Starting phenix.real_space_refine on Thu Mar 13 21:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz2_37944/03_2025/8wz2_37944.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 65 5.16 5 C 5956 2.51 5 N 1605 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9355 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "L" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 147 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 66 Time building chain proxies: 5.88, per 1000 atoms: 0.63 Number of scatterers: 9355 At special positions: 0 Unit cell: (115.34, 147.46, 127.02, 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 65 16.00 O 1729 8.00 N 1605 7.00 C 5956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=1.89 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.663A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.575A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.141A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.813A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.246A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.858A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.729A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.679A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.616A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.701A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.853A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'L' and resid 99 through 111 Processing helix chain 'R' and resid 10 through 19 removed outlier: 3.933A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 30 Processing helix chain 'R' and resid 41 through 72 Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 removed outlier: 3.733A pdb=" N ILE R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 116 through 149 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 149 through 157 removed outlier: 4.067A pdb=" N TRP R 155 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 183 Proline residue: R 179 - end of helix removed outlier: 3.838A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.992A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS R 212 " --> pdb=" O PRO R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 262 through 298 removed outlier: 3.759A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.591A pdb=" N GLU R 297 " --> pdb=" O HIS R 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR R 298 " --> pdb=" O MET R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.717A pdb=" N TYR R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 334 removed outlier: 3.657A pdb=" N CYS R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 344 removed outlier: 3.930A pdb=" N LEU R 344 " --> pdb=" O LYS R 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.105A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.867A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.554A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.662A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.694A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.965A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.470A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.309A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 7.130A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 184 through 191 removed outlier: 3.622A pdb=" N LEU R 202 " --> pdb=" O GLN R 185 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS R 196 " --> pdb=" O ASP R 191 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1356 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: 2.91 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1519 1.27 - 1.41: 2399 1.41 - 1.54: 5462 1.54 - 1.68: 67 1.68 - 1.81: 99 Bond restraints: 9546 Sorted by residual: bond pdb=" C GLU R 203 " pdb=" N GLU R 204 " ideal model delta sigma weight residual 1.331 1.578 -0.248 1.48e-02 4.57e+03 2.81e+02 bond pdb=" C ALA R 27 " pdb=" O ALA R 27 " ideal model delta sigma weight residual 1.236 1.136 0.100 1.15e-02 7.56e+03 7.62e+01 bond pdb=" C GLU R 23 " pdb=" O GLU R 23 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.26e-02 6.30e+03 2.76e+01 bond pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.18e-02 7.18e+03 2.51e+01 bond pdb=" CA ARG R 22 " pdb=" C ARG R 22 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.37e-02 5.33e+03 1.63e+01 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12803 2.23 - 4.45: 92 4.45 - 6.68: 20 6.68 - 8.91: 4 8.91 - 11.13: 12 Bond angle restraints: 12931 Sorted by residual: angle pdb=" O ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 122.45 112.32 10.13 1.07e+00 8.73e-01 8.95e+01 angle pdb=" C ILE R 199 " pdb=" N CYS R 200 " pdb=" CA CYS R 200 " ideal model delta sigma weight residual 123.00 133.83 -10.83 1.38e+00 5.25e-01 6.16e+01 angle pdb=" N THR R 37 " pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 110.08 99.53 10.55 1.38e+00 5.25e-01 5.84e+01 angle pdb=" N ILE R 26 " pdb=" CA ILE R 26 " pdb=" C ILE R 26 " ideal model delta sigma weight residual 110.62 103.17 7.45 1.02e+00 9.61e-01 5.34e+01 angle pdb=" CA ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 116.59 126.91 -10.32 1.44e+00 4.82e-01 5.13e+01 ... (remaining 12926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5562 17.98 - 35.96: 91 35.96 - 53.94: 19 53.94 - 71.93: 4 71.93 - 89.91: 1 Dihedral angle restraints: 5677 sinusoidal: 2189 harmonic: 3488 Sorted by residual: dihedral pdb=" N GLN R 24 " pdb=" C GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual 122.80 132.29 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C GLN R 24 " pdb=" N GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU R 39 " pdb=" CG GLU R 39 " pdb=" CD GLU R 39 " pdb=" OE1 GLU R 39 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 1468 0.340 - 0.679: 0 0.679 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.698: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CG LEU R 54 " pdb=" CB LEU R 54 " pdb=" CD1 LEU R 54 " pdb=" CD2 LEU R 54 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" CB VAL R 79 " pdb=" CA VAL R 79 " pdb=" CG1 