Starting phenix.real_space_refine on Wed Sep 17 10:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.map" model { file = "/net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jj9_61520/09_2025/9jj9_61520.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 21 5.16 5 C 4821 2.51 5 N 1414 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7716 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3625 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 26, 'TRANS': 460} Chain breaks: 6 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 469 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3598 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 26, 'TRANS': 458} Chain breaks: 5 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'9EF': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.87, per 1000 atoms: 0.24 Number of scatterers: 7716 At special positions: 0 Unit cell: (100.92, 100.34, 67.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 1 15.00 O 1459 8.00 N 1414 7.00 C 4821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 373.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1858 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 44.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 43 through 53 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.108A pdb=" N ARG B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 removed outlier: 3.651A pdb=" N THR B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.514A pdb=" N ILE B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 214 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.849A pdb=" N ALA B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.816A pdb=" N GLN B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 319 " --> pdb=" O VAL B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 4.024A pdb=" N ILE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 484 through 501 Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.691A pdb=" N GLU B 506 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'C' and resid 954 through 960 removed outlier: 4.024A pdb=" N HIS C 957 " --> pdb=" O LEU C 954 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 958 " --> pdb=" O THR C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 977 Processing helix chain 'C' and resid 979 through 989 Processing helix chain 'C' and resid 1008 through 1015 removed outlier: 3.709A pdb=" N PHE C1015 " --> pdb=" O GLU C1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 103 through 110 removed outlier: 3.652A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.517A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.826A pdb=" N ARG A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.093A pdb=" N ARG A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.209A pdb=" N THR A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.166A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 214 Processing helix chain 'A' and resid 229 through 240 removed outlier: 4.016A pdb=" N ALA A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.668A pdb=" N GLN A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 removed outlier: 4.071A pdb=" N ILE A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 484 through 501 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.798A pdb=" N GLU A 506 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 507' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 533 through 545 Processing sheet with id=AA1, first strand: chain 'B' and resid 412 through 414 removed outlier: 5.652A pdb=" N LEU B 359 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 329 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 328 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B 444 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 291 " --> pdb=" O ASN B 444 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N HIS B 446 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 289 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL B 448 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 32 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 268 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 34 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 266 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N CYS B 36 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY B 264 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 224 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N MET B 191 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 142 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N MET A 191 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 142 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 224 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY A 264 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N CYS A 36 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 266 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 34 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 268 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 32 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 448 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 289 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N HIS A 446 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A 291 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 444 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 432 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 328 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 327 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N GLY A 362 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 329 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 359 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.509A pdb=" N THR B 59 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.560A pdb=" N ALA B 419 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 478 through 482 Processing sheet with id=AA6, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 482 358 hydrogen bonds defined for protein. 