Starting phenix.real_space_refine on Thu Mar 13 08:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.map" model { file = "/net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flq_29283/03_2025/8flq_29283.cif" } resolution = 2.55 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= 0.070 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 58 5.16 5 C 5709 2.51 5 N 1569 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1906 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2568 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 424 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2858 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 5.97, per 1000 atoms: 0.66 Number of scatterers: 8992 At special positions: 0 Unit cell: (72.8, 96.2, 173.55, 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 58 16.00 O 1656 8.00 N 1569 7.00 C 5709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 43.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.567A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.504A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.592A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.257A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.120A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.851A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.517A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 53 Processing helix chain 'R' and resid 167 through 172 removed outlier: 4.053A pdb=" N LYS R 172 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.482A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.588A pdb=" N SER R 246 " --> pdb=" O ALA R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.529A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.538A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.516A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 359 Processing helix chain 'R' and resid 360 through 392 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.385A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 479 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.345A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.549A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.292A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.235A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.551A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.093A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.674A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.619A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 removed outlier: 3.664A pdb=" N GLU R 111 " --> pdb=" O TRP R 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 494 hydrogen bonds defined for protein. 1407 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: 2.69 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2941 1.34 - 1.46: 2250 1.46 - 1.58: 3904 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9177 Sorted by residual: bond pdb=" N VAL B 187 " pdb=" CA VAL B 187 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N SER B 160 " pdb=" CA SER B 160 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.91e+00 bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.56e-02 4.11e+03 6.62e+00 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12017 1.37 - 2.75: 349 2.75 - 4.12: 65 4.12 - 5.49: 12 5.49 - 6.87: 4 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 114.67 109.69 4.98 1.10e+00 8.26e-01 2.05e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 113.19 108.03 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" C ILE R 190 " pdb=" N TYR R 191 " pdb=" CA TYR R 191 " ideal model delta sigma weight residual 121.14 114.27 6.87 1.75e+00 3.27e-01 1.54e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" C TYR B 59 " ideal model delta sigma weight residual 113.41 109.21 4.20 1.22e+00 6.72e-01 1.19e+01 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 120.00 -6.10 1.80e+00 3.09e-01 1.15e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4907 17.66 - 35.32: 415 35.32 - 52.98: 64 52.98 - 70.63: 16 70.63 - 88.29: 9 Dihedral angle restraints: 5411 sinusoidal: 2081 harmonic: 3330 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 143.52 -50.52 1 1.00e+01 1.00e-02 3.50e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 970 0.039 - 0.077: 308 0.077 - 0.116: 87 0.116 - 0.155: 18 0.155 - 0.193: 3 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB ILE R 190 " pdb=" CA ILE R 190 " pdb=" CG1 ILE R 190 " pdb=" CG2 ILE R 190 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA VAL B 187 " pdb=" N VAL B 187 " pdb=" C VAL B 187 " pdb=" CB VAL B 187 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1383 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 376 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ILE R 376 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE R 376 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU R 377 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 378 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C PHE R 378 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE R 378 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE R 379 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 377 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C LEU R 377 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU R 377 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE R 378 " -0.010 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 926 2.75 - 3.29: 9083 3.29 - 3.82: 16195 3.82 - 4.36: 19609 4.36 - 4.90: 32721 Nonbonded interactions: 78534 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.254 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLU R 302 " pdb=" O HOH R 701 " model vdw 2.265 3.040 ... (remaining 78529 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 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 : 0.003 0.046 9177 Z= 0.215 Angle : 0.569 6.865 12447 Z= 0.352 Chirality : 0.042 0.193 1386 Planarity : 0.004 0.036 1588 Dihedral : 13.874 88.292 3241 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.21 % Allowed : 0.53 % Favored : 99.25 % 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: 1.35 (0.25), residues: 1124 helix: 2.39 (0.24), residues: 443 sheet: -0.26 (0.33), residues: 214 loop : 0.08 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.013 0.001 TYR A 358 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.001 Fit side-chains REVERT: R 32 MET cc_start: 0.4510 (ptt) cc_final: 0.4234 (tpp) outliers start: 2 outliers final: 2 residues processed: 128 average time/residue: 1.2943 time to fit residues: 176.8461 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 101 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.195245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148823 restraints weight = 9849.872| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.32 r_work: 0.3593 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9177 Z= 0.157 Angle : 0.486 5.915 12447 Z= 0.272 Chirality : 0.041 0.175 1386 Planarity : 0.004 0.035 1588 Dihedral : 4.388 23.868 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1124 helix: 2.90 (0.24), residues: 438 sheet: -0.34 (0.31), residues: 231 loop : 0.22 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.010 0.001 HIS A 357 PHE 0.022 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.005 Fit side-chains REVERT: B 66 ASP cc_start: 0.7100 (p0) cc_final: 0.6347 (m-30) REVERT: B 255 LEU cc_start: 0.8168 (mp) cc_final: 0.7916 (mt) REVERT: B 303 ASP cc_start: 0.7837 (m-30) cc_final: 0.7502 (m-30) REVERT: R 32 MET cc_start: 0.6556 (ptt) cc_final: 0.4433 (tpp) REVERT: R 221 TYR cc_start: 0.7549 (m-10) cc_final: 0.6547 (t80) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 1.1584 time to fit residues: 149.3372 Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.193639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146577 restraints weight = 9992.078| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.29 r_work: 0.3567 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9177 Z= 0.172 Angle : 0.481 6.210 12447 Z= 0.266 Chirality : 0.041 0.190 1386 Planarity : 0.003 0.036 1588 Dihedral : 4.367 23.012 1249 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.07 % Allowed : 9.91 % Favored : 89.02 % 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: 1.68 (0.26), residues: 1124 helix: 2.96 (0.24), residues: 437 sheet: -0.43 (0.31), residues: 238 loop : 0.21 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.009 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.054 Fit side-chains REVERT: B 66 ASP cc_start: 0.7189 (p0) cc_final: 0.6455 (m-30) REVERT: B 303 ASP cc_start: 0.7830 (m-30) cc_final: 0.7492 (m-30) REVERT: R 32 MET cc_start: 0.6530 (ptt) cc_final: 0.4547 (tpp) REVERT: R 221 TYR cc_start: 0.7679 (m-10) cc_final: 0.6714 (t80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 1.1830 time to fit residues: 149.2321 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 101 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 78 optimal weight: 7.