VAL R 79 " pdb=" CG2 VAL R 79 " both_signs ideal model delta sigma weight residual False -2.63 -1.12 -1.50 2.00e-01 2.50e+01 5.66e+01 chirality pdb=" CB VAL R 279 " pdb=" CA VAL R 279 " pdb=" CG1 VAL R 279 " pdb=" CG2 VAL R 279 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.56e+01 ... (remaining 1468 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 21 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C THR R 21 " -0.061 2.00e-02 2.50e+03 pdb=" O THR R 21 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG R 22 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 29 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C TYR R 29 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR R 29 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 183 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL R 183 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL R 183 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN R 184 " -0.013 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 102 2.60 - 3.18: 8324 3.18 - 3.75: 14214 3.75 - 4.33: 20031 4.33 - 4.90: 33654 Nonbonded interactions: 76325 Sorted by model distance: nonbonded pdb=" O MET R 295 " pdb=" OG SER R 299 " model vdw 2.029 3.040 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.044 3.040 nonbonded pdb=" OH TYR R 190 " pdb=" OE1 GLU R 195 " model vdw 2.125 3.040 nonbonded pdb=" OG SER R 73 " pdb=" OD1 ASN R 342 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 242 " pdb=" ND2 ASN A 246 " model vdw 2.137 3.120 ... (remaining 76320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.410 Find NCS groups from input model: 0.130 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.004 0.248 9546 Z= 0.295 Angle : 0.580 11.132 12931 Z= 0.363 Chirality : 0.082 1.698 1471 Planarity : 0.002 0.035 1638 Dihedral : 7.423 89.908 3418 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1181 helix: 0.54 (0.24), residues: 420 sheet: -0.61 (0.30), residues: 265 loop : -1.76 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 181 HIS 0.012 0.001 HIS A 324 PHE 0.021 0.001 PHE B 239 TYR 0.024 0.001 TYR R 36 ARG 0.006 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.997 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: B 235 ASN cc_start: 0.7658 (m-40) cc_final: 0.7291 (m-40) REVERT: B 251 ASP cc_start: 0.7324 (p0) cc_final: 0.7118 (p0) REVERT: R 207 SER cc_start: 0.7551 (t) cc_final: 0.6633 (t) outliers start: 1 outliers final: 2 residues processed: 410 average time/residue: 1.4009 time to fit residues: 609.0811 Evaluate side-chains 224 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 23 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 273 ASN B 300 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 167 HIS E 194 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 ASN R 125 GLN R 338 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.102913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077778 restraints weight = 20882.241| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.63 r_work: 0.3065 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9546 Z= 0.233 Angle : 0.636 7.485 12931 Z= 0.326 Chirality : 0.042 0.155 1471 Planarity : 0.005 0.112 1638 Dihedral : 4.306 96.281 1300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.30 % Allowed : 19.08 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1181 helix: 1.49 (0.24), residues: 427 sheet: -0.14 (0.31), residues: 265 loop : -1.48 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 46 HIS 0.007 0.002 HIS E 34 PHE 0.016 0.001 PHE A 189 TYR 0.021 0.001 TYR R 194 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8411 (tp40) REVERT: A 185 PHE cc_start: 0.6755 (m-10) cc_final: 0.6507 (m-80) REVERT: A 226 ASP cc_start: 0.8616 (t0) cc_final: 0.8405 (t0) REVERT: A 242 SER cc_start: 0.9134 (m) cc_final: 0.8813 (p) REVERT: A 247 ARG cc_start: 0.8416 (ptt90) cc_final: 0.7930 (tmm-80) REVERT: A 248 TRP cc_start: 0.8215 (m100) cc_final: 0.7989 (m100) REVERT: B 267 MET cc_start: 0.8863 (tpp) cc_final: 0.8493 (tpp) REVERT: E 42 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8253 (mmmm) REVERT: E 72 ASP cc_start: 0.8404 (t0) cc_final: 0.8036 (t0) REVERT: E 82 MET cc_start: 0.8887 (mtp) cc_final: 0.8657 (mtp) REVERT: E 244 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8216 (tmmt) REVERT: G 17 GLN cc_start: 0.8045 (tp40) cc_final: 0.7654 (tp40) REVERT: G 21 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7429 (mt-10) REVERT: G 45 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8812 (mppt) REVERT: R 32 ARG cc_start: 0.7568 (tpt170) cc_final: 0.7267 (tpt90) REVERT: R 68 TYR cc_start: 0.8780 (t80) cc_final: 0.8355 (t80) REVERT: R 120 MET cc_start: 0.8632 (ttp) cc_final: 0.8192 (ppp) REVERT: R 187 GLU cc_start: 0.5719 (tm-30) cc_final: 0.4791 (tm-30) REVERT: R 188 ILE cc_start: 0.9483 (mt) cc_final: 0.9281 (tp) REVERT: R 200 CYS cc_start: 0.7372 (m) cc_final: 0.6456 (m) REVERT: R 312 MET cc_start: 0.9206 (mtm) cc_final: 0.9000 (mtm) outliers start: 33 outliers final: 11 residues processed: 268 average time/residue: 1.2560 time to fit residues: 358.8298 Evaluate side-chains 221 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 210 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 186 GLN R 63 ASN R 290 HIS R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.072782 restraints weight = 21036.184| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.58 r_work: 0.2959 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9546 Z= 0.232 Angle : 0.633 13.106 12931 Z= 0.320 Chirality : 0.042 0.173 1471 Planarity : 0.004 0.034 1638 Dihedral : 4.456 90.120 1300 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.60 % Allowed : 19.48 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1181 helix: 1.83 (0.25), residues: 433 sheet: -0.03 (0.31), residues: 265 loop : -1.21 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.006 0.002 HIS E 34 PHE 0.018 0.002 PHE R 61 TYR 0.025 0.002 TYR B 64 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8374 (tp40) REVERT: A 185 PHE cc_start: 0.6825 (m-80) cc_final: 