1011 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: 1.43 Time building geometry restraints manager: 0.89 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: 2655 1.34 - 1.46: 976 1.46 - 1.57: 4195 1.57 - 1.69: 1 1.69 - 1.81: 31 Bond restraints: 7858 Sorted by residual: bond pdb=" OAR 9EF B1001 " pdb=" PAW 9EF B1001 " ideal model delta sigma weight residual 1.676 1.611 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CAU 9EF B1001 " pdb=" CAV 9EF B1001 " ideal model delta sigma weight residual 1.533 1.509 0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C LEU B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.344 -0.013 1.19e-02 7.06e+03 1.26e+00 bond pdb=" CAV 9EF B1001 " pdb=" CAX 9EF B1001 " ideal model delta sigma weight residual 1.553 1.531 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C LEU A 913 " pdb=" N PRO A 914 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.01e-01 ... (remaining 7853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 10559 1.62 - 3.25: 103 3.25 - 4.87: 13 4.87 - 6.49: 3 6.49 - 8.12: 5 Bond angle restraints: 10683 Sorted by residual: angle pdb=" C THR C 962 " pdb=" CA THR C 962 " pdb=" CB THR C 962 " ideal model delta sigma weight residual 116.54 110.09 6.45 1.15e+00 7.56e-01 3.15e+01 angle pdb=" C LEU A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" CA THR C 962 " pdb=" C THR C 962 " pdb=" N ALA C 963 " ideal model delta sigma weight residual 119.52 116.84 2.68 7.90e-01 1.60e+00 1.15e+01 angle pdb=" CAJ 9EF B1001 " pdb=" CAK 9EF B1001 " pdb=" NAP 9EF B1001 " ideal model delta sigma weight residual 112.75 104.63 8.12 3.00e+00 1.11e-01 7.32e+00 angle pdb=" C PRO B 323 " pdb=" N THR B 324 " pdb=" CA THR B 324 " ideal model delta sigma weight residual 122.08 125.97 -3.89 1.47e+00 4.63e-01 7.01e+00 ... (remaining 10678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 4288 23.41 - 46.82: 326 46.82 - 70.23: 46 70.23 - 93.64: 9 93.64 - 117.05: 1 Dihedral angle restraints: 4670 sinusoidal: 1778 harmonic: 2892 Sorted by residual: dihedral pdb=" NAO 9EF B1001 " pdb=" CAJ 9EF B1001 " pdb=" CAK 9EF B1001 " pdb=" NAP 9EF B1001 " ideal model delta sinusoidal sigma weight residual 59.47 176.52 -117.05 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA THR B 324 " pdb=" C THR B 324 " pdb=" N GLU B 325 " pdb=" CA GLU B 325 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CG ARG B 212 " pdb=" CD ARG B 212 " pdb=" NE ARG B 212 " pdb=" CZ ARG B 212 " ideal model delta sinusoidal sigma weight residual 180.00 136.19 43.81 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 839 0.030 - 0.060: 251 0.060 - 0.090: 68 0.090 - 0.119: 63 0.119 - 0.149: 8 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CA THR B 324 " pdb=" N THR B 324 " pdb=" C THR B 324 " pdb=" CB THR B 324 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ILE B 218 " pdb=" N ILE B 218 " pdb=" C ILE B 218 " pdb=" CB ILE B 218 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1226 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 322 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO B 323 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 323 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 323 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 371 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C LEU A 371 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU A 371 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 372 " 0.008 2.00e-02 2.50e+03 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1980 2.81 - 3.33: 6916 3.33 - 3.85: 12756 3.85 - 4.38: 14928 4.38 - 4.90: 26315 Nonbonded interactions: 62895 Sorted by model distance: nonbonded pdb=" O LEU B 135 " pdb=" OG1 THR B 138 " model vdw 2.282 3.040 nonbonded pdb=" NH2 ARG A 494 " pdb=" O PRO A 914 " model vdw 2.301 3.120 nonbonded pdb=" OAI 9EF B1001 " pdb=" OAR 9EF B1001 " model vdw 2.302 3.040 nonbonded pdb=" O VAL A 31 " pdb=" N HIS A 283 " model vdw 2.303 3.120 nonbonded pdb=" O LEU A 135 " pdb=" OG1 THR A 138 " model vdw 2.309 3.040 ... (remaining 62890 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 62 or resid 85 through 157 or resid 165 through \ 545 or resid 908 through 926)) selection = (chain 'B' and (resid 27 through 545 or resid 908 through 926)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.250 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.590 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.002 0.065 7860 Z= 0.095 Angle : 0.449 8.119 10683 Z= 0.233 Chirality : 0.039 0.149 1229 Planarity : 0.004 0.073 1400 Dihedral : 16.014 117.049 2812 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.76 % Allowed : 22.31 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.27), residues: 1003 helix: 2.48 (0.27), residues: 395 sheet: 1.72 (0.44), residues: 132 loop : -0.68 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 388 TYR 0.004 0.000 TYR B 916 PHE 0.004 0.000 PHE C 973 TRP 0.005 0.000 TRP B 48 HIS 0.001 0.000 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 7858) covalent geometry : angle 0.44877 (10683) hydrogen bonds : bond 0.14066 ( 358) hydrogen bonds : angle 