Starting phenix.real_space_refine on Fri Jun 13 11:18:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m66_30114/06_2025/6m66_30114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m66_30114/06_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_30114/06_2025/6m66_30114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m66_30114/06_2025/6m66_30114.map" model { file = "/net/cci-nas-00/data/ceres_data/6m66_30114/06_2025/6m66_30114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m66_30114/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.28, per 1000 atoms: 0.35 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 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: 1.61 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: 4.01 Time building geometry restraints manager: 4.30 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: 0.13 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: 1.290 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.900 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 : 1.548 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: 0.3028 time to fit residues: 106.3979 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 : 1.605 ------------------------------------------------------------------------------- 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 = 0.071807 restraints weight = 67491.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073358 restraints weight = 43892.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074396 restraints weight = 32640.431| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 1.35873 ( 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 : 1.828 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: A 56 GLN cc_start: 0.8109 (mm110) cc_final: 0.7774 (mm110) REVERT: A 128 ARG cc_start: 0.9423 (ttp-110) cc_final: 0.9217 (ttp-110) REVERT: A 141 PHE cc_start: 0.7778 (m-10) cc_final: 0.7568 (m-80) REVERT: A 272 ILE cc_start: 0.9334 (pt) cc_final: 0.8922 (tt) REVERT: B 56 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7723 (mm110) REVERT: B 128 ARG cc_start: 0.9578 (tmm-80) cc_final: 0.9282 (ttp-110) REVERT: B 272 ILE cc_start: 0.9297 (pt) cc_final: 0.8999 (tt) REVERT: C 36 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8574 (tptt) REVERT: C 56 GLN cc_start: 0.7901 (mm110) cc_final: 0.7278 (mm110) REVERT: C 152 ARG cc_start: 0.5814 (ttt180) cc_final: 0.5494 (ptt90) REVERT: D 37 MET cc_start: 0.7899 (ttp) cc_final: 0.7696 (mtp) REVERT: D 128 ARG cc_start: 0.9542 (tmm-80) cc_final: 0.9325 (ttp-110) REVERT: D 141 PHE cc_start: 0.7728 (m-10) cc_final: 0.7465 (m-80) REVERT: D 152 ARG cc_start: 0.5317 (ttt180) cc_final: 0.5033 (ptt90) REVERT: E 56 GLN cc_start: 0.8041 (mm110) cc_final: 0.7697 (mm110) REVERT: E 128 ARG cc_start: 0.9527 (tmm-80) cc_final: 0.9164 (ttp-110) REVERT: E 272 ILE cc_start: 0.9367 (pt) cc_final: 0.9119 (tt) REVERT: F 128 ARG cc_start: 0.9440 (ttp-110) cc_final: 0.9226 (ttp-110) REVERT: F 141 PHE cc_start: 0.7786 (m-10) cc_final: 0.7579 (m-80) REVERT: F 152 ARG cc_start: 0.5619 (ttt180) cc_final: 0.5403 (ptt90) REVERT: G 128 ARG cc_start: 0.9454 (ttp-110) cc_final: 0.9238 (ttp-110) REVERT: G 152 ARG cc_start: 0.5666 (ttt180) cc_final: 0.5410 (ptt90) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3204 time to fit residues: 82.6433 Evaluate side-chains 103 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.093151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.072741 restraints weight = 66040.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073700 restraints weight = 44352.