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.192110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144604 restraints weight = 9922.918| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.38 r_work: 0.3540 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9177 Z= 0.204 Angle : 0.494 6.342 12447 Z= 0.273 Chirality : 0.041 0.206 1386 Planarity : 0.004 0.036 1588 Dihedral : 4.496 25.632 1249 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.96 % Allowed : 11.19 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1124 helix: 2.84 (0.24), residues: 444 sheet: -0.49 (0.31), residues: 239 loop : 0.22 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.009 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 1.283 Fit side-chains REVERT: B 66 ASP cc_start: 0.7242 (p0) cc_final: 0.6539 (m-30) REVERT: B 303 ASP cc_start: 0.7950 (m-30) cc_final: 0.7662 (m-30) REVERT: R 32 MET cc_start: 0.6540 (ptt) cc_final: 0.4649 (tpp) REVERT: R 221 TYR cc_start: 0.7686 (m-10) cc_final: 0.6726 (t80) REVERT: R 463 ASN cc_start: 0.8443 (t0) cc_final: 0.7993 (t0) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 1.7941 time to fit residues: 227.1380 Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 471 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 88 ASN N 39 GLN N 53 GLN R 380 ASN R 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.184213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135224 restraints weight = 9883.753| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.18 r_work: 0.3434 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 9177 Z= 0.595 Angle : 0.719 7.468 12447 Z= 0.392 Chirality : 0.052 0.199 1386 Planarity : 0.005 0.051 1588 Dihedral : 5.427 27.516 1247 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.92 % Allowed : 11.62 % Favored : 86.46 % 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: 0.92 (0.25), residues: 1124 helix: 2.00 (0.23), residues: 443 sheet: -0.52 (0.31), residues: 233 loop : -0.06 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.021 0.002 HIS A 357 PHE 0.029 0.003 PHE R 335 TYR 0.023 0.003 TYR A 358 ARG 0.007 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.903 Fit side-chains REVERT: B 66 ASP cc_start: 0.7360 (p0) cc_final: 0.6773 (m-30) REVERT: B 215 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: B 303 ASP cc_start: 0.7980 (m-30) cc_final: 0.7775 (m-30) REVERT: R 32 MET cc_start: 0.6740 (ptt) cc_final: 0.4687 (tpp) REVERT: R 221 TYR cc_start: 0.7741 (m-10) cc_final: 0.6757 (t80) outliers start: 18 outliers final: 6 residues processed: 113 average time/residue: 1.2202 time to fit residues: 147.5173 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 83 optimal weight: 0.0010 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.192830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145937 restraints weight = 9889.890| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.44 r_work: 0.3562 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9177 Z= 0.149 Angle : 0.490 7.758 12447 Z= 0.271 Chirality : 0.040 0.216 1386 Planarity : 0.004 0.040 1588 Dihedral : 4.543 23.892 1247 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.96 % Allowed : 13.75 % Favored : 85.29 % 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: 1.41 (0.25), residues: 1124 helix: 2.70 (0.24), residues: 437 sheet: -0.56 (0.30), residues: 236 loop : 0.09 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.001 PHE R 335 TYR 0.024 0.001 TYR R 191 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.911 Fit side-chains REVERT: B 215 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: B 303 ASP cc_start: 0.7886 (m-30) cc_final: 0.7642 (m-30) REVERT: R 32 MET cc_start: 0.6610 (ptt) cc_final: 0.4794 (tpp) REVERT: R 221 TYR cc_start: 0.7614 (m-10) cc_final: 0.6689 (t80) outliers start: 9 outliers final: 2 residues processed: 122 average time/residue: 1.1827 time to fit residues: 154.8290 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 215 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 48 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 88 ASN N 39 GLN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140795 restraints weight = 9986.559| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.29 r_work: 0.3504 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9177 Z= 0.259 Angle : 0.534 7.241 12447 Z= 0.293 Chirality : 0.043 0.228 1386 Planarity : 0.004 0.045 1588 Dihedral : 4.703 23.954 1247 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.28 % Allowed : 14.07 % Favored : 84.65 % 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: 1.35 (0.25), residues: 1124 helix: 2.58 (0.24), residues: 444 sheet: -0.63 (0.30), residues: 241 loop : 0.13 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.023 0.002 PHE R 335 TYR 0.020 0.002 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.032 Fit side-chains REVERT: A 297 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6396 (tp) REVERT: B 66 ASP cc_start: 0.7289 (p0) cc_final: 0.6679 (m-30) REVERT: B 215 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: B 263 THR cc_start: 0.7921 (m) cc_final: 0.7584 (m) REVERT: B 303 ASP cc_start: 0.7913 (m-30) cc_final: 0.7662 (m-30) REVERT: R 32 MET cc_start: 0.6575 (ptt) cc_final: 0.4746 (tpp) REVERT: R 221 TYR cc_start: 0.7701 (m-10) cc_final: 0.6748 (t80) REVERT: R 414 MET cc_start: 0.8393 (mtp) cc_final: 0.8171 (mtt) outliers start: 12 outliers