chirality : 0.051 0.219 2471 Planarity : 0.006 0.068 2520 Dihedral : 5.861 21.329 1981 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -1.74 (0.20), residues: 1827 helix: -0.14 (0.15), residues: 1176 sheet: -4.44 (0.54), residues: 84 loop : -2.68 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 127 HIS 0.002 0.001 HIS F 106 PHE 0.034 0.002 PHE D 141 TYR 0.033 0.002 TYR F 234 ARG 0.007 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 736) hydrogen bonds : angle 5.01299 ( 2187) SS BOND : bond 0.00572 ( 14) SS BOND : angle 1.07318 ( 28) covalent geometry : bond 0.00447 (15309) covalent geometry : angle 0.82218 (20825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9410 (ttp-110) cc_final: 0.9175 (ttp-110) REVERT: B 128 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9143 (ttp-110) REVERT: D 128 ARG cc_start: 0.9264 (ttp-110) cc_final: 0.9030 (ttp-110) REVERT: D 217 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8552 (mpp80) REVERT: E 37 MET cc_start: 0.7549 (ttt) cc_final: 0.7125 (mtp) REVERT: E 56 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7605 (mm-40) REVERT: E 128 ARG cc_start: 0.9603 (tmm-80) cc_final: 0.9272 (ttp-110) REVERT: F 56 GLN cc_start: 0.8266 (mm110) cc_final: 0.7887 (mm-40) REVERT: F 128 ARG cc_start: 0.9374 (ttp-110) cc_final: 0.9112 (ttp-110) REVERT: G 122 LEU cc_start: 0.9520 (mt) cc_final: 0.9306 (tt) REVERT: G 128 ARG cc_start: 0.9479 (ttp-110) cc_final: 0.9261 (ttp-110) REVERT: G 152 ARG cc_start: 0.5695 (ttt180) cc_final: 0.5398 (ptt90) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2639 time to fit residues: 60.7267 Evaluate side-chains 88 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7242 > 50: distance: 8 - 26: 31.910 distance: 16 - 42: 24.304 distance: 21 - 26: 35.637 distance: 22 - 53: 32.675 distance: 26 - 27: 62.907 distance: 27 - 28: 41.343 distance: 27 - 30: 36.750 distance: 28 - 29: 55.667 distance: 28 - 34: 51.065 distance: 29 - 58: 63.319 distance: 30 - 31: 40.206 distance: 31 - 32: 44.643 distance: 31 - 33: 58.006 distance: 34 - 35: 45.873 distance: 35 - 36: 26.954 distance: 35 - 38: 28.983 distance: 36 - 37: 25.114 distance: 36 - 42: 45.373 distance: 37 - 66: 46.326 distance: 38 - 39: 45.498 distance: 39 - 40: 44.955 distance: 39 - 41: 43.207 distance: 42 - 43: 44.214 distance: 43 - 44: 45.560 distance: 43 - 46: 57.969 distance: 44 - 45: 39.949 distance: 44 - 53: 46.401 distance: 46 - 47: 38.675 distance: 47 - 48: 54.297 distance: 47 - 49: 48.604 distance: 48 - 50: 50.138 distance: 49 - 51: 46.517 distance: 50 - 52: 30.712 distance: 51 - 52: 23.575 distance: 53 - 54: 50.439 distance: 54 - 55: 26.364 distance: 54 - 57: 36.260 distance: 55 - 56: 55.632 distance: 55 - 58: 43.816 distance: 56 - 82: 44.914 distance: 58 - 59: 6.637 distance: 59 - 60: 24.929 distance: 59 - 62: 41.125 distance: 60 - 61: 44.457 distance: 60 - 66: 32.408 distance: 61 - 94: 27.946 distance: 62 - 63: 56.585 distance: 62 - 64: 54.160 distance: 63 - 65: 31.310 distance: 66 - 67: 51.255 distance: 67 - 68: 45.474 distance: 67 - 70: 43.817 distance: 68 - 69: 57.634 distance: 68 - 74: 35.084 distance: 70 - 71: 57.956 distance: 71 - 72: 13.397 distance: 71 - 73: 56.132 distance: 74 - 75: 59.343 distance: 75 - 76: 37.073 distance: 75 - 78: 46.088 distance: 76 - 77: 46.593 distance: 76 - 82: 50.409 distance: 78 - 79: 25.005 distance: 79 - 80: 56.259 distance: 79 - 81: 40.470 distance: 82 - 83: 49.916 distance: 83 - 84: 39.200 distance: 83 - 86: 27.726 distance: 84 - 85: 7.051 distance: 84 - 94: 54.668 distance: 86 - 87: 53.116 distance: 87 - 88: 56.415 distance: 87 - 89: 46.215 distance: 88 - 90: 56.665 distance: 89 - 91: 44.714 distance: 90 - 92: 45.182 distance: 91 - 92: 59.499 distance: 92 - 93: 19.970 distance: 94 - 95: 24.093 distance: 95 - 96: 13.001 distance: 95 - 98: 69.497 distance: 96 - 97: 42.581 distance: 96 - 102: 50.781 distance: 97 - 124: 18.404 distance: 98 - 99: 40.130 distance: 99 - 100: 54.816 distance: 99 - 101: 44.437 distance: 102 - 103: 39.067 distance: 102 - 108: 44.479 distance: 103 - 104: 36.022 distance: 103 - 106: 52.773 distance: 104 - 105: 26.579 distance: 104 - 109: 31.835 distance: 105 - 132: 27.559 distance: 106 - 107: 44.011 distance: 107 - 108: 35.126