Starting phenix.real_space_refine on Mon May 12 05:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flq_29283/05_2025/8flq_29283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flq_29283/05_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_29283/05_2025/8flq_29283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flq_29283/05_2025/8flq_29283.map" model { file = "/net/cci-nas-00/data/ceres_data/8flq_29283/05_2025/8flq_29283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flq_29283/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.36, per 1000 atoms: 0.60 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: 2.15 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.47 Time building geometry restraints manager: 2.51 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: 1.620 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.780 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- 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 9183 Z= 0.198 Angle : 0.569 6.865 12459 Z= 0.353 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 Details of bonding type rmsd hydrogen bonds : bond 0.13542 ( 494) hydrogen bonds : angle 6.06927 ( 1407) SS BOND : bond 0.00095 ( 6) SS BOND : angle 0.92810 ( 12) covalent geometry : bond 0.00327 ( 9177) covalent geometry : angle 0.56880 (12447) *********************** 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 : 0.984 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: 1.2341 time to fit residues: 168.6001 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 : 0.941 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.194971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148507 restraints weight = 9846.009| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.32 r_work: 0.3588 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9183 Z= 0.121 Angle : 0.486 5.794 12459 Z= 0.271 Chirality : 0.041 0.175 1386 Planarity : 0.004 0.034 1588 Dihedral : 4.393 23.955 1250 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.70 (0.26), residues: 1124 helix: 2.91 (0.24), residues: 438 sheet: -0.33 (0.31), residues: 231 loop : 0.23 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.010 0.001 HIS A 357 PHE 0.022 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 494) hydrogen bonds : angle 4.68894 ( 1407) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.71900 ( 12) covalent geometry : bond 0.00245 ( 9177) covalent geometry : angle 0.48537 (12447) *********************** 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 : 0.935 Fit side-chains REVERT: B 66 ASP cc_start: 0.7106 (p0) cc_final: 0.6361 (m-30) REVERT: B 76 ASP cc_start: 0.8531 (p0) cc_final: 0.8325 (p0) REVERT: B 255 LEU cc_start: 0.8212 (mp) cc_final: 0.7957 (mt) REVERT: B 303 ASP cc_start: 0.7839 (m-30) cc_final: 0.7501 (m-30) REVERT: R 32 MET cc_start: 0.6558 (ptt) cc_final: 0.4434 (tpp) REVERT: R 221 TYR cc_start: 0.7552 (m-10) cc_final: 0.6554 (t80) outliers start: 7 outliers final: 5 residues processed: 120 average time/residue: 1.1478 time to fit residues: 147.7334 Evaluate side-chains 117 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 0.7980 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 84 ASN R 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147366 restraints weight = 10011.610| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.35 r_work: 0.3578 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9183 Z= 0.115 Angle : 0.474 6.177 12459 Z= 0.262 Chirality : 0.040 0.187 1386 Planarity : 0.003 0.036 1588 Dihedral : 4.318 22.773 1249 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.85 % Allowed : 10.02 % Favored : 89.13 % 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: 1.73 (0.26), residues: 1124 helix: 2.98 (0.24), residues: 437 sheet: -0.33 (0.31), residues: 234 loop : 0.21 (0.31), residues: 453 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 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 494) hydrogen bonds : angle 4.48181 ( 1407) SS BOND : bond 0.00093 ( 6) SS BOND : angle 1.17640 ( 12) covalent geometry : bond 0.00241 ( 9177) covalent geometry : angle 0.47245 (12447) *********************** 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 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.921 Fit side-chains REVERT: B 66 ASP cc_start: 0.7183 (p0) cc_final: 0.6435 (m-30) REVERT: B 76 ASP cc_start: 0.8602 (p0) cc_final: 0.8347 (p0) REVERT: B 303 ASP cc_start: 0.7835 (m-30) cc_final: 0.7493 (m-30) REVERT: R 32 MET cc_start: 0.6521 (ptt) cc_final: 0.4545 (tpp) REVERT: R 221 TYR cc_start: 0.7666 (m-10) cc_final: 0.6709 (t80) outliers start: 8 outliers final: 4 residues processed: 113 average time/residue: 1.1851 time to fit residues: 143.6165 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 : 0.903 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 107 optimal weight: 0.0000 chunk 78 optimal weight: 6.