0.6508 (m-10) REVERT: A 242 SER cc_start: 0.9111 (m) cc_final: 0.8825 (p) REVERT: A 247 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8123 (tmm-80) REVERT: A 261 GLN cc_start: 0.8253 (pt0) cc_final: 0.7967 (pt0) REVERT: B 28 LYS cc_start: 0.8902 (tmmm) cc_final: 0.8623 (ttmm) REVERT: B 177 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8619 (mm-30) REVERT: B 252 ASP cc_start: 0.8343 (t0) cc_final: 0.8057 (t0) REVERT: E 42 LYS cc_start: 0.8708 (mmmm) cc_final: 0.8310 (mmmm) REVERT: E 72 ASP cc_start: 0.8543 (t0) cc_final: 0.8081 (t0) REVERT: E 244 LYS cc_start: 0.8933 (ttpp) cc_final: 0.8201 (tmmt) REVERT: G 16 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8342 (tm-30) REVERT: G 17 GLN cc_start: 0.8154 (tp40) cc_final: 0.7761 (tp40) REVERT: G 21 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7360 (mt-10) REVERT: G 45 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8913 (mppt) REVERT: R 32 ARG cc_start: 0.7493 (tpt170) cc_final: 0.6869 (tpt90) REVERT: R 77 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8122 (mmt180) REVERT: R 187 GLU cc_start: 0.5884 (tm-30) cc_final: 0.4886 (tm-30) REVERT: R 188 ILE cc_start: 0.9479 (mt) cc_final: 0.9266 (tp) REVERT: R 200 CYS cc_start: 0.7666 (m) cc_final: 0.6693 (m) REVERT: R 204 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8409 (mm-30) REVERT: R 210 HIS cc_start: 0.8074 (m170) cc_final: 0.7854 (m90) REVERT: R 312 MET cc_start: 0.9122 (mtm) cc_final: 0.8895 (mtm) outliers start: 36 outliers final: 13 residues processed: 254 average time/residue: 1.2395 time to fit residues: 335.2848 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 186 GLN R 63 ASN R 81 ASN R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065148 restraints weight = 21075.138| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.54 r_work: 0.2858 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9546 Z= 0.352 Angle : 0.655 9.285 12931 Z= 0.339 Chirality : 0.044 0.193 1471 Planarity : 0.004 0.036 1638 Dihedral : 4.156 21.469 1298 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.10 % Allowed : 21.88 % Favored : 74.03 % 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: 0.54 (0.25), residues: 1181 helix: 1.88 (0.25), residues: 428 sheet: 0.13 (0.32), residues: 270 loop : -0.89 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 87 HIS 0.007 0.002 HIS B 188 PHE 0.021 0.002 PHE E 203 TYR 0.020 0.002 TYR E 190 ARG 0.010 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 PHE cc_start: 0.7081 (m-80) cc_final: 0.6745 (m-10) REVERT: A 261 GLN cc_start: 0.8389 (pt0) cc_final: 0.8121 (pt0) REVERT: B 28 LYS cc_start: 0.9020 (tmmm) cc_final: 0.8781 (ttmm) REVERT: B 177 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 252 ASP cc_start: 0.8661 (t0) cc_final: 0.8355 (t0) REVERT: B 271 HIS cc_start: 0.8833 (t70) cc_final: 0.8585 (t-90) REVERT: E 42 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8294 (mmmm) REVERT: E 72 ASP cc_start: 0.8565 (t0) cc_final: 0.8223 (t0) REVERT: E 220 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7757 (mm-30) REVERT: E 223 ASP cc_start: 0.8408 (m-30) cc_final: 0.8067 (m-30) REVERT: E 234 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6987 (mt-10) REVERT: E 244 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8180 (tmmt) REVERT: G 17 GLN cc_start: 0.8411 (tp40) cc_final: 0.7999 (tp40) REVERT: G 28 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8609 (mtpp) REVERT: G 41 GLU cc_start: 0.8804 (pp20) cc_final: 0.8504 (pp20) REVERT: G 45 LYS cc_start: 0.9264 (mtmm) cc_final: 0.9013 (mppt) REVERT: G 57 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7461 (mp0) REVERT: R 32 ARG cc_start: 0.7466 (tpt170) cc_final: 0.6978 (tpt90) REVERT: R 68 TYR cc_start: 0.8908 (t80) cc_final: 0.8497 (t80) REVERT: R 72 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8009 (ttt90) REVERT: R 77 ARG cc_start: 0.8664 (ttt180) cc_final: 0.8159 (mmt180) REVERT: R 187 GLU cc_start: 0.6123 (tm-30) cc_final: 0.5186 (tm-30) REVERT: R 188 ILE cc_start: 0.9462 (mt) cc_final: 0.9260 (tp) REVERT: R 200 CYS cc_start: 0.7864 (m) cc_final: 0.6971 (m) REVERT: R 204 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8568 (mm-30) REVERT: R 210 HIS cc_start: 0.8275 (m170) cc_final: 0.7869 (m170) REVERT: R 338 ASN cc_start: 0.8419 (t0) cc_final: 0.7622 (t160) outliers start: 41 outliers final: 17 residues processed: 243 average time/residue: 1.4903 time to fit residues: 384.4311 Evaluate side-chains 207 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 194 ASN R 63 ASN R 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067125 restraints weight = 21030.097| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.55 r_work: 0.2843 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9546 Z= 0.209 Angle : 0.624 9.982 12931 Z= 0.319 Chirality : 0.042 0.177 1471 Planarity : 0.003 0.037 1638 Dihedral : 3.907 19.849 1298 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.90 % Allowed : 23.08 % Favored : 73.03 % 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: 0.72 (0.25), residues: 1181 helix: 2.03 (0.25), residues: 427 sheet: 0.30 (0.32), residues: 272 loop : -0.83 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.005 0.001 HIS R 198 PHE 0.014 0.001 PHE R 61 TYR 0.018 0.001 TYR R 36 ARG 0.010 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8920 (m-30) cc_final: 0.8553 (m-30) REVERT: A 28 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8535 (tp40) REVERT: A 185 PHE cc_start: 0.7031 (m-80) cc_final: 0.6694 (m-10) REVERT: A 242 SER cc_start: 0.9220 (m) cc_final: 0.8974 (p) REVERT: A 247 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7637 (ppp80) REVERT: A 261 GLN cc_start: 0.8417 (pt0) cc_final: 0.8076 (pt0) REVERT: B 28 LYS cc_start: 0.8984 (tmmm) cc_final: 0.8754 (ttmm) REVERT: B 177 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8550 (mm-30) REVERT: B 239 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: B 252 ASP cc_start: 0.8613 (t0) cc_final: 0.8284 (t0) REVERT: E 42 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8272 (mmmm) REVERT: E 