Starting phenix.real_space_refine on Thu Jan 16 08:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz2_37944/01_2025/8wz2_37944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz2_37944/01_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_37944/01_2025/8wz2_37944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz2_37944/01_2025/8wz2_37944.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz2_37944/01_2025/8wz2_37944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz2_37944/01_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-5571/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: 6.18, per 1000 atoms: 0.66 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 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: 1.12 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: 2.96 Time building geometry restraints manager: 2.90 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: 3.500 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- 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 : 1.119 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: 1.4605 time to fit residues: 634.2883 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 : 2.074 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.103567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078909 restraints weight = 20792.947| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.57 r_work: 0.3063 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8407 (tp40) REVERT: A 185 PHE cc_start: 0.6762 (m-10) cc_final: 0.6516 (m-80) REVERT: A 226 ASP cc_start: 0.8612 (t0) cc_final: 0.8402 (t0) REVERT: A 242 SER cc_start: 0.9134 (m) cc_final: 0.8813 (p) REVERT: A 247 ARG cc_start: 0.8398 (ptt90) cc_final: 0.7920 (tmm-80) REVERT: A 248 TRP cc_start: 0.8209 (m100) cc_final: 0.7982 (m100) REVERT: B 267 MET cc_start: 0.8859 (tpp) cc_final: 0.8492 (tpp) REVERT: E 42 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8259 (mmmm) REVERT: E 72 ASP cc_start: 0.8414 (t0) cc_final: 0.8046 (t0) REVERT: E 82 MET cc_start: 0.8892 (mtp) cc_final: 0.8661 (mtp) REVERT: E 244 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8214 (tmmt) REVERT: G 17 GLN cc_start: 0.8046 (tp40) cc_final: 0.7652 (tp40) REVERT: G 21 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7429 (mt-10) REVERT: G 45 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8811 (mppt) REVERT: R 32 ARG cc_start: 0.7564 (tpt170) cc_final: 0.7263 (tpt90) REVERT: R 68 TYR cc_start: 0.8779 (t80) cc_final: 0.8352 (t80) REVERT: R 120 MET cc_start: 0.8636 (ttp) cc_final: 0.8195 (ppp) REVERT: R 187 GLU cc_start: 0.5720 (tm-30) cc_final: 0.4793 (tm-30) REVERT: R 188 ILE cc_start: 0.9483 (mt) cc_final: 0.9281 (tp) REVERT: R 200 CYS cc_start: 0.7370 (m) cc_final: 0.6458 (m) REVERT: R 312 MET cc_start: 0.9210 (mtm) cc_final: 0.9005 (mtm) outliers start: 33 outliers final: 11 residues processed: 268 average time/residue: 1.2938 time to fit residues: 369.2146 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 : 1.183 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 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: 0.0170 chunk 45 optimal weight: 3.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 R 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074743 restraints weight = 20991.422| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.54 r_work: 0.2981 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9546 Z= 0.220 Angle : 0.628 13.016 12931 Z= 0.316 Chirality : 0.042 0.171 1471 Planarity : 0.004 0.035 1638 Dihedral : 4.416 89.704 1300 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.80 % Allowed : 19.28 % 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: 0.33 (0.24), residues: 1181 helix: 1.93 (0.25), residues: 429 sheet: -0.04 (0.32), residues: 266 loop : -1.21 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.006 0.001 HIS E 34 PHE 0.019 0.001 PHE R 61 TYR 0.025 0.002 TYR B 64 ARG 0.009 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 271 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8398 (tp40) REVERT: A 185 PHE cc_start: 0.6874 (m-80) cc_final: 0.6559 (m-10) REVERT: A 242 SER cc_start: 0.9104 (m) cc_final: 0.8814 (p) REVERT: A 247 ARG cc_start: 0.8544 (ptt90) cc_final: 0.8092 (tmm-80) REVERT: A 248 TRP cc_start: 0.8422 (m100) cc_final: 0.8219 (m100) REVERT: A 261 GLN cc_start: 0.8238 (pt0) cc_final: 