Starting phenix.real_space_refine on Wed Aug 5 12:24:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c6q_45254/08_2026/9c6q_45254.map" } resolution = 3.18 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= 0.006 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 12 5.49 5 S 24 5.16 5 C 6189 2.51 5 N 1721 2.21 5 O 1895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9841 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 241 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 9600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9600 Classifications: {'peptide': 1190} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1155} Time building chain proxies: 1.70, per 1000 atoms: 0.17 Number of scatterers: 9841 At special positions: 0 Unit cell: (90.3495, 106.531, 133.951, 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 24 16.00 P 12 15.00 O 1895 8.00 N 1721 7.00 C 6189 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=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 280.1 milliseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 49.7% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.564A pdb=" N PHE C 8 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 9 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 37 removed outlier: 3.558A pdb=" N THR C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 55 through 78 removed outlier: 3.565A pdb=" N ALA C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 111 Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.777A pdb=" N LEU C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 Processing helix chain 'C' and resid 162 through 178 removed outlier: 3.827A pdb=" N GLN C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 208 removed outlier: 3.518A pdb=" N ASN C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 200 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 3.691A pdb=" N ALA C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 4.085A pdb=" N LYS C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 234' Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.798A pdb=" N VAL C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.508A pdb=" N PHE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 321 Processing helix chain 'C' and resid 322 through 337 removed outlier: 3.799A pdb=" N ASN C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 433 removed outlier: 3.508A pdb=" N PHE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.840A pdb=" N GLU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.863A pdb=" N GLY C 536 " --> pdb=" O MET C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 564 removed outlier: 3.640A pdb=" N GLU C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 605 through 616 Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 637 through 657 removed outlier: 3.523A pdb=" N SER C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 674 No H-bonds generated for 'chain 'C' and resid 672 through 674' Processing helix chain 'C' and resid 675 through 693 Processing helix chain 'C' and resid 704 through 711 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.698A pdb=" N SER C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 723 " --> pdb=" O HIS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 738 removed outlier: 3.532A pdb=" N ALA C 738 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 808 removed outlier: 4.359A pdb=" N ASN C 793 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 794 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.554A pdb=" N MET C 824 " --> pdb=" O ARG C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 836 Processing helix chain 'C' and resid 839 through 855 removed outlier: 3.807A pdb=" N SER C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 879 Processing helix chain 'C' and resid 891 through 901 removed outlier: 3.619A pdb=" N SER C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.409A pdb=" N ARG C 913 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 938 " --> pdb=" O VAL C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 960 removed outlier: 3.531A pdb=" N ILE C 947 " --> pdb=" O SER C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1002 No H-bonds generated for 'chain 'C' and resid 1000 through 1002' Processing helix chain 'C' and resid 1009 through 1014 removed outlier: 3.972A pdb=" N CYS C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C1014 " --> pdb=" O GLU C1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1009 through 1014' Processing helix chain 'C' and resid 1014 through 1020 