5.77546 ( 1011) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.314 Fit side-chains REVERT: B 155 TYR cc_start: 0.6818 (t80) cc_final: 0.6384 (t80) REVERT: B 157 ARG cc_start: 0.5452 (mmt180) cc_final: 0.4956 (mmp-170) REVERT: B 247 GLN cc_start: 0.7785 (tp40) cc_final: 0.7495 (mm-40) REVERT: B 440 MET cc_start: 0.5939 (ptm) cc_final: 0.4674 (tpt) REVERT: B 524 GLU cc_start: 0.7162 (mp0) cc_final: 0.6787 (mp0) REVERT: A 158 ARG cc_start: 0.5260 (ptt90) cc_final: 0.4920 (ttp-170) REVERT: A 262 GLU cc_start: 0.7785 (pt0) cc_final: 0.7386 (pm20) REVERT: A 306 ARG cc_start: 0.7685 (mtm180) cc_final: 0.6995 (mtp-110) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.5970 time to fit residues: 50.6697 Evaluate side-chains 76 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.179603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144629 restraints weight = 7804.983| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.73 r_work: 0.3625 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7860 Z= 0.109 Angle : 0.485 6.640 10683 Z= 0.249 Chirality : 0.042 0.137 1229 Planarity : 0.005 0.070 1400 Dihedral : 6.863 128.995 1151 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.31 % Allowed : 18.38 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1003 helix: 2.23 (0.27), residues: 406 sheet: 0.74 (0.44), residues: 133 loop : -0.81 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 388 TYR 0.014 0.001 TYR A 155 PHE 0.008 0.001 PHE A 95 TRP 0.010 0.001 TRP A 122 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7858) covalent geometry : angle 0.48488 (10683) hydrogen bonds : bond 0.03689 ( 358) hydrogen bonds : angle 4.39769 ( 1011) Misc. bond : bond 0.00094 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.225 Fit side-chains REVERT: B 148 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6938 (mtt-85) REVERT: B 157 ARG cc_start: 0.5776 (mmt180) cc_final: 0.5086 (mmp-170) REVERT: B 169 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6595 (t) REVERT: B 191 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6757 (ptm) REVERT: B 247 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7570 (mm-40) REVERT: B 273 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6314 (ptp90) REVERT: B 440 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.4833 (tpt) REVERT: A 158 ARG cc_start: 0.5298 (ptt90) cc_final: 0.4959 (ttp-170) outliers start: 34 outliers final: 12 residues processed: 95 average time/residue: 0.5783 time to fit residues: 58.3214 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.0270 chunk 39 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 overall best weight: 1.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136693 restraints weight = 7870.672| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.72 r_work: 0.3536 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7860 Z= 0.172 Angle : 0.607 7.544 10683 Z= 0.308 Chirality : 0.045 0.140 1229 Planarity : 0.006 0.069 1400 Dihedral : 7.624 164.227 1145 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.69 % Allowed : 18.76 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1003 helix: 1.58 (0.26), residues: 412 sheet: 0.81 (0.42), residues: 124 loop : -1.11 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 388 TYR 0.017 0.002 TYR B 316 PHE 0.014 0.002 PHE A 95 TRP 0.015 0.001 TRP A 122 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7858) covalent geometry : angle 0.60661 (10683) hydrogen bonds : bond 0.04791 ( 358) hydrogen bonds : angle 4.64434 ( 1011) Misc. bond : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.314 Fit side-chains REVERT: B 148 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7118 (mtt-85) REVERT: B 247 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: B 385 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7642 (mp) REVERT: B 402 ASN cc_start: 0.7129 (t0) cc_final: 0.6909 (t0) REVERT: B 440 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.4991 (tpt) REVERT: A 158 ARG cc_start: 0.5653 (ptt90) cc_final: 0.5064 (ttp-170) outliers start: 37 outliers final: 16 residues processed: 94 average time/residue: 0.5397 time to fit residues: 54.2415 Evaluate side-chains 82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137111 restraints weight = 7604.672| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.81 r_work: 0.3510 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7860 Z= 0.122 Angle : 0.515 6.291 10683 Z= 0.263 Chirality : 0.043 0.144 1229 Planarity : 0.005 0.068 1400 Dihedral : 7.297 158.819 1145 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.18 % Allowed : 18.25 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1003 helix: 1.70 (0.26), residues: 412 sheet: 0.26 (0.42), residues: 134 loop : -1.09 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 388 TYR 0.012 0.001 TYR B 316 PHE 0.009 0.001 PHE A 95 TRP 0.012 0.001 TRP A 122 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7858) covalent geometry : angle 0.51469 (10683) hydrogen bonds : bond 0.03780 ( 358) hydrogen bonds : angle 4.44970 ( 1011) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.309 Fit side-chains REVERT: B 148 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7026 (mtt-85) REVERT: B 157 ARG cc_start: 0.5756 (mmt180) cc_final: 0.5155 (mmp-170) REVERT: B 402 ASN cc_start: 0.7174 (t0) cc_final: 0.6958 (t0) REVERT: B 440 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.4886 (tpp) REVERT: A 158 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.5014 (ttp-170) outliers start: 33 outliers final: 17 residues processed: 94 average time/residue: 0.5901 time