final: 3 residues processed: 112 average time/residue: 1.4870 time to fit residues: 178.8732 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148261 restraints weight = 10081.005| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.36 r_work: 0.3587 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9177 Z= 0.141 Angle : 0.471 6.296 12447 Z= 0.260 Chirality : 0.040 0.237 1386 Planarity : 0.003 0.039 1588 Dihedral : 4.274 22.720 1247 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.85 % Allowed : 14.93 % Favored : 84.22 % 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: 1.59 (0.25), residues: 1124 helix: 2.85 (0.24), residues: 438 sheet: -0.47 (0.31), residues: 231 loop : 0.17 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.021 0.001 TYR R 191 ARG 0.010 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.942 Fit side-chains REVERT: A 297 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6350 (tp) REVERT: B 303 ASP cc_start: 0.7978 (m-30) cc_final: 0.7706 (m-30) REVERT: R 32 MET cc_start: 0.6557 (ptt) cc_final: 0.4736 (tpp) REVERT: R 221 TYR cc_start: 0.7682 (m-10) cc_final: 0.6788 (t80) REVERT: R 414 MET cc_start: 0.8346 (mtp) cc_final: 0.8138 (mtt) outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 1.1448 time to fit residues: 141.5889 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.192987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146165 restraints weight = 9951.966| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.48 r_work: 0.3559 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9177 Z= 0.169 Angle : 0.483 6.230 12447 Z= 0.265 Chirality : 0.041 0.237 1386 Planarity : 0.003 0.040 1588 Dihedral : 4.310 22.435 1247 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.75 % Allowed : 15.03 % Favored : 84.22 % 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: 1.57 (0.25), residues: 1124 helix: 2.79 (0.24), residues: 444 sheet: -0.47 (0.30), residues: 236 loop : 0.18 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.006 Fit side-chains REVERT: A 297 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6347 (tp) REVERT: B 303 ASP cc_start: 0.7996 (m-30) cc_final: 0.7734 (m-30) REVERT: R 32 MET cc_start: 0.6552 (ptt) cc_final: 0.4720 (tpp) REVERT: R 221 TYR cc_start: 0.7655 (m-10) cc_final: 0.6739 (t80) REVERT: R 414 MET cc_start: 0.8338 (mtp) cc_final: 0.8117 (mtt) outliers start: 7 outliers final: 3 residues processed: 111 average time/residue: 1.2021 time to fit residues: 143.1972 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.189847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141440 restraints weight = 9905.069| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.30 r_work: 0.3511 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9177 Z= 0.262 Angle : 0.542 6.643 12447 Z= 0.296 Chirality : 0.043 0.240 1386 Planarity : 0.004 0.044 1588 Dihedral : 4.643 23.599 1247 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.85 % Allowed : 15.25 % Favored : 83.90 % 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: 1.42 (0.25), residues: 1124 helix: 2.66 (0.24), residues: 444 sheet: -0.61 (0.30), residues: 246 loop : 0.17 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.002 PHE R 335 TYR 0.020 0.002 TYR R 191 ARG 0.009 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.927 Fit side-chains REVERT: A 297 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6443 (tp) REVERT: B 66 ASP cc_start: 0.7237 (p0) cc_final: 0.6678 (m-30) REVERT: B 263 THR cc_start: 0.7957 (m) cc_final: 0.7691 (m) REVERT: B 303 ASP cc_start: 0.7986 (m-30) cc_final: 0.7717 (m-30) REVERT: R 32 MET cc_start: 0.6593 (ptt) cc_final: 0.4769 (tpp) REVERT: R 221 TYR cc_start: 0.7757 (m-10) cc_final: 0.6839 (t80) REVERT: R 414 MET cc_start: 0.8384 (mtp) cc_final: 0.8176 (mtt) outliers start: 8 outliers final: 3 residues processed: 110 average time/residue: 1.1151 time to fit residues: 132.1730 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN R 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.193369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146745 restraints weight = 9975.590| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.34 r_work: 0.3580 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9177 Z= 0.154 Angle : 0.482 6.279 12447 Z= 0.265 Chirality : 0.041 0.236 1386 Planarity : 0.003 0.040 1588 Dihedral : 4.341 22.604 1247 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.85 % Allowed : 15.46 % Favored : 83.69 % 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: 1.54 (0.25), residues: 1124 helix: 2.78 (0.24), residues: 444 sheet: -0.50 (0.31), residues: 236 loop : 0.15 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.009 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8288.41 seconds wall clock time: 144 minutes 25.55 seconds (8665.55 seconds total)