0.7962 (pt0) REVERT: B 28 LYS cc_start: 0.8898 (tmmm) cc_final: 0.8622 (ttmm) REVERT: B 177 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 252 ASP cc_start: 0.8290 (t0) cc_final: 0.7992 (t0) REVERT: B 267 MET cc_start: 0.9229 (tpp) cc_final: 0.8894 (tpp) REVERT: E 42 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8340 (mmmm) REVERT: E 72 ASP cc_start: 0.8536 (t0) cc_final: 0.8080 (t0) REVERT: E 244 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8216 (tmmt) REVERT: G 17 GLN cc_start: 0.8146 (tp40) cc_final: 0.7797 (tp40) REVERT: G 21 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7497 (mt-10) REVERT: R 32 ARG cc_start: 0.7505 (tpt170) cc_final: 0.6879 (tpt90) REVERT: R 68 TYR cc_start: 0.8690 (t80) cc_final: 0.8485 (t80) REVERT: R 74 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8357 (mmmt) REVERT: R 77 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8139 (mpt180) REVERT: R 187 GLU cc_start: 0.5906 (tm-30) cc_final: 0.4948 (tm-30) REVERT: R 188 ILE cc_start: 0.9486 (mt) cc_final: 0.9279 (tp) REVERT: R 200 CYS cc_start: 0.7657 (m) cc_final: 0.6718 (m) REVERT: R 204 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8402 (mm-30) REVERT: R 210 HIS cc_start: 0.8066 (m170) cc_final: 0.7854 (m90) REVERT: R 312 MET cc_start: 0.9111 (mtm) cc_final: 0.8882 (mtm) outliers start: 38 outliers final: 16 residues processed: 256 average time/residue: 1.2655 time to fit residues: 345.4515 Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 20 SER 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 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: 0.9990 chunk 78 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 186 GLN R 63 ASN R 81 ASN R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.061519 restraints weight = 21371.028| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.50 r_work: 0.2775 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 9546 Z= 0.576 Angle : 0.753 9.623 12931 Z= 0.395 Chirality : 0.048 0.250 1471 Planarity : 0.005 0.045 1638 Dihedral : 5.438 98.772 1300 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.09 % Allowed : 21.28 % Favored : 73.63 % 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: 0.32 (0.24), residues: 1181 helix: 1.59 (0.24), residues: 426 sheet: 0.06 (0.31), residues: 279 loop : -0.94 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 87 HIS 0.010 0.003 HIS B 96 PHE 0.023 0.002 PHE E 203 TYR 0.028 0.002 TYR E 190 ARG 0.009 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 261 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8894 (tp-100) REVERT: A 185 PHE cc_start: 0.7161 (m-80) cc_final: 0.6825 (m-10) REVERT: A 261 GLN cc_start: 0.8367 (pt0) cc_final: 0.8115 (pt0) REVERT: B 177 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 219 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8410 (mpp80) REVERT: B 252 ASP cc_start: 0.8784 (t0) cc_final: 0.8468 (t0) REVERT: E 42 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8293 (mmmm) REVERT: E 72 ASP cc_start: 0.8490 (t0) cc_final: 0.7949 (t0) REVERT: E 220 GLU cc_start: 0.8215 (mm-30) cc_final: 0.8005 (mm-30) REVERT: E 234 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7367 (mt-10) REVERT: E 244 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8135 (tmmt) REVERT: G 13 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9171 (tppp) REVERT: G 41 GLU cc_start: 0.8904 (pp20) cc_final: 0.8642 (pp20) REVERT: G 45 LYS cc_start: 0.9321 (mtmm) cc_final: 0.9093 (mppt) REVERT: G 57 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7450 (mp0) REVERT: R 32 ARG cc_start: 0.7464 (tpt170) cc_final: 0.6946 (tpt90) REVERT: R 77 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8180 (mpt180) REVERT: R 91 ASP cc_start: 0.8753 (t70) cc_final: 0.8461 (t70) REVERT: R 106 ASN cc_start: 0.9148 (m-40) cc_final: 0.8735 (p0) REVERT: R 109 ASP cc_start: 0.8788 (p0) cc_final: 0.8577 (p0) REVERT: R 124 VAL cc_start: 0.9103 (t) cc_final: 0.8803 (p) REVERT: R 160 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7659 (tpm170) REVERT: R 187 GLU cc_start: 0.6127 (tm-30) cc_final: 0.5215 (tm-30) REVERT: R 200 CYS cc_start: 0.8037 (m) cc_final: 0.7169 (m) REVERT: R 204 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8573 (mm-30) REVERT: R 210 HIS cc_start: 0.8308 (m170) cc_final: 0.7879 (m170) REVERT: R 312 MET cc_start: 0.9277 (mtm) cc_final: 0.9056 (mtm) REVERT: R 338 ASN cc_start: 0.8537 (t0) cc_final: 0.7745 (t160) outliers start: 51 outliers final: 16 residues processed: 244 average time/residue: 1.3128 time to fit residues: 340.4893 Evaluate side-chains 200 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 269 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 219 ARG 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 144 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 34 HIS E 186 GLN E 194 ASN R 63 ASN R 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 156 GLN R 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064754 restraints weight = 21101.006| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.54 r_work: 0.2851 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9546 Z= 0.220 Angle : 0.634 8.961 12931 Z= 0.326 Chirality : 0.043 0.180 1471 Planarity : 0.004 0.040 1638 Dihedral : 4.214 20.832 1298 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.90 % Allowed : 24.08 % 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: 0.57 (0.24), residues: 1181 helix: 1.74 (0.25), residues: 432 sheet: 0.39 (0.33), residues: 247 loop : -0.83 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 170 HIS 0.006 0.001 HIS E 34 PHE 0.015 0.001 PHE R 61 TYR 0.017 0.001 TYR R 36 ARG 0.009 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 242 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8908 (tp-100) REVERT: A 28 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8522 (tp40) REVERT: A 185 PHE cc_start: 0.7167 (m-80) cc_final: 0.6845 (m-10) REVERT: A 197 HIS cc_start: 0.8106 (m170) cc_final: 0.7852 (m90) REVERT: A 247 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7707 (ppp80) REVERT: A 261 GLN cc_start: 0.8440 (pt0) cc_final: 0.8126 (pt0) REVERT: B 177 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 239 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: B 252 ASP cc_start: 0.8747 (t0) cc_final: 0.8423 (t0) REVERT: E 42 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8304 (mmmm) REVERT: E 72 ASP cc_start: 0.8498 (t0) cc_final: 0.7955 (t0) REVERT: E 220 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7856 (mm-30) REVERT: E 223 ASP cc_start: 0.8395 (m-30) cc_final: 0.8055 (m-30) REVERT: E 234 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7249 (mt-10) REVERT: E 244 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8111 (tmmt) REVERT: G 13 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9367 (mmmm) REVERT: G 16 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8398 (tm-30) REVERT: G 41 GLU cc_start: 0.8904 (pp20) cc_final: 0.8598 (pp20) REVERT: G 45 LYS cc_start: 0.9322 (mtmm) cc_final: 0.9083 (mppt) REVERT: R 68 TYR cc_start: 0.8883 (t80) cc_final: 0.7897 (t80) REVERT: R 72 ARG cc_start: 0.8463 (ttt90) cc_final: 0.8260 (ptm160) REVERT: R 76 MET cc_start: 0.8347 (mmt) cc_final: 0.8101 (mmt) REVERT: R 77 ARG cc_start: 0.8648 (ttt180) cc_final: 0.8193 (mpt180) REVERT: R 124 VAL cc_start: 0.9062 (t) cc_final: 0.8834 (p) REVERT: R 187 GLU cc_start: 0.6153 (tm-30) cc_final: 0.5279 (tm-30) REVERT: R 204 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8601 (mm-30) REVERT: R 210 HIS cc_start: 0.8275 (m170) cc_final: 0.7795 (m170) REVERT: R 312 MET cc_start: 0.9252 (mtm) cc_final: 0.9033 (mtm) outliers start: 29 outliers final: 13 residues processed: 235 average time/residue: 1.3252 time to fit residues: 331.6674 Evaluate side-chains 205 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 264 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 40.0000 chunk 89 optimal weight: 0.0030 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 R 81 ASN ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063709 restraints weight = 21036.410| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.52 r_work: 0.2826 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9546 Z= 0.295 Angle : 0.655 9.245 12931 Z= 0.334 Chirality : 0.043 0.181 1471 Planarity : 0.004 0.043 1638 Dihedral : 4.174 19.733 1298 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.30 % Allowed : 23.48 % Favored : 72.23 % 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: 0.70 (0.25), residues: 1181 helix: 1.83 (0.25), residues: 431 sheet: 0.43 (0.33), residues: 261 loop : -0.74 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.006 0.001 HIS R 198 PHE 0.015 0.001 PHE R 61 TYR 0.018 0.001 TYR E 