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.195046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148273 restraints weight = 9940.306| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.37 r_work: 0.3600 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9183 Z= 0.108 Angle : 0.457 6.245 12459 Z= 0.253 Chirality : 0.040 0.205 1386 Planarity : 0.003 0.037 1588 Dihedral : 4.252 26.383 1249 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.07 % Allowed : 10.55 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.26), residues: 1124 helix: 3.07 (0.24), residues: 438 sheet: -0.33 (0.31), residues: 235 loop : 0.27 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 494) hydrogen bonds : angle 4.35368 ( 1407) SS BOND : bond 0.00081 ( 6) SS BOND : angle 0.98779 ( 12) covalent geometry : bond 0.00226 ( 9177) covalent geometry : angle 0.45662 (12447) *********************** 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 121 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.054 Fit side-chains REVERT: B 66 ASP cc_start: 0.7179 (p0) cc_final: 0.6436 (m-30) REVERT: B 76 ASP cc_start: 0.8603 (p0) cc_final: 0.8346 (p0) REVERT: B 303 ASP cc_start: 0.7781 (m-30) cc_final: 0.7424 (m-30) REVERT: R 32 MET cc_start: 0.6518 (ptt) cc_final: 0.4655 (tpp) REVERT: R 221 TYR cc_start: 0.7678 (m-10) cc_final: 0.6734 (t80) outliers start: 10 outliers final: 4 residues processed: 116 average time/residue: 1.2112 time to fit residues: 150.6080 Evaluate side-chains 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 471 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN N 53 GLN N 82 GLN R 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.187315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138407 restraints weight = 9860.145| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.21 r_work: 0.3473 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9183 Z= 0.282 Angle : 0.615 6.506 12459 Z= 0.337 Chirality : 0.047 0.208 1386 Planarity : 0.004 0.044 1588 Dihedral : 4.957 25.421 1247 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.28 % Allowed : 11.51 % Favored : 87.21 % 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: 1.29 (0.25), residues: 1124 helix: 2.45 (0.24), residues: 444 sheet: -0.55 (0.31), residues: 238 loop : 0.11 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 234 HIS 0.015 0.002 HIS A 357 PHE 0.025 0.002 PHE R 335 TYR 0.019 0.002 TYR A 358 ARG 0.005 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 494) hydrogen bonds : angle 4.79095 ( 1407) SS BOND : bond 0.00085 ( 6) SS BOND : angle 1.30142 ( 12) covalent geometry : bond 0.00641 ( 9177) covalent geometry : angle 0.61434 (12447) *********************** 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: 12 poor density : 111 time to evaluate : 0.968 Fit side-chains REVERT: B 66 ASP cc_start: 0.7290 (p0) cc_final: 0.6707 (m-30) REVERT: B 76 ASP cc_start: 0.8715 (p0) cc_final: 0.8419 (p0) REVERT: B 135 VAL cc_start: 0.8361 (t) cc_final: 0.8122 (p) REVERT: B 263 THR cc_start: 0.8008 (m) cc_final: 0.7737 (m) REVERT: B 303 ASP cc_start: 0.7889 (m-30) cc_final: 0.7594 (m-30) REVERT: R 32 MET cc_start: 0.6669 (ptt) cc_final: 0.4694 (tpp) REVERT: R 221 TYR cc_start: 0.7707 (m-10) cc_final: 0.6743 (t80) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 1.1494 time to fit residues: 143.1163 Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 83 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 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 = 0.4208 r_free = 0.4208 target = 0.193274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146161 restraints weight = 9857.426| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.45 r_work: 0.3562 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9183 Z= 