removed outlier: 3.900A pdb=" N LEU C1018 " --> pdb=" O SER C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1032 Processing helix chain 'C' and resid 1045 through 1052 removed outlier: 3.799A pdb=" N THR C1050 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C1051 " --> pdb=" O ILE C1047 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C1052 " --> pdb=" O MET C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 3.584A pdb=" N ALA C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1112 through 1127 removed outlier: 4.536A pdb=" N SER C1116 " --> pdb=" O SER C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1176 through 1187 removed outlier: 3.649A pdb=" N VAL C1180 " --> pdb=" O ASN C1176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.723A pdb=" N ALA C 43 " --> pdb=" O ALA C 537 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 539 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 267 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU C 540 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 269 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE C 542 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 271 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU C 87 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE C 270 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.833A pdb=" N THR C 92 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 3.720A pdb=" N LEU C 521 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 354 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 342 through 344 removed outlier: 3.844A pdb=" N LYS C 382 " --> pdb=" O ASP C 377 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 377 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 384 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 595 through 601 removed outlier: 6.811A pdb=" N VAL C 595 " --> pdb=" O ILE C 866 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU C 868 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 597 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL C 870 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS C 599 " --> pdb=" O VAL C 870 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 773 " --> pdb=" O TYR C 662 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 731 " --> pdb=" O SER C 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 744 through 745 removed outlier: 3.628A pdb=" N TYR C 744 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 974 through 975 Processing sheet with id=AA9, first strand: chain 'C' and resid 997 through 998 Processing sheet with id=AB1, first strand: chain 'C' and resid 1072 through 1074 removed outlier: 3.797A pdb=" N THR C1072 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C1089 " --> pdb=" O THR C1072 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C1086 " --> pdb=" O LEU C1099 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C1099 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N PHE C1131 " --> pdb=" O ILE C1162 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE C1164 " --> pdb=" O PHE C1131 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR C1133 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C1163 " --> pdb=" O ARG C1145 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C1145 " --> pdb=" O GLU C1163 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1182 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: 1.75 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2047 1.33 - 1.45: 2395 1.45 - 1.57: 5558 1.57 - 1.69: 23 1.69 - 1.81: 39 Bond restraints: 10062 Sorted by residual: bond pdb=" C GLU C 465 " pdb=" N SER C 466 " ideal model delta sigma weight residual 1.335 1.697 -0.362 1.38e-02 5.25e+03 6.88e+02 bond pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 1.334 1.525 -0.191 1.41e-02 5.03e+03 1.84e+02 bond pdb=" C3' DT A 15 " pdb=" C2' DT A 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" N GLU C 463 " pdb=" CA GLU C 463 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.23e+00 bond pdb=" N PHE C 459 " pdb=" CA PHE C 459 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.26e-02 6.30e+03 6.10e+00 ... (remaining 10057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 13621 4.41 - 8.82: 24 8.82 - 13.22: 1 13.22 - 17.63: 2 17.63 - 22.04: 1 Bond angle restraints: 13649 Sorted by residual: angle pdb=" CA LEU C 456 " pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 118.14 96.10 22.04 1.31e+00 5.83e-01 2.83e+02 angle pdb=" O LEU C 456 " pdb=" C LEU C 456 " pdb=" N THR C 457 " ideal model delta sigma weight