72 ASP cc_start: 0.8571 (t0) cc_final: 0.8071 (t0) REVERT: E 220 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7959 (mm-30) REVERT: E 223 ASP cc_start: 0.8349 (m-30) cc_final: 0.7376 (m-30) REVERT: E 234 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6857 (mt-10) REVERT: E 244 LYS cc_start: 0.8896 (ttpp) cc_final: 0.8108 (tmmt) REVERT: G 41 GLU cc_start: 0.8818 (pp20) cc_final: 0.8492 (pp20) REVERT: G 45 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8983 (mppt) REVERT: R 68 TYR cc_start: 0.8932 (t80) cc_final: 0.8016 (t80) REVERT: R 72 ARG cc_start: 0.8493 (ttt90) cc_final: 0.8191 (ttm-80) REVERT: R 77 ARG cc_start: 0.8662 (ttt180) cc_final: 0.8214 (mpt180) REVERT: R 160 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7477 (tpm170) REVERT: R 188 ILE cc_start: 0.9467 (mt) cc_final: 0.9208 (tp) REVERT: R 210 HIS cc_start: 0.8272 (m170) cc_final: 0.7816 (m170) REVERT: R 225 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8426 (tt) REVERT: R 312 MET cc_start: 0.9135 (mtm) cc_final: 0.8918 (mtm) outliers start: 39 outliers final: 15 residues processed: 236 average time/residue: 1.4524 time to fit residues: 367.2949 Evaluate side-chains 216 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 194 ASN R 63 ASN R 81 ASN R 338 ASN R 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.060730 restraints weight = 21373.833| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.49 r_work: 0.2761 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 9546 Z= 0.563 Angle : 0.737 8.973 12931 Z= 0.383 Chirality : 0.048 0.225 1471 Planarity : 0.005 0.060 1638 Dihedral : 4.477 22.952 1298 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.50 % Allowed : 23.78 % Favored : 71.73 % 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: 0.45 (0.24), residues: 1181 helix: 1.67 (0.25), residues: 427 sheet: 0.21 (0.32), residues: 265 loop : -0.88 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 87 HIS 0.008 0.002 HIS G 43 PHE 0.013 0.002 PHE R 61 TYR 0.028 0.002 TYR E 190 ARG 0.010 0.001 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8643 (mt-10) REVERT: A 22 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8892 (tp-100) REVERT: A 27 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9088 (ttpp) REVERT: A 185 PHE cc_start: 0.7149 (m-80) cc_final: 0.6843 (m-10) REVERT: A 247 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7836 (ppp80) REVERT: A 261 GLN cc_start: 0.8428 (pt0) cc_final: 0.8115 (pt0) REVERT: B 28 LYS cc_start: 0.9129 (tmmm) cc_final: 0.8927 (ttmm) REVERT: B 177 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 219 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8865 (mpp80) REVERT: B 252 ASP cc_start: 0.8803 (t0) cc_final: 0.8517 (t0) REVERT: E 42 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8283 (mmmm) REVERT: E 72 ASP cc_start: 0.8566 (t0) cc_final: 0.8047 (t0) REVERT: E 112 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8883 (mm-40) REVERT: E 153 GLU cc_start: 0.8502 (pm20) cc_final: 0.8137 (pm20) REVERT: E 201 ASP cc_start: 0.8895 (p0) cc_final: 0.8430 (t70) REVERT: E 220 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7979 (mm-30) REVERT: E 223 ASP cc_start: 0.8536 (m-30) cc_final: 0.8080 (m-30) REVERT: E 234 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7361 (mt-10) REVERT: E 244 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8120 (tmmt) REVERT: G 8 ILE cc_start: 0.9333 (pp) cc_final: 0.9127 (pp) REVERT: G 13 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9095 (mmmm) REVERT: G 16 GLU cc_start: 0.9235 (pt0) cc_final: 0.8993 (pp20) REVERT: G 19 LYS cc_start: 0.9548 (ttpp) cc_final: 0.9225 (tmmt) REVERT: G 20 MET cc_start: 0.9017 (ptp) cc_final: 0.8526 (ptp) REVERT: G 57 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7323 (mp0) REVERT: R 68 TYR cc_start: 0.8990 (t80) cc_final: 0.8028 (t80) REVERT: R 72 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8236 (ttm170) REVERT: R 77 ARG cc_start: 0.8651 (ttt180) cc_final: 0.8206 (mpt180) REVERT: R 160 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7658 (tpm170) REVERT: R 188 ILE cc_start: 0.9475 (mt) cc_final: 0.9225 (tp) REVERT: R 191 ASP cc_start: 0.7090 (p0) cc_final: 0.6830 (p0) REVERT: R 193 LEU cc_start: 0.9078 (pt) cc_final: 0.8845 (pp) REVERT: R 210 HIS cc_start: 0.8435 (m170) cc_final: 0.7868 (m170) REVERT: R 312 MET cc_start: 0.9292 (mtm) cc_final: 0.9072 (mtm) outliers start: 45 outliers final: 22 residues processed: 226 average time/residue: 1.2679 time to fit residues: 305.2461 Evaluate side-chains 208 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 132 GLU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 50.0000 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065192 restraints weight = 20838.229| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.52 r_work: 0.2877 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9546 Z= 0.225 Angle : 0.655 10.262 12931 Z= 0.333 Chirality : 0.043 0.184 1471 Planarity : 0.003 0.040 1638 Dihedral : 4.182 19.086 1298 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.90 % Allowed : 25.67 % Favored : 71.43 % 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: 0.62 (0.24), residues: 1181 helix: 1.73 (0.25), residues: 433 sheet: 0.42 (0.33), residues: 254 loop : -0.77 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.006 0.001 HIS R 198 PHE 0.013 0.001 PHE R 61 TYR 0.018 0.001 TYR R 36 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 22 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8930 (tp-100) REVERT: A 28 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8532 (tp40) REVERT: A 185 PHE cc_start: 0.7233 (m-80) cc_final: 0.6921 (m-10) REVERT: A 197 HIS cc_start: 0.8132 (m170) cc_final: 0.7887 (m90) REVERT: A 247 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7833 (ppp80) REVERT: A 261 GLN cc_start: 0.8442 (pt0) cc_final: 0.8120 (pt0) REVERT: B 177 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 239 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: B 252 ASP cc_start: 0.8724 (t0) cc_final: 0.8458 (t0) REVERT: E 42 