0.108 Angle : 0.481 7.711 12459 Z= 0.265 Chirality : 0.040 0.221 1386 Planarity : 0.004 0.038 1588 Dihedral : 4.436 23.561 1247 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.96 % Allowed : 12.90 % Favored : 86.14 % 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: 2.86 (0.24), residues: 437 sheet: -0.53 (0.30), residues: 236 loop : 0.19 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 494) hydrogen bonds : angle 4.45229 ( 1407) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.83465 ( 12) covalent geometry : bond 0.00220 ( 9177) covalent geometry : angle 0.48011 (12447) *********************** 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 120 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.992 Fit side-chains REVERT: B 76 ASP cc_start: 0.8595 (p0) cc_final: 0.8313 (p0) REVERT: B 303 ASP cc_start: 0.7852 (m-30) cc_final: 0.7540 (m-30) REVERT: R 32 MET cc_start: 0.6621 (ptt) cc_final: 0.4812 (tpt) REVERT: R 221 TYR cc_start: 0.7657 (m-10) cc_final: 0.6700 (t80) outliers start: 9 outliers final: 3 residues processed: 116 average time/residue: 1.1702 time to fit residues: 145.7932 Evaluate side-chains 107 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 191 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.191670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144020 restraints weight = 9989.190| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.45 r_work: 0.3543 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9183 Z= 0.142 Angle : 0.499 6.697 12459 Z= 0.273 Chirality : 0.041 0.231 1386 Planarity : 0.004 0.038 1588 Dihedral : 4.482 23.514 1247 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.75 % Allowed : 13.22 % Favored : 86.03 % 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: 1.53 (0.26), residues: 1124 helix: 2.77 (0.24), residues: 444 sheet: -0.59 (0.30), residues: 241 loop : 0.22 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 494) hydrogen bonds : angle 4.44808 ( 1407) SS BOND : bond 0.00083 ( 6) SS BOND : angle 0.88603 ( 12) covalent geometry : bond 0.00311 ( 9177) covalent geometry : angle 0.49816 (12447) *********************** 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 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.008 Fit side-chains REVERT: A 297 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6356 (tp) REVERT: B 76 ASP cc_start: 0.8662 (p0) cc_final: 0.8379 (p0) REVERT: B 303 ASP cc_start: 0.7934 (m-30) cc_final: 0.7652 (m-30) REVERT: R 32 MET cc_start: 0.6608 (ptt) cc_final: 0.4810 (tpt) REVERT: R 221 TYR cc_start: 0.7686 (m-10) cc_final: 0.6728 (t80) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 1.1301 time to fit residues: 134.3613 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 297 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.193142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146090 restraints weight = 10076.857| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.42 r_work: 0.3557 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9183 Z= 0.121 Angle : 0.479 6.322 12459 Z= 0.263 Chirality : 0.041 0.240 1386 Planarity : 0.003 0.038 1588 Dihedral : 4.363 23.091 1247 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.75 % Allowed : 13.86 % Favored : 85.39 % 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: 1.61 (0.26), residues: 1124 helix: 2.91 (0.24), residues: 438 sheet: -0.53 (0.30), residues: 239 loop : 0.19 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 494) hydrogen bonds : angle 4.38201 ( 1407) SS BOND : bond 0.00069 ( 6) SS BOND : angle 0.84596 ( 12) covalent geometry : bond 0.00259 ( 9177) covalent geometry : angle 0.47897 (12447) *********************** 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 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.927 Fit side-chains REVERT: A 297 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6345 (tp) REVERT: B 76 ASP cc_start: 0.8609 (p0) cc_final: 0.8321 (p0) REVERT: B 303 ASP cc_start: 0.7934 (m-30) cc_final: 0.7678 (m-30) REVERT: R 32 MET cc_start: 0.6590 (ptt) cc_final: 0.4812 (tpt) REVERT: R 221 TYR cc_start: 0.7694 (m-10) cc_final: 0.6781 (t80) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 1.0407 time to fit residues: 125.7754 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.0470 chunk 6 