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.074287 restraints weight = 32678.826| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15323 Z= 0.200 Angle : 0.838 8.773 20853 Z= 0.409 Chirality : 0.050 0.207 2471 Planarity : 0.007 0.055 2520 Dihedral : 6.452 22.095 1981 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.24 % Allowed : 6.52 % Favored : 93.24 % 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: -2.83 (0.18), residues: 1827 helix: -1.03 (0.14), residues: 1162 sheet: -4.35 (0.48), residues: 84 loop : -3.03 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 127 HIS 0.002 0.001 HIS E 106 PHE 0.021 0.001 PHE D 109 TYR 0.030 0.002 TYR D 234 ARG 0.003 0.000 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 736) hydrogen bonds : angle 5.32924 ( 2187) SS BOND : bond 0.00396 ( 14) SS BOND : angle 1.33526 ( 28) covalent geometry : bond 0.00438 (15309) covalent geometry : angle 0.83676 (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 160 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 1.593 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: A 56 GLN cc_start: 0.8082 (mm110) cc_final: 0.7671 (mm110) REVERT: A 128 ARG cc_start: 0.9438 (ttp-110) cc_final: 0.9193 (ttp-110) REVERT: A 141 PHE cc_start: 0.7698 (m-10) cc_final: 0.7416 (m-80) REVERT: A 272 ILE cc_start: 0.9400 (pt) cc_final: 0.9077 (tt) REVERT: B 128 ARG cc_start: 0.9590 (tmm-80) cc_final: 0.9312 (ttp-110) REVERT: B 144 GLU cc_start: 0.9431 (tm-30) cc_final: 0.9222 (tm-30) REVERT: C 36 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8763 (tptt) REVERT: C 152 ARG cc_start: 0.5845 (ttt180) cc_final: 0.5528 (ptt90) REVERT: D 141 PHE cc_start: 0.7648 (m-10) cc_final: 0.7382 (m-80) REVERT: D 152 ARG cc_start: 0.5348 (ttt180) cc_final: 0.5051 (ptt90) REVERT: D 217 ARG cc_start: 0.9130 (mtt180) cc_final: 0.8674 (mpp80) REVERT: E 56 GLN cc_start: 0.8192 (mm110) cc_final: 0.7808 (mm110) REVERT: E 128 ARG cc_start: 0.9567 (tmm-80) cc_final: 0.9243 (ttp-110) REVERT: F 128 ARG cc_start: 0.9428 (ttp-110) cc_final: 0.9153 (ttp-110) REVERT: F 152 ARG cc_start: 0.5547 (ttt180) cc_final: 0.5285 (ptt90) REVERT: G 128 ARG cc_start: 0.9502 (ttp-110) cc_final: 0.9286 (ttp-110) REVERT: G 152 ARG cc_start: 0.5629 (ttt180) cc_final: 0.5378 (ptt90) outliers start: 4 outliers final: 4 residues processed: 160 average time/residue: 0.3013 time to fit residues: 69.2820 Evaluate side-chains 107 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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: 0.0270 chunk 180 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 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: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- 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** B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.095609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075470 restraints weight = 65568.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076306 restraints weight = 44290.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.077353 restraints weight = 32659.054| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15323 Z= 0.142 Angle : 0.793 9.647 20853 Z= 0.382 Chirality : 0.049 0.203 2471 Planarity : 0.006 0.056 2520 Dihedral : 6.043 21.042 1981 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.67 % 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: -2.34 (0.19), residues: 1827 helix: -0.62 (0.14), residues: 1162 sheet: -4.22 (0.52), residues: 84 loop : -2.91 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 127 HIS 0.001 0.000 HIS E 134 PHE 0.024 0.001 PHE F 141 TYR 0.017 0.001 TYR B 234 ARG 0.012 0.000 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 736) hydrogen bonds : angle 5.07247 ( 2187) SS BOND : bond 0.00360 ( 14) SS BOND : angle 1.42831 ( 28) covalent geometry : bond 0.00303 (15309) covalent geometry : angle 0.79159 (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 169 