residual 122.43 138.64 -16.21 1.34e+00 5.57e-01 1.46e+02 angle pdb=" C LEU C 456 " pdb=" N THR C 457 " pdb=" CA THR C 457 " ideal model delta sigma weight residual 120.71 103.17 17.54 1.67e+00 3.59e-01 1.10e+02 angle pdb=" C PHE C 999 " pdb=" CA PHE C 999 " pdb=" CB PHE C 999 " ideal model delta sigma weight residual 116.63 110.70 5.93 1.16e+00 7.43e-01 2.61e+01 angle pdb=" C LYS C 590 " pdb=" N ASP C 591 " pdb=" CA ASP C 591 " ideal model delta sigma weight residual 122.09 129.84 -7.75 1.86e+00 2.89e-01 1.73e+01 ... (remaining 13644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 5277 16.85 - 33.71: 577 33.71 - 50.56: 139 50.56 - 67.42: 38 67.42 - 84.27: 16 Dihedral angle restraints: 6047 sinusoidal: 2551 harmonic: 3496 Sorted by residual: dihedral pdb=" CA ILE C 294 " pdb=" C ILE C 294 " pdb=" N TRP C 295 " pdb=" CA TRP C 295 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA THR C 780 " pdb=" C THR C 780 " pdb=" N GLN C 781 " pdb=" CA GLN C 781 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE C 459 " pdb=" C PHE C 459 " pdb=" N ASN C 460 " pdb=" CA ASN C 460 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1150 0.044 - 0.089: 269 0.089 - 0.133: 76 0.133 - 0.178: 6 0.178 - 0.222: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA VAL C 354 " pdb=" N VAL C 354 " pdb=" C VAL C 354 " pdb=" CB VAL C 354 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR C 80 " pdb=" CA THR C 80 " pdb=" OG1 THR C 80 " pdb=" CG2 THR C 80 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA LEU C 356 " pdb=" N LEU C 356 " pdb=" C LEU C 356 " pdb=" CB LEU C 356 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 1499 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 456 " 0.029 2.00e-02 2.50e+03 7.35e-02 5.41e+01 pdb=" C LEU C 456 " -0.126 2.00e-02 2.50e+03 pdb=" O LEU C 456 " 0.057 2.00e-02 2.50e+03 pdb=" N THR C 457 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 473 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.82e+00 pdb=" CG ASP C 473 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 473 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 473 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 181 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 182 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " 0.025 5.00e-02 4.00e+02 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 175 2.69 - 3.24: 9101 3.24 - 3.80: 13587 3.80 - 4.35: 17694 4.35 - 4.90: 30147 Nonbonded interactions: 70704 Sorted by model distance: nonbonded pdb=" OE2 GLU C 465 " pdb=" OH TYR C 469 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR C 733 " pdb=" O GLU C 777 " model vdw 2.145 3.040 nonbonded pdb=" O CYS C1013 " pdb=" OH TYR C1103 " model vdw 2.168 3.040 nonbonded pdb=" N LEU C 456 " pdb=" N THR C 457 " model vdw 2.265 2.560 nonbonded pdb=" O TYR C 662 " pdb=" OG SER C 773 " model vdw 2.269 3.040 ... (remaining 70699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.900 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: 0.510 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 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 : 0.005 0.362 10062 Z= 0.345 Angle : 0.647 22.041 13649 Z= 0.394 Chirality : 0.041 0.222 1502 Planarity : 0.004 0.074 1736 Dihedral : 15.428 84.274 3783 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.07 (0.25), residues: 1188 helix: 1.92 (0.24), residues: 524 sheet: -0.03 (0.49), residues: 120 loop : -2.18 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1145 TYR 0.027 0.001 TYR C 469 PHE 0.019 0.001 PHE C 8 TRP 0.021 0.002 TRP C 428 HIS 0.005 0.001 HIS C 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.34 (10062) covalent geometry : angle 0.64690 / 0.39 (13649) hydrogen bonds : bond 0.18526 / 18.34 ( 410) hydrogen bonds : angle 5.83313 / 4.56 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: C 119 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6978 (ttt-90) REVERT: C 422 LYS cc_start: 0.5476 (mtmm) cc_final: 0.4753 (mmtt) REVERT: C 517 LYS cc_start: 0.7411 (mmmt) cc_final: 0.6813 (mmtm) REVERT: C 599 LYS cc_start: 0.7391 (ttmm) cc_final: 0.7076 (tptt) REVERT: C 948 GLN cc_start: 0.7513 (tp40) cc_final: 0.7221 (mm-40) REVERT: C 952 ASP cc_start: 0.7998 (m-30) cc_final: 0.7730 (m-30) REVERT: C 1022 GLN cc_start: 0.5712 (pt0) cc_final: 0.5332 (pm20) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.0908 time to fit residues: 21.9523 Evaluate side-chains 93 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 463 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 ASN C 70 GLN C 335 ASN C 364 HIS C 462 GLN C 575 GLN C 668 