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.194475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148005 restraints weight = 9942.360| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.47 r_work: 0.3576 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9183 Z= 0.107 Angle : 0.462 6.247 12459 Z= 0.254 Chirality : 0.040 0.242 1386 Planarity : 0.003 0.036 1588 Dihedral : 4.206 22.513 1247 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.75 % Allowed : 14.07 % Favored : 85.18 % 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: 1.70 (0.26), residues: 1124 helix: 2.99 (0.24), residues: 438 sheet: -0.43 (0.31), residues: 237 loop : 0.19 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 494) hydrogen bonds : angle 4.30296 ( 1407) SS BOND : bond 0.00066 ( 6) SS BOND : angle 0.78081 ( 12) covalent geometry : bond 0.00223 ( 9177) covalent geometry : angle 0.46132 (12447) *********************** 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 : 0.929 Fit side-chains REVERT: A 297 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6288 (tp) REVERT: B 59 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8689 (t80) REVERT: B 76 ASP cc_start: 0.8618 (p0) cc_final: 0.8337 (p0) REVERT: B 303 ASP cc_start: 0.7934 (m-30) cc_final: 0.7658 (m-30) REVERT: N 39 GLN cc_start: 0.7726 (tt0) cc_final: 0.7470 (tp40) REVERT: R 32 MET cc_start: 0.6557 (ptt) cc_final: 0.4813 (tpt) REVERT: R 221 TYR cc_start: 0.7699 (m-10) cc_final: 0.6747 (t80) outliers start: 7 outliers final: 2 residues processed: 112 average time/residue: 1.0988 time to fit residues: 132.7415 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145524 restraints weight = 9935.284| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.38 r_work: 0.3553 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.003 0.030 9183 Z= 0.132 Angle : 0.487 6.293 12459 Z= 0.267 Chirality : 0.041 0.243 1386 Planarity : 0.003 0.044 1588 Dihedral : 4.336 22.584 1247 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.64 % Allowed : 14.61 % Favored : 84.75 % 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: 1.65 (0.26), residues: 1124 helix: 2.96 (0.24), residues: 438 sheet: -0.53 (0.31), residues: 239 loop : 0.21 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.022 0.002 TYR R 191 ARG 0.010 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 494) hydrogen bonds : angle 4.36600 ( 1407) SS BOND : bond 0.00056 ( 6) SS BOND : angle 0.85564 ( 12) covalent geometry : bond 0.00286 ( 9177) covalent geometry : angle 0.48671 (12447) ********************** 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 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.916 Fit side-chains REVERT: A 297 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6359 (tp) REVERT: B 76 ASP cc_start: 0.8645 (p0) cc_final: 0.8351 (p0) REVERT: B 303 ASP cc_start: 0.7939 (m-30) cc_final: 0.7672 (m-30) REVERT: N 39 GLN cc_start: 0.7739 (tt0) cc_final: 0.7471 (tp40) REVERT: R 32 MET cc_start: 0.6575 (ptt) cc_final: 0.4805 (tpt) REVERT: R 221 TYR cc_start: 0.7738 (m-10) cc_final: 0.6798 (t80) outliers start: 6 outliers final: 4 residues processed: 108 average time/residue: 1.0942 time to fit residues: 127.5310 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain N residue 69 THR 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: 0.9980 chunk 92 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.194299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147610 restraints weight = 10003.656| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.41 r_work: 0.3576 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9183 Z= 0.109 Angle : 0.469 6.445 12459 Z= 0.257 Chirality : 0.040 0.243 1386 Planarity : 0.003 0.037 1588 Dihedral : 4.208 22.260 1247 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.75 % Allowed : 14.61 % 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: 1.73 (0.26), residues: 1124 helix: 3.01 (0.24), residues: 438 sheet: -0.40 (0.31), residues: 232 loop : 0.20 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 494) hydrogen bonds : angle 4.29972 ( 1407) SS BOND : bond 0.00056 ( 6) SS BOND : angle 0.79824 ( 12) covalent geometry : bond 0.00231 ( 9177) covalent geometry : angle 0.46816 (12447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7635.28 seconds wall clock time: 131 minutes 56.59 seconds (7916.59 seconds total)