190 ARG 0.008 0.001 ARG B 134 *********************** 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 238 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8627 (mt-10) REVERT: A 22 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8876 (tp-100) REVERT: A 28 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8572 (tp-100) REVERT: A 185 PHE cc_start: 0.7214 (m-80) cc_final: 0.6905 (m-10) REVERT: A 247 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7815 (ppp80) REVERT: A 261 GLN cc_start: 0.8457 (pt0) cc_final: 0.8132 (pt0) REVERT: B 177 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8534 (mm-30) REVERT: B 252 ASP cc_start: 0.8739 (t0) cc_final: 0.8439 (t0) REVERT: E 42 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8262 (mmmm) REVERT: E 72 ASP cc_start: 0.8526 (t0) cc_final: 0.7982 (t0) REVERT: E 112 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8789 (mm-40) REVERT: E 220 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7873 (mm-30) REVERT: E 223 ASP cc_start: 0.8418 (m-30) cc_final: 0.7337 (m-30) REVERT: E 234 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7303 (mt-10) REVERT: E 244 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8114 (tmmt) REVERT: G 12 ARG cc_start: 0.9046 (tmm-80) cc_final: 0.8113 (tmm-80) REVERT: G 13 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9011 (mmmm) REVERT: G 19 LYS cc_start: 0.9525 (ttpp) cc_final: 0.9218 (tmmt) REVERT: G 41 GLU cc_start: 0.8973 (pp20) cc_final: 0.8667 (pp20) REVERT: G 45 LYS cc_start: 0.9318 (mtmm) cc_final: 0.9042 (mppt) REVERT: G 57 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7277 (mp0) REVERT: R 68 TYR cc_start: 0.8939 (t80) cc_final: 0.8565 (t80) REVERT: R 72 ARG cc_start: 0.8468 (ttt90) cc_final: 0.8014 (ttt90) REVERT: R 160 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7588 (tpm170) REVERT: R 197 GLU cc_start: 0.8497 (mp0) cc_final: 0.8133 (mp0) REVERT: R 210 HIS cc_start: 0.8412 (m170) cc_final: 0.7876 (m170) REVERT: R 312 MET cc_start: 0.9281 (mtm) cc_final: 0.9053 (mtm) outliers start: 43 outliers final: 24 residues processed: 226 average time/residue: 1.2414 time to fit residues: 299.6368 Evaluate side-chains 215 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 A residue 355 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 151 LEU 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 61 ASP 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 116 PHE Chi-restraints excluded: chain R residue 120 MET Chi-restraints excluded: chain R residue 121 VAL 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 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 306 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** 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 = 0.3490 r_free = 0.3490 target = 0.091217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.064737 restraints weight = 21123.655| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.52 r_work: 0.2846 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9546 Z= 0.235 Angle : 0.658 9.599 12931 Z= 0.334 Chirality : 0.043 0.182 1471 Planarity : 0.004 0.043 1638 Dihedral : 4.088 19.186 1298 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.40 % Allowed : 25.47 % 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: 0.76 (0.25), residues: 1181 helix: 1.88 (0.25), residues: 431 sheet: 0.48 (0.33), residues: 254 loop : -0.70 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS R 198 PHE 0.014 0.001 PHE R 97 TYR 0.019 0.001 TYR R 36 ARG 0.006 0.001 ARG G 12 *********************** 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 236 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8615 (mt-10) REVERT: A 22 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8869 (tp-100) REVERT: A 28 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8538 (tp-100) REVERT: A 185 PHE cc_start: 0.7209 (m-80) cc_final: 0.6901 (m-10) REVERT: A 247 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7842 (ppp80) REVERT: A 261 GLN cc_start: 0.8469 (pt0) cc_final: 0.8137 (pt0) REVERT: A 314 ASP cc_start: 0.9224 (t0) cc_final: 0.8954 (m-30) REVERT: B 177 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8533 (mm-30) REVERT: B 239 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: B 252 ASP cc_start: 0.8712 (t0) cc_final: 0.8424 (t0) REVERT: E 42 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8278 (mmmm) REVERT: E 64 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8528 (ttmm) REVERT: E 72 ASP cc_start: 0.8568 (t0) cc_final: 0.8033 (t0) REVERT: E 92 MET cc_start: 0.8202 (ttm) cc_final: 0.7950 (tpp) REVERT: E 201 ASP cc_start: 0.8891 (p0) cc_final: 0.8545 (t70) REVERT: E 220 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8229 (mm-30) REVERT: E 223 ASP cc_start: 0.8461 (m-30) cc_final: 0.8116 (m-30) REVERT: E 234 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7280 (mt-10) REVERT: E 244 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8126 (tmmt) REVERT: G 12 ARG cc_start: 0.8794 (tmm-80) cc_final: 0.8398 (tmm-80) REVERT: G 13 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9044 (mmmm) REVERT: G 19 LYS cc_start: 0.9524 (ttpp) cc_final: 0.9199 (tmmt) REVERT: G 28 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8453 (mmmm) REVERT: G 41 GLU cc_start: 0.8994 (pp20) cc_final: 0.8658 (pp20) REVERT: G 45 LYS cc_start: 0.9278 (mtmm) cc_final: 0.9044 (mppt) REVERT: G 57 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7313 (mp0) REVERT: R 77 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8153 (mpt180) REVERT: R 155 TRP cc_start: 0.8974 (p-90) cc_final: 0.8582 (p-90) REVERT: R 160 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7567 (tpm170) REVERT: R 210 HIS cc_start: 0.8403 (m170) cc_final: 0.7890 (m170) REVERT: R 225 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8444 (tt) REVERT: R 312 MET cc_start: 0.9236 (mtm) cc_final: 0.9009 (mtm) outliers start: 34 outliers final: 20 residues processed: 224 average time/residue: 1.2493 time to fit residues: 298.8655 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER 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 G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG 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 200 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE 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: 0.4980 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** 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 = 0.3475 r_free = 0.3475 target = 0.090439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.063912 restraints weight = 21409.699| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.54 r_work: 0.2827 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9546 Z= 0.287 Angle : 0.675 10.032 12931 Z= 0.345 Chirality : 0.043 0.181 1471 Planarity : 0.004 0.044 1638 Dihedral : 4.105 19.011 1296 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.60 % Allowed : 26.07 % Favored : 70.33 % 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 (0.24), residues: 1181 helix: 1.79 (0.25), residues: 431 sheet: 0.37 (0.32), residues: 256 loop : -0.69 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 170 HIS 0.006 0.001 HIS R 198 PHE 0.013 0.001 PHE R 61 TYR 0.018 0.001 TYR R 68 ARG 0.006 0.001 ARG A 356 *********************** 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 234 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8984 (m-30) cc_final: 0.8508 (m-30) REVERT: A 20 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8624 (mt-10) REVERT: A 22 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8871 (tp-100) REVERT: A 28 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8547 (tp-100) REVERT: A 185 PHE cc_start: 0.7203 (m-80) cc_final: 0.6901 (m-10) REVERT: A 247 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7904 (ppp80) REVERT: B 177 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8552 (mm-30) REVERT: B 239 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: B 252 ASP cc_start: 0.8721 (t0) cc_final: 0.8440 (t0) REVERT: E 42 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8345 (mmmm) REVERT: E 64 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8499 (ttmm) REVERT: E 72 ASP cc_start: 0.8548 (t0) cc_final: 0.7979 (t0) REVERT: E 92 MET cc_start: 0.8208 (ttm) cc_final: 0.7939 (tpp) REVERT: E 201 ASP cc_start: 0.8904 (p0) cc_final: 0.8565 (t0) REVERT: E 220 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8110 (mm-30) REVERT: E 223 ASP cc_start: 0.8456 (m-30) cc_final: 0.8080 (m-30) REVERT: E 234 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 244 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8068 (tmmt) REVERT: G 12 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8579 (tmm-80) REVERT: G 13 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9109 (mmmm) REVERT: G 19 LYS cc_start: 0.9490 (ttpp) cc_final: 0.9227 (tmmt) REVERT: G 20 MET cc_start: 0.9183 (ptp) cc_final: 0.8972 (ptp) REVERT: G 28 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8473 (mmmm) REVERT: G 57 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7164 (mp0) REVERT: R 77 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8187 (mpt180) REVERT: R 155 TRP cc_start: 0.8976 (p-90) cc_final: 0.8602 (p-90) REVERT: R 160 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7561 (tpm170) REVERT: R 210 HIS cc_start: 0.8444 (m170) cc_final: 0.7920 (m170) REVERT: R 225 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8427 (tt) REVERT: R 312 MET cc_start: 0.9235 (mtm) cc_final: 0.9022 (mtm) outliers start: 36 outliers final: 26 residues processed: 224 average time/residue: 1.2411 time to fit residues: 296.5632 Evaluate side-chains 223 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE 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 A residue 355 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 151 LEU 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 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 104 LEU 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 200 CYS Chi-restraints excluded: chain R residue 225 LEU 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: 7.9990 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062893 restraints weight = 21382.783| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.52 r_work: 0.2807 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9546 Z= 0.346 Angle : 0.713 10.675 12931 Z= 0.364 Chirality : 0.045 0.187 1471 Planarity : 0.004 0.044 1638 Dihedral : 4.224 19.748 1296 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.90 % Allowed : 27.07 % Favored : 70.03 % 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: 0.63 (0.25), residues: 1181 helix: 1.70 (0.25), residues: 432 sheet: 0.27 (0.32), residues: 263 loop : -0.62 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 205 HIS 0.006 0.002 HIS R 198 PHE 0.016 0.001 PHE R 61 TYR 0.019 0.002 TYR R 36 ARG 0.006 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 225 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8967 (m-30) cc_final: 0.8460 (m-30) REVERT: A 20 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8640 (mt-10) REVERT: A 22 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8885 (tp-100) REVERT: A 28 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8580 (tp-100) REVERT: A 185 PHE cc_start: 0.7214 (m-80) cc_final: 0.6917 (m-10) REVERT: A 247 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7963 (ppp80) REVERT: B 177 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8551 (mm-30) REVERT: B 252 ASP cc_start: 0.8758 (t0) cc_final: 0.8469 (t0) REVERT: E 42 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8359 (mmmm) REVERT: E 64 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8505 (ttmm) REVERT: E 72 ASP cc_start: 0.8555 (t0) cc_final: 0.8038 (t0) REVERT: E 92 MET cc_start: 0.8229 (ttm) cc_final: 0.7960 (tpp) REVERT: E 201 ASP cc_start: 0.8934 (p0) cc_final: 0.8622 (t0) REVERT: E 220 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 223 ASP cc_start: 0.8370 (m-30) cc_final: 0.8003 (m-30) REVERT: E 244 LYS cc_start: 0.8907 (ttpp) cc_final: 0.8095 (tmmt) REVERT: G 19 LYS cc_start: 0.9490 (ttpp) cc_final: 0.9239 (tmmt) REVERT: G 20 MET cc_start: 0.9154 (ptp) cc_final: 0.8942 (ptp) REVERT: G 28 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8520 (mmmm) REVERT: G 41 GLU cc_start: 0.8953 (pp20) cc_final: 0.8673 (pp20) REVERT: G 57 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7345 (mp0) REVERT: R 68 TYR cc_start: 0.8962 (t80) cc_final: 0.8205 (t80) REVERT: R 72 ARG cc_start: 0.8552 (ttt90) cc_final: 0.8206 (ttm-80) REVERT: R 120 MET cc_start: 0.8999 (ttp) cc_final: 0.8141 (tmm) REVERT: R 155 TRP cc_start: 0.8980 (p-90) cc_final: 0.8607 (p-90) REVERT: R 160 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7573 (tpm170) REVERT: R 225 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8433 (tt) REVERT: R 312 MET cc_start: 0.9273 (mtm) cc_final: 0.9065 (mtm) outliers start: 29 outliers final: 26 residues processed: 218 average time/residue: 1.2904 time to fit residues: 300.8596 Evaluate side-chains 223 