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8456 (mmmm) REVERT: E 64 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8573 (ttmm) REVERT: E 72 ASP cc_start: 0.8657 (t0) cc_final: 0.8174 (t0) REVERT: E 201 ASP cc_start: 0.8862 (p0) cc_final: 0.8460 (t70) REVERT: E 220 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8002 (mm-30) REVERT: E 223 ASP cc_start: 0.8434 (m-30) cc_final: 0.8073 (m-30) REVERT: E 234 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7227 (mt-10) REVERT: E 244 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8113 (tmmt) REVERT: G 16 GLU cc_start: 0.9180 (pt0) cc_final: 0.8936 (tm-30) REVERT: G 19 LYS cc_start: 0.9550 (ttpp) cc_final: 0.9153 (tmmt) REVERT: G 20 MET cc_start: 0.8976 (ptp) cc_final: 0.7597 (ptm) REVERT: G 41 GLU cc_start: 0.8804 (pp20) cc_final: 0.8577 (pp20) REVERT: G 45 LYS cc_start: 0.9307 (mtmm) cc_final: 0.9006 (mppt) REVERT: G 57 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7475 (mp0) REVERT: R 68 TYR cc_start: 0.9051 (t80) cc_final: 0.8159 (t80) REVERT: R 72 ARG cc_start: 0.8520 (ttt90) cc_final: 0.8235 (ttm170) REVERT: R 77 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8223 (mpt180) REVERT: R 160 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7578 (tpm170) REVERT: R 188 ILE cc_start: 0.9471 (mt) cc_final: 0.9197 (tp) REVERT: R 210 HIS cc_start: 0.8465 (m170) cc_final: 0.7941 (m170) REVERT: R 225 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8478 (tt) REVERT: R 312 MET cc_start: 0.9223 (mtm) cc_final: 0.8949 (mtm) REVERT: R 338 ASN cc_start: 0.8314 (t0) cc_final: 0.8065 (t160) outliers start: 29 outliers final: 20 residues processed: 215 average time/residue: 1.2191 time to fit residues: 279.5813 Evaluate side-chains 214 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 306 ASP Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 40 optimal weight: 0.0770 chunk 90 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063688 restraints weight = 21341.380| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.52 r_work: 0.2825 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9546 Z= 0.282 Angle : 0.677 9.398 12931 Z= 0.343 Chirality : 0.043 0.180 1471 Planarity : 0.004 0.043 1638 Dihedral : 4.123 18.710 1296 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.00 % Allowed : 25.87 % Favored : 71.13 % 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: 0.66 (0.25), residues: 1181 helix: 1.75 (0.25), residues: 433 sheet: 0.37 (0.32), residues: 265 loop : -0.69 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.006 0.001 HIS R 198 PHE 0.013 0.001 PHE R 97 TYR 0.017 0.001 TYR E 190 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8623 (mt-10) REVERT: A 28 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8550 (tp40) REVERT: A 185 PHE cc_start: 0.7199 (m-80) cc_final: 0.6880 (m-10) REVERT: A 247 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7911 (ppp80) REVERT: B 177 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 219 ARG cc_start: 0.9204 (mmm-85) cc_final: 0.8579 (mpp80) REVERT: B 239 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 252 ASP cc_start: 0.8733 (t0) cc_final: 0.8458 (t0) REVERT: E 42 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8368 (mmmm) REVERT: E 64 LYS cc_start: 0.8737 (mtpp) cc_final: 0.8520 (ttmm) REVERT: E 72 ASP cc_start: 0.8571 (t0) cc_final: 0.8090 (t0) REVERT: E 92 MET cc_start: 0.8189 (ttm) cc_final: 0.7927 (tpp) REVERT: E 201 ASP cc_start: 0.8881 (p0) cc_final: 0.8501 (t70) REVERT: E 220 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7958 (mm-30) REVERT: E 223 ASP cc_start: 0.8390 (m-30) cc_final: 0.7988 (m-30) REVERT: E 234 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7180 (mt-10) REVERT: E 244 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8102 (tmmt) REVERT: G 19 LYS cc_start: 0.9518 (ttpp) cc_final: 0.9222 (tmmt) REVERT: G 20 MET cc_start: 0.9005 (ptp) cc_final: 0.8550 (ptp) REVERT: G 28 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8461 (mmmm) REVERT: G 57 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7378 (mp0) REVERT: R 68 TYR cc_start: 0.9085 (t80) cc_final: 0.8252 (t80) REVERT: R 72 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8249 (ttm170) REVERT: R 77 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8212 (mpt180) REVERT: R 91 ASP cc_start: 0.8836 (t70) cc_final: 0.8378 (t70) REVERT: R 160 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7597 (tpm170) REVERT: R 188 ILE cc_start: 0.9469 (mt) cc_final: 0.9197 (tp) REVERT: R 210 HIS cc_start: 0.8454 (m170) cc_final: 0.7942 (m170) REVERT: R 270 ARG cc_start: 0.8404 (tpp80) cc_final: 0.8190 (tpp80) REVERT: R 312 MET cc_start: 0.9239 (mtm) cc_final: 0.9012 (mtm) outliers start: 30 outliers final: 21 residues processed: 219 average time/residue: 1.2269 time to fit residues: 286.7534 Evaluate side-chains 212 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 306 ASP Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.0170 chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 87 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.065254 restraints weight = 21127.416| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.55 r_work: 0.2861 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9546 Z= 0.223 Angle : 0.694 12.435 12931 Z= 0.349 Chirality : 0.043 0.179 1471 Planarity : 0.003 0.042 1638 Dihedral : 4.017 18.328 1296 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.60 % Allowed : 26.77 % Favored : 70.63 % 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: 0.68 (0.25), residues: 1181 helix: 1.74 (0.25), residues: 433 sheet: 0.47 (0.33), residues: 252 loop : -0.69 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.007 0.001 HIS R 198 PHE 0.013 0.001 PHE R 61 TYR 0.020 0.001 TYR R 36 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 28 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8535 (tp-100) REVERT: A 185 PHE cc_start: 0.7197 (m-80) cc_final: 0.6908 (m-10) REVERT: A 247 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7879 (ppp80) REVERT: B 49 GLN cc_start: 0.7925 (pm20) cc_final: 0.7665 (pm20) REVERT: B 135 GLU cc_start: 0.8892 (mp0) cc_final: 0.8629 (mp0) REVERT: B 177 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 239 PHE cc_start: 0.9296 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 252 ASP cc_start: 0.8645 (t0) cc_final: 0.8403 (t0) REVERT: E 42 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8342 (mmmm) REVERT: E 64 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8486 (ttmm) REVERT: E 72 ASP cc_start: 0.8567 (t0) cc_final: 0.8077 (t0) REVERT: E 92 MET cc_start: 0.8209 (ttm) cc_final: 0.7946 (tpp) REVERT: E 201 ASP cc_start: 0.8884 (p0) cc_final: 0.8526 (t0) REVERT: E 220 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8193 (mm-30) REVERT: E 234 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7073 (mt-10) REVERT: E 244 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8046 (tmmt) REVERT: G 16 GLU cc_start: 0.9006 (pp20) cc_final: 0.8680 (pp20) REVERT: G 19 LYS cc_start: 0.9492 (ttpp) cc_final: 0.9217 (tmmt) REVERT: G 20 MET cc_start: 0.8918 (ptp) cc_final: 0.8622 (ptp) REVERT: G 28 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8477 (mmmm) REVERT: G 57 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7273 (mp0) REVERT: R 68 TYR cc_start: 0.9088 (t80) cc_final: 0.8275 (t80) REVERT: R 72 ARG cc_start: 0.8548 (ttt90) cc_final: 0.8232 (ttm170) REVERT: R 77 ARG cc_start: 0.8633 (ttt180) cc_final: 0.8194 (mmt180) REVERT: R 91 ASP cc_start: 0.8793 (t70) cc_final: 0.8259 (t70) REVERT: R 155 TRP cc_start: 0.8967 (p-90) cc_final: 0.8585 (p-90) REVERT: R 160 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7556 (tpm170) REVERT: R 188 ILE cc_start: 0.9469 (mt) cc_final: 0.9194 (tp) REVERT: R 225 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8447 (tt) REVERT: R 270 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8147 (tpp80) REVERT: R 312 MET cc_start: 0.9234 (mtm) cc_final: 0.9009 (mtm) outliers start: 26 outliers final: 20 residues processed: 222 average time/residue: 1.3274 time to fit residues: 316.8341 Evaluate side-chains 221 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 306 ASP Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 50.0000 chunk 74 optimal weight: 0.0030 chunk 11 optimal weight: 0.0020 chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066458 restraints weight = 21224.461| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.51 r_work: 0.2831 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9546 Z= 0.209 Angle : 0.698 12.512 12931 Z= 0.352 Chirality : 0.043 0.177 1471 Planarity : 0.004 0.043 1638 Dihedral : 3.956 18.092 1296 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.60 % Allowed : 27.47 % Favored : 69.93 % 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: 0.71 (0.25), residues: 1181 helix: 1.68 (0.25), residues: 440 sheet: 0.54 (0.32), residues: 251 loop : -0.66 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.007 0.001 HIS R 198 PHE 0.016 0.001 PHE R 61 TYR 0.017 0.001 TYR R 194 ARG 0.009 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8476 (tp40) REVERT: A 185 PHE cc_start: 0.7110 (m-80) cc_final: 0.6817 (m-10) REVERT: A 247 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7878 (ppp80) REVERT: A 314 ASP cc_start: 0.9215 (t0) cc_final: 0.8950 (m-30) REVERT: B 49 GLN cc_start: 0.7927 (pm20) cc_final: 0.7686 (pm20) REVERT: B 135 GLU cc_start: 0.8847 (mp0) cc_final: 0.8537 (mp0) REVERT: B 177 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8637 (mm-30) REVERT: B 239 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 252 ASP cc_start: 0.8612 (t0) cc_final: 0.8379 (t0) REVERT: E 42 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8276 (mmmm) REVERT: E 64 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8413 (ttmm) REVERT: E 72 ASP cc_start: 0.8489 (t0) cc_final: 0.8003 (t0) REVERT: E 92 MET cc_start: 0.8142 (ttm) cc_final: 0.7737 (tpp) REVERT: E 201 ASP cc_start: 0.8905 (p0) cc_final: 0.8541 (t0) REVERT: E 220 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7957 (mm-30) REVERT: E 223 ASP cc_start: 0.8217 (m-30) cc_final: 0.7862 (m-30) REVERT: E 234 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6969 (mt-10) REVERT: E 244 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8392 (ttpp) REVERT: G 16 GLU cc_start: 0.9097 (pp20) cc_final: 0.8579 (pp20) REVERT: G 19 LYS cc_start: 0.9488 (ttpp) cc_final: 0.9216 (tmmt) REVERT: G 20 MET cc_start: 0.8923 (ptp) cc_final: 0.8455 (ptp) REVERT: G 28 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8431 (mmmm) REVERT: G 57 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7323 (mp0) REVERT: R 68 TYR cc_start: 0.9080 (t80) cc_final: 0.8290 (t80) REVERT: R 72 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8178 (ttm170) REVERT: R 91 ASP cc_start: 0.8720 (t70) cc_final: 0.8291 (t70) REVERT: R 120 MET cc_start: 0.8715 (tmm) cc_final: 0.8198 (tmm) REVERT: R 155 TRP cc_start: 0.8920 (p-90) cc_final: 0.8539 (p-90) REVERT: R 160 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7507 (tpm170) REVERT: R 188 ILE cc_start: 0.9452 (mt) cc_final: 0.9178 (tp) REVERT: R 225 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (tt) REVERT: R 270 ARG cc_start: 0.8308 (tpp80) cc_final: 0.8091 (tpp80) REVERT: R 312 MET cc_start: 0.9188 (mtm) cc_final: 0.8963 (mtm) outliers start: 26 outliers final: 16 residues processed: 222 average time/residue: 1.1897 time to fit residues: 281.9942 Evaluate side-chains 216 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 64, in __init__ weight = self.w, xray_structure = self.xray_structure) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 70.8618 > 50: distance: 11 - 36: 3.150 distance: 31 - 55: 3.229 distance: 39 - 62: 3.014 distance: 53 - 82: 3.074 distance: 58 - 88: 3.128 distance: 74 - 105: 3.201 distance: 85 - 113: 3.170 distance: 91 - 122: 6.531 distance: 99 - 100: 3.085 distance: 100 - 131: 32.740 distance: 108 - 140: 31.339 distance: 115 - 122: 4.118 distance: 116 - 148: 3.528 distance: 122 - 123: 9.105 distance: 123 - 124: 32.617 distance: 123 - 126: 9.575 distance: 124 - 125: 50.850 distance: 124 - 131: 