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8071 (mm110) cc_final: 0.7678 (mm110) REVERT: A 128 ARG cc_start: 0.9458 (ttp-110) cc_final: 0.9194 (ttp-110) REVERT: A 217 ARG cc_start: 0.9268 (mtm180) cc_final: 0.8508 (mtm-85) REVERT: B 36 LYS cc_start: 0.8850 (tmmt) cc_final: 0.8637 (tptm) REVERT: B 56 GLN cc_start: 0.7983 (mm110) cc_final: 0.7245 (mm-40) REVERT: B 128 ARG cc_start: 0.9569 (tmm-80) cc_final: 0.9319 (ttp-110) REVERT: B 144 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9185 (tm-30) REVERT: B 272 ILE cc_start: 0.9218 (pt) cc_final: 0.8938 (pt) REVERT: C 56 GLN cc_start: 0.8215 (mm110) cc_final: 0.7672 (mm-40) REVERT: D 36 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8734 (tptt) REVERT: D 128 ARG cc_start: 0.9401 (ttp-110) cc_final: 0.9178 (ttp-110) REVERT: D 141 PHE cc_start: 0.7638 (m-10) cc_final: 0.7376 (m-80) REVERT: D 152 ARG cc_start: 0.5272 (ttt180) cc_final: 0.4987 (ptt90) REVERT: D 217 ARG cc_start: 0.9205 (mtt180) cc_final: 0.8576 (mpp80) REVERT: E 128 ARG cc_start: 0.9589 (tmm-80) cc_final: 0.9257 (ttp-110) REVERT: F 128 ARG cc_start: 0.9450 (ttp-110) cc_final: 0.9179 (ttp-110) REVERT: F 217 ARG cc_start: 0.9238 (mtt180) cc_final: 0.9036 (mtm180) REVERT: G 56 GLN cc_start: 0.8417 (mt0) cc_final: 0.8087 (mm110) REVERT: G 122 LEU cc_start: 0.9521 (mt) cc_final: 0.9314 (tt) REVERT: G 128 ARG cc_start: 0.9522 (ttp-110) cc_final: 0.9310 (ttp-110) REVERT: G 152 ARG cc_start: 0.5563 (ttt180) cc_final: 0.5318 (ptt90) REVERT: G 280 ASN cc_start: 0.8880 (t0) cc_final: 0.8520 (t0) outliers start: 3 outliers final: 0 residues processed: 167 average time/residue: 0.2836 time to fit residues: 68.9377 Evaluate side-chains 110 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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: 0.9990 chunk 146 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 174 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- 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** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** 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 = 0.4004 r_free = 0.4004 target = 0.095674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.075344 restraints weight = 66475.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.077072 restraints weight = 41922.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078363 restraints weight = 30564.289| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15323 Z= 0.137 Angle : 0.762 9.435 20853 Z= 0.374 Chirality : 0.047 0.187 2471 Planarity : 0.006 0.055 2520 Dihedral : 5.649 19.266 1981 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.12 % Allowed : 3.02 % 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: -0.37 (0.15), residues: 1155 sheet: -4.14 (0.53), residues: 84 loop : -2.83 (0.24), 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 0.029 0.001 PHE D 334 TYR 0.031 0.002 TYR G 234 ARG 0.003 0.000 ARG F 254 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 736) hydrogen bonds : angle 4.92030 ( 2187) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.09962 ( 28) covalent geometry : bond 0.00286 (15309) covalent geometry : angle 0.76165 (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: 2 poor density : 174 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9419 (ttp-110) cc_final: 0.9179 (ttp-110) REVERT: B 56 GLN cc_start: 0.7824 (mm110) cc_final: 0.6993 (mm-40) REVERT: B 128 ARG cc_start: 0.9412 (tmm-80) cc_final: 0.9143 (ttp-110) REVERT: B 272 ILE cc_start: 0.9148 (pt) cc_final: 0.8785 (pt) REVERT: C 56 GLN cc_start: 0.7947 (mm110) cc_final: 0.7425 (mm-40) REVERT: C 217 ARG cc_start: 0.9069 (mtm180) cc_final: 0.8479 (mtm-85) REVERT: D 141 PHE cc_start: 0.7651 (m-10) cc_final: 0.7256 (m-80) REVERT: D 152 ARG cc_start: 