to fit residues: 58.9213 Evaluate side-chains 85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135535 restraints weight = 7565.832| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.79 r_work: 0.3492 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7860 Z= 0.142 Angle : 0.550 6.822 10683 Z= 0.280 Chirality : 0.044 0.160 1229 Planarity : 0.005 0.072 1400 Dihedral : 7.526 162.625 1145 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.69 % Allowed : 18.50 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.26), residues: 1003 helix: 1.48 (0.26), residues: 418 sheet: 0.13 (0.42), residues: 134 loop : -1.18 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.017 0.002 TYR A 155 PHE 0.010 0.001 PHE A 95 TRP 0.013 0.001 TRP A 122 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7858) covalent geometry : angle 0.55031 (10683) hydrogen bonds : bond 0.04142 ( 358) hydrogen bonds : angle 4.49720 ( 1011) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.296 Fit side-chains REVERT: B 140 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7426 (tp) REVERT: B 148 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7138 (mtt-85) REVERT: B 157 ARG cc_start: 0.5780 (mmt180) cc_final: 0.5242 (mmp-170) REVERT: B 402 ASN cc_start: 0.7259 (t0) cc_final: 0.7048 (t0) REVERT: B 440 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.4941 (tpt) REVERT: A 158 ARG cc_start: 0.5666 (ptt90) cc_final: 0.5108 (ttp80) outliers start: 37 outliers final: 21 residues processed: 96 average time/residue: 0.5374 time to fit residues: 55.1187 Evaluate side-chains 88 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133221 restraints weight = 7514.606| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.75 r_work: 0.3462 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7860 Z= 0.201 Angle : 0.640 7.475 10683 Z= 0.324 Chirality : 0.047 0.150 1229 Planarity : 0.006 0.073 1400 Dihedral : 7.945 166.040 1145 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.58 % Allowed : 17.74 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.25), residues: 1003 helix: 1.17 (0.26), residues: 417 sheet: 0.11 (0.41), residues: 129 loop : -1.28 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 318 TYR 0.017 0.002 TYR B 316 PHE 0.013 0.002 PHE A 95 TRP 0.016 0.002 TRP A 122 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7858) covalent geometry : angle 0.64037 (10683) hydrogen bonds : bond 0.04909 ( 358) hydrogen bonds : angle 4.69030 ( 1011) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 0.296 Fit side-chains REVERT: B 140 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7523 (tp) REVERT: B 148 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7268 (mtt-85) REVERT: B 247 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7633 (mm-40) REVERT: B 402 ASN cc_start: 0.7433 (t0) cc_final: 0.7194 (t0) REVERT: B 440 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5146 (tpt) REVERT: B 520 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.5862 (mmt90) REVERT: C 975 ASP cc_start: 0.5101 (OUTLIER) cc_final: 0.4742 (m-30) REVERT: A 157 ARG cc_start: 0.5773 (OUTLIER) cc_final: 0.4821 (mmt180) REVERT: A 158 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5189 (ttp-170) REVERT: A 925 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7770 (pp) outliers start: 44 outliers final: 25 residues processed: 98 average time/residue: 0.5802 time to fit residues: 60.4246 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 520 ARG Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 925 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 34 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137444 restraints weight = 7525.837| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.75 r_work: 0.3513 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7860 Z= 0.110 Angle : 0.505 6.443 10683 Z= 0.259 Chirality : 0.042 0.146 1229 Planarity : 0.005 0.074 1400 Dihedral : 7.439 160.148 1145 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.31 % Allowed : 19.01 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 1003 helix: 1.53 (0.27), residues: 412 sheet: 0.11 (0.42), residues: 129 loop : -1.27 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 136 TYR 0.018 0.001 TYR A 155 PHE 0.007 0.001 PHE A 95 TRP 0.012 0.001 TRP B 48 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7858) covalent geometry : angle 0.50518 (10683) hydrogen bonds : bond 0.03605 ( 358) hydrogen bonds : angle 4.46032 ( 1011) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.308 Fit side-chains REVERT: B 140 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7431 (tt) REVERT: B 148 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7072 (mtt-85) REVERT: B 157 ARG cc_start: 0.5804 (mmt180) cc_final: 0.5259 (mmp-170) REVERT: B 314 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6605 (ptp-110) REVERT: B 411 ASN cc_start: 0.7366 (t0) cc_final: 0.7068 (t0) REVERT: B 440 MET cc_start: 0.6044 (ptm) cc_final: 0.4870 (tpp) REVERT: A 158 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5023 (ttp-170) outliers start: 34 outliers final: 21 residues processed: 96 average time/residue: 0.5493 time to fit residues: 56.2941 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135916 restraints weight = 7551.715| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.76 r_work: 0.3496 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7860 Z= 0.131 Angle : 0.534 6.664 10683 Z= 0.272 Chirality : 0.043 0.146 1229 Planarity : 0.005 0.073 1400 Dihedral : 7.511 163.208 1145 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.07 % Allowed : 18.38 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1003 helix: 1.55 (0.27), residues: 405 sheet: 0.09 (0.41), residues: 128 loop : -1.27 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 318 TYR 0.012 0.002 TYR B 316 PHE 0.009 0.001 PHE A 95 TRP 0.012 0.001 TRP A 122 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7858) covalent geometry : angle 0.53375 (10683) hydrogen bonds : bond 0.03933 ( 358) hydrogen bonds : angle 4.46027 ( 1011) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 0.346 Fit side-chains REVERT: B 140 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7468 (tp) REVERT: B 148 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7129 (mtt-85) REVERT: B 157 ARG cc_start: 0.5799 (mmt180) cc_final: 0.5272 (mmp-170) REVERT: B 314 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6627 (ptp-110) REVERT: B 440 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.4913 (tpt) REVERT: A 158 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5032 (ttp-170) outliers start: 40 outliers final: 24 residues processed: 93 average time/residue: 0.5699 time to fit residues: 56.5362 Evaluate side-chains 90 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 921 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.0060 chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137824 restraints weight = 7500.084| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.78 r_work: 0.3520 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7860 Z= 0.106 Angle : 0.496 6.162 10683 Z= 0.254 Chirality : 0.042 0.144 1229 Planarity : 0.005 0.074 1400 Dihedral : 7.294 161.645 1145 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.55 % Allowed : 20.15 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1003 helix: 1.76 (0.27), residues: 400 sheet: 0.16 (0.42), residues: 128 loop : -1.19 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 274 TYR 0.018 0.001 TYR A 155 PHE 0.007 0.001 PHE A 95 TRP 0.012 0.001 TRP B 48 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7858) covalent geometry : angle 0.49588 (10683) hydrogen bonds : bond 0.03464 ( 358) hydrogen bonds : angle 4.35944 ( 1011) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.304 Fit side-chains REVERT: B 148 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7059 (mtt-85) REVERT: B 157 ARG cc_start: 0.5719 (mmt180) cc_final: 0.5212 (mmp-170) REVERT: B 247 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: B 314 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6603 (ptp-110) REVERT: B 440 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.4826 (tpp) REVERT: A 158 ARG cc_start: 0.5703 (ptt90) cc_final: 0.5061 (ttp-170) outliers start: 28 outliers final: 20 residues processed: 85 average time/residue: 0.5861 time to fit residues: 52.9592 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.172115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136637 restraints weight = 7510.048| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.76 r_work: 0.3502 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7860 Z= 0.128 Angle : 0.529 6.507 10683 Z= 0.270 Chirality : 0.043 0.147 1229 Planarity : 0.005 0.074 1400 Dihedral : 7.404 163.183 1145 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.55 % Allowed : 20.28 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.26), residues: 1003 helix: 1.78 (0.27), residues: 394 sheet: 0.10 (0.41), residues: 128 loop : -1.17 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 274 TYR 0.012 0.001 TYR B 316 PHE 0.008 0.001 PHE A 95 TRP 0.012 0.001 TRP A 122 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7858) covalent geometry : angle 0.52906 (10683) hydrogen bonds : bond 0.03841 ( 358) hydrogen bonds : angle 4.41538 ( 1011) Misc. bond : bond 0.00047 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.307 Fit side-chains REVERT: B 148 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7123 (mtt-85) REVERT: B 157 ARG cc_start: 0.5792 (mmt180) cc_final: 0.5271 (mmp-170) REVERT: B 314 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6627 (ptp-110) REVERT: B 440 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.4894 (tpt) REVERT: A 158 ARG cc_start: 0.5768 (ptt90) cc_final: 0.5100 (ttp-170) REVERT: A 925 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7722 (pp) outliers start: 28 outliers final: 22 residues processed: 84 average time/residue: 0.5789 time to fit residues: 51.8326 Evaluate side-chains 87 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 925 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.172816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137457 restraints weight = 7501.917| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.75 r_work: 0.3513 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7860 Z= 0.116 Angle : 0.511 6.283 10683 Z= 0.261 Chirality : 0.042 0.147 1229 Planarity : 0.005 0.074 1400 Dihedral : 7.325 162.544 1145 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.68 % Allowed : 20.28 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1003 helix: 1.73 (0.27), residues: 401 sheet: 0.09 (0.42), residues: 129 loop : -1.21 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 274 TYR 0.019 0.002 TYR A 155 PHE 0.008 0.001 PHE A 95 TRP 0.012 0.001 TRP A 122 HIS 0.003 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7858) covalent geometry : angle 0.51136 (10683) hydrogen bonds : bond 0.03639 ( 358) hydrogen bonds : angle 4.38465 ( 1011) Misc. bond : bond 0.00040 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.49 seconds wall clock time: 51 minutes 18.98 seconds (3078.98 seconds total)