4.998 distance: 125 - 157: 20.055 distance: 131 - 132: 55.982 distance: 132 - 133: 38.606 distance: 132 - 135: 38.878 distance: 133 - 134: 38.963 distance: 133 - 140: 32.666 distance: 134 - 166: 32.579 distance: 135 - 136: 67.758 distance: 136 - 137: 56.310 distance: 137 - 138: 47.586 distance: 137 - 139: 69.555 distance: 140 - 141: 17.298 distance: 141 - 142: 20.039 distance: 141 - 144: 21.095 distance: 142 - 143: 3.330 distance: 143 - 174: 3.165 distance: 151 - 183: 3.140 distance: 267 - 741: 3.754 distance: 286 - 770: 3.366 distance: 305 - 306: 3.125 distance: 344 - 372: 3.107 distance: 350 - 351: 5.536 distance: 351 - 381: 7.112 distance: 352 - 354: 3.794 distance: 363 - 364: 3.155 distance: 370 - 371: 3.758 distance: 385 - 386: 4.086 distance: 387 - 388: 6.600 distance: 433 - 571: 3.104 distance: 436 - 568: 3.075 distance: 613 - 614: 6.124 distance: 613 - 616: 7.049 distance: 614 - 615: 4.529 distance: 614 - 620: 3.068 distance: 617 - 618: 19.354 distance: 617 - 619: 17.969 distance: 620 - 621: 3.555 distance: 654 - 682: 3.018 distance: 677 - 697: 3.159 distance: 685 - 708: 3.066 distance: 835 - 869: 3.126 distance: 863 - 890: 3.046 distance: 885 - 918: 3.053 distance: 1030 - 1613: 3.191 distance: 1042 - 1616: 3.363 distance: 1045 - 1632: 3.049 distance: 1080 - 1111: 3.220 distance: 1087 - 1090: 5.283 distance: 1090 - 1091: 3.338 distance: 1091 - 1092: 9.672 distance: 1092 - 1093: 8.832 distance: 1092 - 1094: 8.414 distance: 1106 - 1133: 3.016 distance: 1136 - 1162: 3.031 distance: 1422 - 1456: 3.035 distance: 1433 - 1467: 3.025 distance: 1438 - 1475: 3.117 distance: 1447 - 1486: 3.202 distance: 1470 - 1504: 3.294 distance: 1489 - 1522: 3.169 distance: 1643 - 1644: 5.357 distance: 1644 - 1645: 3.203 distance: 1644 - 1653: 5.344 distance: 1654 - 1655: 5.328 distance: 1655 - 1656: 16.315 distance: 1655 - 1660: 4.287 distance: 1660 - 1661: 3.432 distance: 1691 - 1692: 5.572 distance: 1691 - 1693: 3.213 distance: 1697 - 1727: 3.273 distance: 1730 - 1765: 3.296 distance: 1741 - 1773: 3.067 distance: 1749 - 1779: 3.025 distance: 1791 - 1820: 3.697 distance: 1793 - 1794: 7.527 distance: 1793 - 1795: 8.666 distance: 1799 - 1829: 3.018 distance: 1832 - 1864: 3.166 distance: 1840 - 1873: 3.064 distance: 1898 - 1899: 3.272 distance: 1928 - 1961: 4.822 distance: 1936 - 1970: 5.097 distance: 1945 - 1979: 5.363 distance: 1952 - 1961: 4.591 distance: 1953 - 1984: 6.400 distance: 1961 - 1962: 3.354 distance: 1962 - 1963: 3.341 distance: 1964 - 1993: 9.057 distance: 1965 - 1966: 3.953 distance: 1966 - 1967: 3.383 distance: 1967 - 1968: 3.052 distance: 1970 - 1971: 5.305 distance: 1971 - 1972: 5.913 distance: 1972 - 1973: 6.838 distance: 1973 - 2002: 10.151 distance: 1974 - 1975: 6.208 distance: 1975 - 1976: 3.471 distance: 1976 - 1977: 20.330 distance: 1976 - 1978: 12.470 distance: 1980 - 1981: 3.029 distance: 1981 - 1982: 3.469 distance: 1982 - 2010: 3.822 distance: 1984 - 1985: 5.915 distance: 1987 - 2019: 3.323 distance: 1988 - 1989: 13.833 distance: 1989 - 1990: 8.297 distance: 1990 - 1991: 9.837 distance: 1990 - 1992: 7.738 distance: 1996 - 2027: 3.439 distance: 2017 - 2018: 3.410 distance: 2039 - 2068: 3.016 distance: 2047 - 2079: 3.262 distance: 2227 - 2229: 21.012 distance: 2245 - 2246: 8.058 distance: 2246 - 2247: 9.724 distance: 2280 - 4475: 3.150 distance: 2298 - 4458: 3.569 distance: 2370 - 2475: 3.231 distance: 2373 - 2472: 3.523 distance: 2383 - 2462: 3.076 distance: 2386 - 2459: 3.383 distance: 2451 - 2540: 3.124 distance: 2466 - 2524: 3.381 distance: 2469 - 2521: 3.233 distance: 2631 - 2632: 4.127 distance: 2777 - 2858: 3.216 distance: 2789 - 2844: 3.162 distance: 2838 - 2982: 3.143 distance: 2899 - 2900: 3.142 distance: 2903 - 2904: 3.423 distance: 2910 - 2911: 6.555 distance: 2911 - 2912: 5.701 distance: 2911 - 2914: 9.194 distance: 2914 - 2915: 10.315 distance: 2915 - 2916: 11.128 distance: 2916 - 2917: 9.913 distance: 2916 - 2918: 5.360 distance: 3049 - 3143: 3.044 distance: 3058 - 3132: 3.222 distance: 3061 - 3129: 3.149 distance: 3121 - 3203: 3.247 distance: 3136 - 3190: 3.103 distance: 3181 - 3292: 3.315 distance: 3429 - 3512: 3.035 distance: 3447 - 3495: 3.367 distance: 3450 - 3492: 3.208 distance: 3463 - 3464: 3.616 distance: 3464 - 3468: 7.428 distance: 3468 - 3469: 3.463 distance: 3487 - 3606: 3.400 distance: 3527 - 3528: 5.158 distance: 3528 - 3529: 6.267 distance: 3528 - 3530: 6.256 distance: 3539 - 3540: 4.200 distance: 3540 - 3549: 7.412 distance: 3549 - 3550: 10.864 distance: 3550 - 3551: 6.885 distance: 3550 - 3553: 8.701 distance: 3553 - 3554: 8.071 distance: 3554 - 3555: 3.639 distance: 3555 - 3556: 9.369 distance: 3555 - 3557: 19.506 distance: 3666 - 3773: 3.018 distance: 3747 - 3836: 3.058 distance: 3763 - 3817: 3.226 distance: 3808 - 3928: 3.934 distance: 3811 - 3925: 3.398 distance: 3825 - 3913: 3.663 distance: 3969 - 3970: 6.531 distance: 3970 - 3971: 6.117 distance: 3970 - 3973: 8.444 distance: 3971 - 3972: 4.505 distance: 3971 - 3977: 4.153 distance: 3973 - 3974: 5.568 distance: 3973 - 3975: 4.320 distance: 4100 - 4162: 3.605 distance: 4103 - 4159: 3.127 distance: 4109 - 4148: 3.931 distance: 4139 - 4140: 4.451 distance: 4139 - 4141: 3.734 distance: 4141 - 4143: 4.199 distance: 4153 - 4261: 3.471 distance: 4325 - 4412: 3.399 distance: 4339 - 4400: 3.062 distance: 4374 - 4375: 3.766 distance: 4375 - 4377: 6.104 distance: 4377 - 4378: 4.330 distance: 4383 - 4384: 8.822 distance: 4390 - 4486: 3.211 distance: 4402 - 4469: 3.423 distance: 4405 - 4466: 3.292 distance: 4529 - 4651: 3.001 distance: 4551 - 4552: 4.186 distance: 4559 - 5396: 3.336 distance: 4571 - 5411: 3.142 distance: 4608 - 5124: 3.130 distance: 4611 - 5121: 3.673 distance: 4628 - 5107: 3.239 distance: 4633 - 4635: 4.934 distance: 4719 - 5255: 3.403 distance: 4724 - 4725: 3.503 distance: 4731 - 5237: 3.494 distance: 4734 - 5234: 3.785 distance: 4744 - 4847: 3.295 distance: 4755 - 5219: 3.020 distance: 4758 - 5216: 3.034 distance: 4762 - 4827: 3.324 distance: 4765 - 4824: 3.238 distance: 4798 - 4799: 3.009 distance: 4799 - 4800: 3.052 distance: 4800 - 4801: 3.952 distance: 4800 - 4802: 4.498 distance: 4859 - 4923: 3.178 distance: 4862 - 4920: 3.532 distance: 5009 - 5112: 3.262 distance: 5021 - 5096: 3.028 distance: 5041 - 5078: 3.169 distance: 5163 - 5167: 3.505 distance: 5167 - 5168: 6.022 distance: 5168 - 5169: 6.225 distance: 5168 - 5171: 8.982 distance: 5169 - 5176: 4.139 distance: 5171 - 5172: 10.975 distance: 5172 - 5173: 3.284 distance: 5173 - 5174: 22.196 distance: 5173 - 5175: 15.524 distance: 5191 - 5403: 3.114 distance: 5204 - 5389: 3.468 distance: 5207 - 5386: 3.298 distance: 5327 - 5336: 3.123 distance: 5337 - 5338: 3.435 distance: 5337 - 5340: 6.763 distance: 5341 - 5342: 12.797 distance: 5341 - 5343: 10.948 distance: 5435 - 5441: 3.337 distance: 5438 - 5439: 7.398 distance: 5438 - 5440: 9.415 distance: 5567 - 5571: 4.782 distance: 5571 - 5572: 4.501 distance: 5571 - 6006: 6.481 distance: 5575 - 5576: 11.244 distance: 5576 - 5578: 11.961 distance: 5585 - 5988: 3.151 distance: 5588 - 5985: 3.027 distance: 5708 - 6133: 3.385 distance: 5711 - 6130: 3.058 distance: 5734 - 6115: 3.430 distance: 5737 - 6112: 3.133 distance: 5753 - 6096: 3.083 distance: 5897 - 5899: 7.358 distance: 5899 - 5900: 17.103 distance: 5900 - 5901: 35.780 distance: 5900 - 5903: 16.256 distance: 5901 - 5902: 23.412 distance: 5901 - 5906: 22.115 distance: 5903 - 5904: 3.058 distance: 5903 - 5905: 3.380 distance: 5906 - 5907: 5.843 distance: 5906 - 5912: 3.326 distance: 6054 - 6074: 3.509 distance: 6065 - 6066: 3.582 distance: 6066 - 6067: 3.751 distance: 6066 - 6069: 4.693 distance: 6069 - 6070: 5.158 distance: 6070 - 6071: 5.302 distance: 6071 - 6072: 6.127 distance: 6079 - 6080: 3.606 distance: 6089 - 6251: 3.167 distance: 6103 - 6232: 3.247 distance: 6275 - 6276: 4.664 distance: 6283 - 6304: 5.897 distance: 6285 - 6286: 3.681 distance: 6286 - 6287: 3.319 distance: 6286 - 6289: 3.835 distance: 6287 - 6288: 6.628 distance: 6287 - 6291: 7.334 distance: 6288 - 6313: 3.589 distance: 6291 - 6292: 7.898 distance: 6292 - 6293: 6.026 distance: 6292 - 6295: 18.403 distance: 6293 - 6294: 11.211 distance: 6294 - 6318: 17.252 distance: 6295 - 6296: 5.080 distance: 6295 - 6297: 26.634 distance: 6296 - 6298: 8.446 distance: 6299 - 6300: 4.985 distance: 6300 - 6301: 3.730 distance: 6301 - 6304: 3.826 distance: 6302 - 6329: 4.657 distance: 6304 - 6305: 7.808 distance: 6305 - 6306: 5.791 distance: 6305 - 6308: 10.218 distance: 6306 - 6313: 5.877 distance: 6307 - 6338: 5.014 distance: 6308 - 6309: 7.905 distance: 6309 - 6310: 4.998 distance: 6310 - 6311: 17.103 distance: 6310 - 6312: 4.429 distance: 6319 - 6320: 3.327 distance: 6319 - 6322: 3.027 distance: 6320 - 6329: 3.066 distance: 6322 - 6323: 9.992 distance: 6323 - 6324: 31.226 distance: 6324 - 6325: 14.497 distance: 6325 - 6326: 13.795 distance: 6326 - 6327: 5.515 distance: 6326 - 6328: 3.631 distance: 6329 - 6330: 5.945 distance: 6330 - 6333: 3.097 distance: 6332 - 6362: 3.338 distance: 6333 - 6334: 6.022 distance: 6334 - 6335: 4.975 distance: 6335 - 6336: 8.695 distance: 6336 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3.090 distance: 6577 - 6584: 3.466 distance: 6584 - 6585: 8.279 distance: 6585 - 6586: 5.047 distance: 6585 - 6588: 11.830 distance: 6588 - 6589: 11.358 distance: 6589 - 6590: 4.165 distance: 6590 - 6591: 23.309 distance: 6590 - 6592: 15.917 distance: 6613 - 6614: 6.620 distance: 6663 - 6664: 3.247 distance: 6669 - 6670: 3.495 distance: 6721 - 6738: 3.116 distance: 6915 - 6932: 3.013 distance: 6944 - 6945: 4.353 distance: 6977 - 6978: 3.323 distance: 6977 - 6987: 3.587 distance: 6980 - 6981: 5.376 distance: 6980 - 6982: 9.912 distance: 6981 - 6983: 5.844 distance: 6982 - 6984: 6.974 distance: 6983 - 6985: 3.115 distance: 6991 - 6993: 5.749 distance: 6994 - 6995: 7.295 distance: 6994 - 7000: 3.016 distance: 6995 - 6996: 22.889 distance: 6995 - 6998: 8.813 distance: 6996 - 6997: 19.958 distance: 6996 - 7001: 19.372 distance: 6998 - 6999: 3.706 distance: 7001 - 7002: 7.133 distance: 7028 - 7054: 3.068 distance: 7035 - 7036: 3.030 distance: 7070 - 7097: 3.106 distance: 7085 - 7108: 3.800 distance: 7103 - 7108: 3.213 distance: 7108 - 7109: 6.107 distance: 7109 - 7110: 3.402 distance: 7109 - 7112: 5.604 distance: 7110 - 7111: 10.647 distance: 7111 - 7140: 11.527 distance: 7112 - 7113: 10.559 distance: 7113 - 7114: 21.770 distance: 7113 - 7115: 13.807 distance: 7116 - 7117: 3.008 distance: 7119 - 7148: 3.509 distance: 7137 - 7140: 4.241 distance: 7138 - 7161: 3.119 distance: 7140 - 7141: 13.351 distance: 7141 - 7142: 13.632 distance: 7141 - 7144: 12.862 distance: 7142 - 7148: 4.019 distance: 7143 - 7172: 3.660 distance: 7144 - 7145: 8.460 distance: 7145 - 7146: 15.223 distance: 7145 - 7147: 13.204 distance: 7151 - 7176: 5.386 distance: 7164 - 7189: 3.005 distance: 7174 - 7176: 3.473 distance: 7176 - 7177: 11.231 distance: 7177 - 7178: 13.151 distance: 7177 - 7180: 13.603 distance: 7178 - 7179: 3.159 distance: 7178 - 7184: 5.137 distance: 7179 - 7204: 3.090 distance: 7180 - 7181: 9.104 distance: 7181 - 7182: 11.292 distance: 7181 - 7183: 7.321 distance: 7200 - 7234: 3.041 distance: 7261 - 7265: 3.363 distance: 7265 - 7266: 4.928 distance: 7266 - 7269: 4.351 distance: 7268 - 7287: 3.067 distance: 7269 - 7270: 5.888 distance: 7270 - 7271: 3.144 distance: 7271 - 7272: 10.451 distance: 7272 - 7273: 5.195 distance: 7315 - 7346: 3.016 distance: 7338 - 7366: 3.025 distance: 7349 - 7374: 3.093 distance: 7371 - 7373: 7.147 distance: 7382 - 7409: 3.106 distance: 7390 - 7417: 3.127 distance: 7412 - 7443: 4.046 distance: 7420 - 7454: 3.355 distance: 7422 - 7424: 3.114 distance: 7443 - 7444: 3.122 distance: 7444 - 7445: 3.718 distance: 7444 - 7447: 4.657 distance: 7447 - 7448: 3.550 distance: 7448 - 7449: 4.339 distance: 7463 - 7489: 3.248 distance: 7471 - 7497: 3.058 distance: 7478 - 7505: 3.454 distance: 7485 - 7514: 3.683 distance: 7495 - 7496: 3.152 distance: 7511 - 7512: 3.842 distance: 7511 - 7513: 3.601 distance: 7566 - 7567: 4.087 distance: 7567 - 7570: 3.953 distance: 7570 - 7571: 3.254 distance: 7590 - 7621: 3.011 distance: 7601 - 7629: 5.777 distance: 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