ASN C 951 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.215677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174534 restraints weight = 11035.595| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.93 r_work: 0.3530 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10062 Z= 0.139 Angle : 0.581 7.721 13649 Z= 0.307 Chirality : 0.040 0.151 1502 Planarity : 0.004 0.039 1736 Dihedral : 9.435 77.411 1437 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.80 % Allowed : 5.79 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: 0.01 (0.25), residues: 1188 helix: 1.97 (0.23), residues: 530 sheet: 0.38 (0.49), residues: 115 loop : -2.24 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1145 TYR 0.016 0.001 TYR C 744 PHE 0.020 0.002 PHE C 8 TRP 0.018 0.001 TRP C 643 HIS 0.015 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (10062) covalent geometry : angle 0.58116 / 0.31 (13649) hydrogen bonds : bond 0.04703 / 4.52 ( 410) hydrogen bonds : angle 4.29952 / 3.46 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.299 Fit side-chains REVERT: C 51 THR cc_start: 0.7110 (p) cc_final: 0.6775 (p) REVERT: C 517 LYS cc_start: 0.7456 (mmmt) cc_final: 0.6529 (tmtt) REVERT: C 599 LYS cc_start: 0.7641 (ttmm) cc_final: 0.7293 (tptt) REVERT: C 683 GLN cc_start: 0.6696 (mt0) cc_final: 0.6170 (tp-100) REVERT: C 882 SER cc_start: 0.7413 (p) cc_final: 0.6919 (t) REVERT: C 948 GLN cc_start: 0.7767 (tp40) cc_final: 0.7380 (mm-40) REVERT: C 952 ASP cc_start: 0.8246 (m-30) cc_final: 0.7993 (m-30) REVERT: C 1022 GLN cc_start: 0.5772 (pt0) cc_final: 0.5395 (pm20) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 0.0848 time to fit residues: 12.9202 Evaluate side-chains 98 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 747 ASN Chi-restraints excluded: chain C residue 774 ILE Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 89 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.7664 > 50:) chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 370 HIS C 951 GLN C1042 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.209779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167235 restraints weight = 10900.906| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.16 r_work: 0.3408 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10062 Z= 0.183 Angle : 0.646 9.342 13649 Z= 0.340 Chirality : 0.043 0.199 1502 Planarity : 0.004 0.043 1736 Dihedral : 9.588 75.457 1434 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.90 % Allowed : 8.26 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.35 (0.24), residues: 1188 helix: 1.59 (0.23), residues: 531 sheet: 0.26 (0.48), residues: 114 loop : -2.35 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C1001 TYR 0.017 0.002 TYR C 892 PHE 0.047 0.002 PHE C 916 TRP 0.022 0.002 TRP C 643 HIS 0.008 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (10062) covalent geometry : angle 0.64645 / 0.34 (13649) hydrogen bonds : bond 0.06614 / 6.29 ( 410) hydrogen bonds : angle 4.21968 / 3.50 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: C 51 THR cc_start: 0.7391 (p) cc_final: 0.7080 (p) REVERT: C 517 LYS cc_start: 0.7484 (mmmt) cc_final: 0.6540 (tmtt) REVERT: C 521 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7768 (mp) REVERT: C 599 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7824 (tttp) REVERT: C 683 GLN cc_start: 0.6861 (mt0) cc_final: 0.6329 (tp-100) REVERT: C 931 LYS cc_start: 0.7690 (tppt) cc_final: 0.7077 (ttpt) REVERT: C 952 ASP cc_start: 0.8428 (m-30) cc_final: 0.8157 (m-30) REVERT: C 954 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7085 (mtt180) REVERT: C 1022 GLN cc_start: 0.6437 (pt0) cc_final: 0.5735 (pm20) outliers start: 20 outliers final: 12 residues processed: 107 average time/residue: 0.0856 time to fit residues: 12.7655 Evaluate side-chains 93 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 774 ILE Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1180 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.211371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.170581 restraints weight = 11067.946| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.87 r_work: 0.3487 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10062 Z= 0.110 Angle : 0.510 9.818 13649 Z= 0.272 Chirality : 0.039 0.135 1502 Planarity : 0.003 0.037 1736 Dihedral : 9.336 74.978 1434 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.23 % Allowed : 10.07 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: -0.01 (0.25), residues: 1188 helix: 1.96 (0.23), residues: 533 sheet: 0.42 (0.48), residues: 114 loop : -2.29 