0.5348 (ttt180) cc_final: 0.5038 (ptt90) REVERT: D 217 ARG cc_start: 0.9167 (mtt180) cc_final: 0.8680 (mpp80) REVERT: E 56 GLN cc_start: 0.8000 (mm110) cc_final: 0.7438 (mm-40) REVERT: E 128 ARG cc_start: 0.9598 (tmm-80) cc_final: 0.9268 (ttp-110) REVERT: F 128 ARG cc_start: 0.9410 (ttp-110) cc_final: 0.9111 (ttp-110) REVERT: G 152 ARG cc_start: 0.5555 (ttt180) cc_final: 0.5323 (ptt90) outliers start: 2 outliers final: 0 residues processed: 176 average time/residue: 0.2704 time to fit residues: 71.4276 Evaluate side-chains 115 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 B 207 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN E 280 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.094156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073689 restraints weight = 66410.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.075354 restraints weight = 41837.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.076621 restraints weight = 29951.345| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15323 Z= 0.164 Angle : 0.774 9.233 20853 Z= 0.381 Chirality : 0.049 0.205 2471 Planarity : 0.006 0.057 2520 Dihedral : 5.711 19.937 1981 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -1.82 (0.19), residues: 1827 helix: -0.21 (0.15), residues: 1176 sheet: -4.26 (0.56), residues: 84 loop : -2.72 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 127 HIS 0.002 0.000 HIS C 106 PHE 0.030 0.001 PHE E 334 TYR 0.028 0.002 TYR G 234 ARG 0.004 0.001 ARG F 217 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 736) hydrogen bonds : angle 4.90273 ( 2187) SS BOND : bond 0.00477 ( 14) SS BOND : angle 0.97434 ( 28) covalent geometry : bond 0.00357 (15309) covalent geometry : angle 0.77333 (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 : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9439 (ttp-110) cc_final: 0.9141 (ttp-110) REVERT: B 56 GLN cc_start: 0.8015 (mm110) cc_final: 0.7212 (mm-40) REVERT: B 272 ILE cc_start: 0.9267 (pt) cc_final: 0.8868 (pt) REVERT: C 56 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7461 (mm-40) REVERT: C 128 ARG cc_start: 0.9322 (ttp-110) cc_final: 0.9106 (ttp-110) REVERT: C 217 ARG cc_start: 0.9098 (mtm180) cc_final: 0.8851 (ttm110) REVERT: D 128 ARG cc_start: 0.9358 (ttp-110) cc_final: 0.9157 (ttp-110) REVERT: D 217 ARG cc_start: 0.9163 (mtt180) cc_final: 0.8616 (mpp80) REVERT: E 40 CYS cc_start: 0.9080 (t) cc_final: 0.8874 (t) REVERT: E 128 ARG cc_start: 0.9615 (tmm-80) cc_final: 0.9296 (ttp-110) REVERT: F 128 ARG cc_start: 0.9409 (ttp-110) cc_final: 0.9113 (ttp-110) REVERT: G 128 ARG cc_start: 0.9474 (ttp-110) cc_final: 0.9244 (ttp-110) REVERT: G 152 ARG cc_start: 0.5609 (ttt180) cc_final: 0.5370 (ptt90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2689 time to fit residues: 65.6648 Evaluate side-chains 99 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** 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 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.092739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071486 restraints weight = 66428.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073071 restraints weight = 43225.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.074092 restraints weight = 32243.096| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15323 Z= 0.201 Angle : 0.825 10.218 20853 Z= 0.405 Chirality : 0.051 0.227 2471 Planarity : 0.006 0.058 2520 Dihedral : 5.901 21.778 1981 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % 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: -1.72 (0.20), residues: 1827 helix: -0.11 (0.15), residues: 1176 sheet: -4.43 (0.56), residues: 84 loop : -2.70 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 127 HIS 0.003 0.001 HIS E 106 PHE 0.030 