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 A residue 355 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 104 LEU 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 200 CYS Chi-restraints excluded: chain R residue 225 LEU 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: 2.9990 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.064301 restraints weight = 21359.559| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.52 r_work: 0.2835 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9546 Z= 0.247 Angle : 0.702 10.080 12931 Z= 0.357 Chirality : 0.043 0.194 1471 Planarity : 0.003 0.043 1638 Dihedral : 4.138 18.381 1296 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 27.77 % Favored : 69.33 % 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: 1.72 (0.25), residues: 432 sheet: 0.32 (0.32), residues: 260 loop : -0.61 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 205 HIS 0.007 0.001 HIS R 198 PHE 0.014 0.001 PHE R 61 TYR 0.019 0.001 TYR R 194 ARG 0.005 0.000 ARG A 356 ********************** 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: 29 poor density : 199 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8957 (m-30) cc_final: 0.8466 (m-30) REVERT: A 20 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 22 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8900 (tp-100) REVERT: A 28 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8583 (tp-100) REVERT: A 185 PHE cc_start: 0.7218 (m-80) cc_final: 0.6920 (m-10) REVERT: A 247 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7938 (ppp80) REVERT: B 177 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 252 ASP cc_start: 0.8691 (t0) cc_final: 0.8443 (t0) REVERT: E 42 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8360 (mmmm) REVERT: E 64 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8373 (ttmm) REVERT: E 72 ASP cc_start: 0.8548 (t0) cc_final: 0.8083 (t0) REVERT: E 92 MET cc_start: 0.8229 (ttm) cc_final: 0.7962 (tpp) REVERT: E 201 ASP cc_start: 0.8935 (p0) cc_final: 0.8653 (t0) REVERT: E 220 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8048 (mm-30) REVERT: E 223 ASP cc_start: 0.8383 (m-30) cc_final: 0.7976 (m-30) REVERT: E 244 LYS cc_start: 0.8880 (ttpp) cc_final: 0.8048 (tmmt) REVERT: G 19 LYS cc_start: 0.9487 (ttpp) cc_final: 0.9227 (tmmt) REVERT: G 28 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8511 (mmmm) REVERT: G 41 GLU cc_start: 0.8963 (pp20) cc_final: 0.8665 (pp20) REVERT: G 57 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7402 (mp0) REVERT: R 91 ASP cc_start: 0.8792 (t70) cc_final: 0.8397 (t70) REVERT: R 155 TRP cc_start: 0.8958 (p-90) cc_final: 0.8583 (p-90) REVERT: R 160 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7492 (tpm170) REVERT: R 225 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8426 (tt) REVERT: R 312 MET cc_start: 0.9248 (mtm) cc_final: 0.9013 (mtm) outliers start: 29 outliers final: 23 residues processed: 220 average time/residue: 1.2476 time to fit residues: 292.8201 Evaluate side-chains 212 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 17 GLU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER 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 G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 104 LEU 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 200 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 81 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 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 = 0.091879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065556 restraints weight = 21090.886| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.52 r_work: 0.2811 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9546 Z= 0.215 Angle : 0.712 13.128 12931 Z= 0.361 Chirality : 0.044 0.196 1471 Planarity : 0.004 0.045 1638 Dihedral : 4.079 18.323 1296 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 28.77 % Favored : 69.03 % 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: 0.67 (0.25), residues: 1181 helix: 1.63 (0.25), residues: 439 sheet: 0.36 (0.33), residues: 255 loop : -0.56 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 205 HIS 0.007 0.001 HIS R 198 PHE 0.015 0.001 PHE R 61 TYR 0.025 0.001 TYR R 68 ARG 0.009 0.001 ARG G 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9087.89 seconds wall clock time: 161 minutes 55.20 seconds (9715.20 seconds total)