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1001 TYR 0.011 0.001 TYR C1103 PHE 0.016 0.001 PHE C 607 TRP 0.022 0.001 TRP C 643 HIS 0.004 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (10062) covalent geometry : angle 0.50961 / 0.27 (13649) hydrogen bonds : bond 0.04492 / 4.33 ( 410) hydrogen bonds : angle 3.92081 / 3.29 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.233 Fit side-chains REVERT: C 51 THR cc_start: 0.7403 (p) cc_final: 0.7082 (p) REVERT: C 708 MET cc_start: 0.8134 (mtt) cc_final: 0.7633 (mtt) REVERT: C 931 LYS cc_start: 0.7657 (tppt) cc_final: 0.7113 (ttpt) REVERT: C 952 ASP cc_start: 0.8452 (m-30) cc_final: 0.8180 (m-30) REVERT: C 954 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7176 (mtt180) REVERT: C 1022 GLN cc_start: 0.6484 (pt0) cc_final: 0.5804 (pm20) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.0876 time to fit residues: 11.1865 Evaluate side-chains 82 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 774 ILE Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1180 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.209345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165129 restraints weight = 11166.359| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 3.26 r_work: 0.3451 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10062 Z= 0.118 Angle : 0.503 8.321 13649 Z= 0.268 Chirality : 0.038 0.133 1502 Planarity : 0.003 0.037 1736 Dihedral : 9.258 73.289 1434 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.52 % Allowed : 10.73 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 are not related in a simple way. whole: 0.10 (0.25), residues: 1188 helix: 2.08 (0.23), residues: 535 sheet: 0.32 (0.47), residues: 124 loop : -2.29 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1087 TYR 0.011 0.001 TYR C 892 PHE 0.016 0.001 PHE C 607 TRP 0.025 0.001 TRP C 428 HIS 0.005 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (10062) covalent geometry : angle 0.50342 / 0.27 (13649) hydrogen bonds : bond 0.04631 / 4.42 ( 410) hydrogen bonds : angle 3.79772 / 3.20 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.220 Fit side-chains REVERT: C 51 THR cc_start: 0.7464 (p) cc_final: 0.7148 (p) REVERT: C 230 GLU cc_start: 0.7802 (tp30) cc_final: 0.7368 (tm-30) REVERT: C 521 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7595 (mp) REVERT: C 708 MET cc_start: 0.8143 (mtt) cc_final: 0.7760 (mtt) REVERT: C 931 LYS cc_start: 0.7705 (tppt) cc_final: 0.7136 (ttpt) REVERT: C 952 ASP cc_start: 0.8461 (m-30) cc_final: 0.8177 (m-30) REVERT: C 954 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7232 (mtt180) REVERT: C 1022 GLN cc_start: 0.6577 (pt0) cc_final: 0.5737 (pm20) outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 0.0706 time to fit residues: 9.4678 Evaluate side-chains 85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1180 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.0040 chunk 28 optimal weight: 0.4980 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.211555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166318 restraints weight = 11203.608| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.49 r_work: 0.3460 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10062 Z= 0.092 Angle : 0.464 9.732 13649 Z= 0.248 Chirality : 0.037 0.134 1502 Planarity : 0.003 0.038 1736 Dihedral : 9.142 72.485 1434 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.95 % Allowed : 11.87 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.28 (0.25), residues: 1188 helix: 2.27 (0.23), residues: 533 sheet: 0.56 (0.49), residues: 114 loop : -2.22 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 587 TYR 0.013 0.001 TYR C 127 PHE 0.021 0.001 PHE C 8 TRP 0.024 0.001 TRP C 428 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (10062) covalent geometry : angle 0.46367 / 0.25 (13649) hydrogen bonds : bond 0.03728 / 3.64 ( 410) hydrogen bonds : angle 3.64217 / 3.09 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: C 51 THR cc_start: 0.7473 (p) cc_final: 0.7154 (p) REVERT: C 230 GLU cc_start: 0.7724 (tp30) cc_final: 0.7343 (tm-30) REVERT: C 683 GLN cc_start: 0.7005 (mt0) cc_final: 0.6582 (tp-100) REVERT: C 931 LYS cc_start: 0.7709 (tppt) cc_final: 0.7056 (ttpt) REVERT: C 952 ASP cc_start: 0.8423 (m-30) cc_final: 0.8102 (m-30) REVERT: C 954 ARG cc_start: 0.7516 (mtm180) cc_final: 0.7218 (mtt90) REVERT: C 1001 ARG cc_start: 0.5995 (mpp-170) cc_final: 0.5101 (mtt180) REVERT: C 1022 GLN cc_start: 0.6483 (pt0) cc_final: 0.5702 (pm20) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.0873 time to fit residues: 