0.002 PHE D 141 TYR 0.029 0.002 TYR E 234 ARG 0.007 0.001 ARG F 217 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 736) hydrogen bonds : angle 5.02472 ( 2187) SS BOND : bond 0.00542 ( 14) SS BOND : angle 1.02190 ( 28) covalent geometry : bond 0.00441 (15309) covalent geometry : angle 0.82462 (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 151 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9413 (ttp-110) cc_final: 0.9182 (ttp-110) REVERT: A 217 ARG cc_start: 0.9109 (mtm180) cc_final: 0.8801 (mtm110) REVERT: B 128 ARG cc_start: 0.9441 (ttp-110) cc_final: 0.9170 (ttp-110) REVERT: C 56 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7843 (mm-40) REVERT: D 128 ARG cc_start: 0.9367 (ttp-110) cc_final: 0.9155 (ttp-110) REVERT: D 217 ARG cc_start: 0.9195 (mtt180) cc_final: 0.8560 (mpp80) REVERT: E 128 ARG cc_start: 0.9612 (tmm-80) cc_final: 0.9277 (ttp-110) REVERT: F 128 ARG cc_start: 0.9384 (ttp-110) cc_final: 0.9109 (ttp-110) REVERT: G 128 ARG cc_start: 0.9449 (ttp-110) cc_final: 0.9213 (ttp-110) REVERT: G 152 ARG cc_start: 0.5683 (ttt180) cc_final: 0.5380 (ptt90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2692 time to fit residues: 60.7196 Evaluate side-chains 89 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 69.2637 > 50: distance: 9 - 26: 28.654 distance: 17 - 42: 25.501 distance: 22 - 26: 28.736 distance: 23 - 53: 23.228 distance: 26 - 27: 51.473 distance: 27 - 28: 45.809 distance: 27 - 30: 10.001 distance: 28 - 29: 51.502 distance: 28 - 34: 52.351 distance: 29 - 58: 30.891 distance: 30 - 31: 10.201 distance: 31 - 32: 8.945 distance: 31 - 33: 16.690 distance: 34 - 35: 42.682 distance: 35 - 36: 45.127 distance: 35 - 38: 11.315 distance: 36 - 37: 49.374 distance: 36 - 42: 44.787 distance: 37 - 66: 8.150 distance: 38 - 39: 27.585 distance: 39 - 40: 28.810 distance: 39 - 41: 27.684 distance: 42 - 43: 35.885 distance: 43 - 44: 28.200 distance: 43 - 46: 27.167 distance: 44 - 45: 18.920 distance: 44 - 53: 32.386 distance: 46 - 47: 44.166 distance: 47 - 48: 47.318 distance: 47 - 49: 23.848 distance: 48 - 50: 20.016 distance: 49 - 51: 6.009 distance: 50 - 52: 8.025 distance: 51 - 52: 9.834 distance: 53 - 54: 40.958 distance: 54 - 55: 23.914 distance: 54 - 57: 25.338 distance: 55 - 56: 24.937 distance: 55 - 58: 17.772 distance: 56 - 82: 40.970 distance: 58 - 59: 33.861 distance: 59 - 60: 6.344 distance: 59 - 62: 48.108 distance: 60 - 61: 26.795 distance: 60 - 66: 35.109 distance: 61 - 94: 22.199 distance: 62 - 63: 31.452 distance: 62 - 64: 34.207 distance: 63 - 65: 8.717 distance: 66 - 67: 21.364 distance: 67 - 68: 62.826 distance: 67 - 70: 57.988 distance: 68 - 69: 41.012 distance: 68 - 74: 69.264 distance: 70 - 71: 69.210 distance: 71 - 73: 12.521 distance: 74 - 75: 35.104 distance: 75 - 76: 36.617 distance: 75 - 78: 44.946 distance: 76 - 77: 16.257 distance: 76 - 82: 51.611 distance: 78 - 79: 33.472 distance: 79 - 80: 30.836 distance: 79 - 81: 25.714 distance: 82 - 83: 30.571 distance: 83 - 84: 14.075 distance: 83 - 86: 20.159 distance: 84 - 85: 30.593 distance: 84 - 94: 34.537 distance: 86 - 87: 35.148 distance: 87 - 88: 24.412 distance: 87 - 89: 23.888 distance: 88 - 90: 10.638 distance: 89 - 91: 9.803 distance: 90 - 92: 20.432 distance: 91 - 92: 30.069 distance: 92 - 93: 5.578 distance: 94 - 95: 26.587 distance: 95 - 96: 32.811 distance: 95 - 98: 37.794 distance: 96 - 97: 20.502 distance: 96 - 102: 20.037 distance: 97 - 124: 12.537 distance: 98 - 99: 41.461 distance: 99 - 100: 20.357 distance: 99 - 101: 18.124 distance: 102 - 103: 38.458 distance: 102 - 108: 27.076 distance: 103 - 104: 57.530 distance: 103 - 106: 40.441 distance: 104 - 105: 43.079 distance: 104 - 109: 29.470 distance: 105 - 132: 23.111 distance: 106 - 107: 12.373 distance: 107 - 108: 19.334