10.7822 Evaluate side-chains 85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.210337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165893 restraints weight = 11103.795| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.21 r_work: 0.3469 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10062 Z= 0.100 Angle : 0.490 10.593 13649 Z= 0.255 Chirality : 0.038 0.135 1502 Planarity : 0.003 0.036 1736 Dihedral : 9.079 71.065 1434 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.14 % Allowed : 12.35 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.34 (0.25), residues: 1188 helix: 2.30 (0.23), residues: 534 sheet: 0.62 (0.50), residues: 114 loop : -2.19 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1001 TYR 0.010 0.001 TYR C 892 PHE 0.016 0.001 PHE C 8 TRP 0.029 0.001 TRP C 428 HIS 0.004 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (10062) covalent geometry : angle 0.48958 / 0.26 (13649) hydrogen bonds : bond 0.04048 / 3.93 ( 410) hydrogen bonds : angle 3.62214 / 3.09 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.377 Fit side-chains REVERT: C 51 THR cc_start: 0.7510 (p) cc_final: 0.7202 (p) REVERT: C 230 GLU cc_start: 0.7758 (tp30) cc_final: 0.7418 (tm-30) REVERT: C 683 GLN cc_start: 0.7045 (mt0) cc_final: 0.6689 (tp-100) REVERT: C 931 LYS cc_start: 0.7725 (tppt) cc_final: 0.7128 (ttpt) REVERT: C 952 ASP cc_start: 0.8419 (m-30) cc_final: 0.8119 (m-30) REVERT: C 954 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7309 (mtt90) REVERT: C 1022 GLN cc_start: 0.6553 (pt0) cc_final: 0.5728 (pm20) REVERT: C 1029 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7362 (mt-10) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.0834 time to fit residues: 9.9098 Evaluate side-chains 82 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 628 HIS Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 0.0030 chunk 64 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.212134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168621 restraints weight = 11102.149| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.24 r_work: 0.3474 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10062 Z= 0.087 Angle : 0.459 12.156 13649 Z= 0.241 Chirality : 0.037 0.161 1502 Planarity : 0.003 0.037 1736 Dihedral : 8.956 70.506 1434 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.66 % Allowed : 13.20 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.49 (0.25), residues: 1188 helix: 2.43 (0.23), residues: 534 sheet: 0.80 (0.51), residues: 114 loop : -2.13 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 587 TYR 0.006 0.001 TYR C 892 PHE 0.013 0.001 PHE C 8 TRP 0.032 0.001 TRP C 428 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00165 / 0.09 (10062) covalent geometry : angle 0.45945 / 0.24 (13649) hydrogen bonds : bond 0.03383 / 3.34 ( 410) hydrogen bonds : angle 3.50755 / 2.98 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.261 Fit side-chains REVERT: C 1 MET cc_start: 0.1515 (ppp) cc_final: 0.1178 (ppp) REVERT: C 51 THR cc_start: 0.7525 (p) cc_final: 0.7214 (p) REVERT: C 230 GLU cc_start: 0.7741 (tp30) cc_final: 0.7417 (tm-30) REVERT: C 683 GLN cc_start: 0.7054 (mt0) cc_final: 0.6685 (tp-100) REVERT: C 931 LYS cc_start: 0.7686 (tppt) cc_final: 0.7096 (ttpt) REVERT: C 952 ASP cc_start: 0.8402 (m-30) cc_final: 0.8100 (m-30) REVERT: C 954 ARG cc_start: 0.7535 (mtm180) cc_final: 0.7282 (mtt90) REVERT: C 1022 GLN cc_start: 0.6556 (pt0) cc_final: 0.5701 (pm20) REVERT: C 1029 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7353 (mt-10) outliers start: 7 outliers final: 5 residues processed: 82 average time/residue: 0.1043 time to fit residues: 11.8460 Evaluate side-chains 80 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.206508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165086 restraints weight = 11036.703| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.85 r_work: 0.3427 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10062 Z= 0.130 Angle : 0.552 12.897 13649 Z= 0.285 Chirality : 0.040 0.133 1502 Planarity : 0.004 0.072 1736 Dihedral : 9.051 69.074 1434 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.52 % Allowed : 12.63 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.27 (0.25), residues: 1188 helix: 2.23 (0.23), residues: 538 sheet: 0.50 (0.50), residues: 114 loop : -2.22 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1001 TYR 0.015 0.001 TYR C 892 PHE 0.025 0.002 PHE C 916 TRP 0.037 0.002 TRP C 428 HIS 0.005 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10062) covalent geometry : angle 0.55225 / 0.29 (13649) hydrogen bonds : bond 0.05025 / 4.77 ( 410) hydrogen bonds : angle 3.75773 / 3.21 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.337 Fit side-chains REVERT: C 1 MET cc_start: 0.1654 (ppp) cc_final: 0.1303 (ppp) REVERT: C 51 THR cc_start: 0.7605 (p) cc_final: 0.7298 (p) REVERT: C 230 GLU cc_start: 0.7798 (tp30) cc_final: 0.7428 (tm-30) REVERT: C 663 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.6390 (tpt) REVERT: C 683 GLN cc_start: 0.7081 (mt0) cc_final: 0.6754 (tp-100) REVERT: C 697 THR cc_start: 0.8276 (p) cc_final: 0.7806 (m) REVERT: C 708 MET cc_start: 0.8141 (mtt) cc_final: 0.7598 (mtt) REVERT: C 931 LYS cc_start: 0.7767 (tppt) cc_final: 0.7191 (ttpt) REVERT: C 952 ASP cc_start: 0.8460 (m-30) cc_final: 0.8146 (m-30) REVERT: C 954 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7369 (mtt90) REVERT: C 1022 GLN cc_start: 0.6784 (pt0) cc_final: 0.5786 (pm20) REVERT: C 1029 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7460 (mt-10) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.0883 time to fit residues: 10.4830 Evaluate side-chains 85 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 115 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.206767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162595 restraints weight = 11053.442| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.29 r_work: 0.3413 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10062 Z= 0.132 Angle : 0.531 14.194 13649 Z= 0.279 Chirality : 0.039 0.132 1502 Planarity : 0.003 0.036 1736 Dihedral : 9.049 68.811 1434 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.14 % Allowed : 12.92 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.13 (0.25), residues: 1188 helix: 2.16 (0.23), residues: 536 sheet: 0.27 (0.50), residues: 117 loop : -2.29 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1001 TYR 0.011 0.001 TYR C 892 PHE 0.016 0.001 PHE C 607 TRP 0.038 0.002 TRP C 428 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10062) covalent geometry : angle 0.53071 / 0.28 (13649) hydrogen bonds : bond 0.04799 / 4.61 ( 410) hydrogen bonds : angle 3.80095 / 3.25 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.245 Fit side-chains REVERT: C 1 MET cc_start: 0.1559 (ppp) cc_final: 0.0891 (ppp) REVERT: C 51 THR cc_start: 0.7608 (p) cc_final: 0.7300 (p) REVERT: C 230 GLU cc_start: 0.7789 (tp30) cc_final: 0.7413 (tm-30) REVERT: C 521 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7599 (mp) REVERT: C 663 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6413 (tpt) REVERT: C 697 THR cc_start: 0.8336 (p) cc_final: 0.7946 (m) REVERT: C 931 LYS cc_start: 0.7849 (tppt) cc_final: 0.7212 (tttt) REVERT: C 952 ASP cc_start: 0.8469 (m-30) cc_final: 0.8099 (m-30) REVERT: C 954 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7332 (mtt180) REVERT: C 1022 GLN cc_start: 0.6990 (pt0) cc_final: 0.5943 (pm20) REVERT: C 1029 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7489 (mt-10) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.0801 time to fit residues: 10.5222 Evaluate side-chains 87 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 597 THR Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1175 THR Chi-restraints excluded: chain C residue 1183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 112 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.8307 > 50:) chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.0170 chunk 2 optimal weight: 0.9980 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.208821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169591 restraints weight = 11129.790| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.78 r_work: 0.3417 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10062 Z= 0.098 Angle : 0.497 13.238 13649 Z= 0.260 Chirality : 0.038 0.132 1502 Planarity : 0.003 0.081 1736 Dihedral : 8.916 68.421 1434 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.95 % Allowed : 13.96 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.32 (0.25), residues: 1188 helix: 2.31 (0.23), residues: 536 sheet: 0.56 (0.51), residues: 114 loop : -2.23 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1001 TYR 0.011 0.001 TYR C 744 PHE 0.013 0.001 PHE C 916 TRP 0.037 0.001 TRP C 428 HIS 0.004 0.001 HIS C 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 (10062) covalent geometry : angle 0.49661 / 0.26 (13649) hydrogen bonds : bond 0.03934 / 3.85 ( 410) hydrogen bonds : angle 3.63016 / 3.09 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.48 seconds wall clock time: 41 minutes 1.94 seconds (2461.94 seconds total)