Starting phenix.real_space_refine on Wed Aug 5 18:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.map" model { file = "/net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkt_48337/08_2026/9mkt_48337.cif" } resolution = 3.26 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= 0.001 sd= 0.018 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 28 5.49 5 S 21 5.16 5 C 6879 2.51 5 N 1792 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 10866 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1242, 10270 Classifications: {'peptide': 1242} Link IDs: {'PTRANS': 28, 'TRANS': 1213} Chain breaks: 7 Chain: "B" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 596 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 10} Link IDs: {'rna2p': 7, 'rna3p': 20} Time building chain proxies: 2.50, per 1000 atoms: 0.23 Number of scatterers: 10866 At special positions: 0 Unit cell: (96.32, 112.66, 129, 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 28 15.00 O 2146 8.00 N 1792 7.00 C 6879 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: 0.89 Conformation dependent library (CDL) restraints added in 496.0 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 9 sheets defined 49.2% alpha, 9.3% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 46 removed outlier: 3.687A pdb=" N ASP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 66 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 91 through 116 removed outlier: 3.915A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 4.368A pdb=" N ILE A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.004A pdb=" N ASN A 156 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.650A pdb=" N ALA A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 178 Processing helix chain 'A' and resid 179 through 188 removed outlier: 4.064A pdb=" N GLU A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.735A pdb=" N ASP A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.543A pdb=" N LYS A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.954A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 346 through 356 removed outlier: 3.757A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 383 removed outlier: 3.626A pdb=" N LYS A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.522A pdb=" N THR A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 436 through 442 removed outlier: 4.065A pdb=" N ILE A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.821A pdb=" N LYS A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix removed outlier: 3.789A pdb=" N GLN A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.506A pdb=" N SER A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 504' Processing helix chain 'A' and resid 520 through 537 removed outlier: 3.557A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.993A pdb=" N PHE A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 587 removed outlier: 4.222A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 664 through 673 Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 749 through 761 removed outlier: 4.022A pdb=" N PHE A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.573A pdb=" N SER A 794 " --> pdb=" O LYS A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.706A pdb=" N ASP A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 907 Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 976 through 1000 removed outlier: 4.086A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1036 removed outlier: 3.562A pdb=" N ASN A1036 " --> pdb=" O ILE A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.704A pdb=" N MET A1067 " --> pdb=" O PHE A1064 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A1068 " --> pdb=" O LYS A1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1068' Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 4.355A pdb=" N SER A1083 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1169 through 1180 Processing helix chain 'A' and resid 1190 through 1198 removed outlier: 4.539A pdb=" N ALA A1194 " --> pdb=" O CYS A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 3.693A pdb=" N GLN A1216 " --> pdb=" O ASN A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.521A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1275 removed outlier: 3.697A pdb=" N ALA A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1299 removed outlier: 4.537A pdb=" N ASN A1299 " --> pdb=" O VAL A1295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.642A pdb=" N TYR A 832 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 21 " --> pdb=" O PHE A 878 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 623 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.642A pdb=" N TYR A 832 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA4, first strand: chain 'A' and resid 841 through 843 removed outlier: 4.070A pdb=" N HIS A 843 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 867 " --> pdb=" O HIS A 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 940 removed outlier: 7.103A pdb=" N LEU A 928 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN A 938 " --> pdb=" O TYR A 926 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR A 926 " --> pdb=" O GLN A 938 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR A 940 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA A 924 " --> pdb=" O THR A 940 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 915 " --> pdb=" O THR A 927 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 916 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A1006 " --> pdb=" O ILE A 916 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ARG A 918 " --> pdb=" O GLU A1006 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AA7, first strand: chain 'A' and resid 1114 through 1118 Processing sheet with id=AA8, first strand: chain 'A' and resid 1150 through 1152 Processing sheet with id=AA9, first strand: chain 'A' and resid 1218 through 1219 423 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2945 1.33 - 1.45: 2044 1.45 - 1.57: 6061 1.57 - 1.69: 55 1.69 - 1.81: 33 Bond restraints: 11138 Sorted by residual: bond pdb=" CA ILE A 71 " pdb=" CB ILE A 71 " ideal model delta sigma weight residual 1.531 1.545 -0.014 1.11e-02 8.12e+03 1.63e+00 bond pdb=" C GLY A 983 " pdb=" O GLY A 983 " ideal model delta sigma weight residual 1.235 1.249 -0.015 1.23e-02 6.61e+03 1.41e+00 bond pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.86e-02 2.89e+03 1.02e+00 bond pdb=" C4 C B -14 " pdb=" C5 C B -14 " ideal model delta sigma weight residual 1.425 1.417 0.008 8.00e-03 1.56e+04 9.82e-01 bond pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.62e-01 ... (remaining 11133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14771 1.67 - 3.34: 282 3.34 - 5.00: 32 5.00 - 6.67: 8 6.67 - 8.34: 3 Bond angle restraints: 15096 Sorted by residual: angle pdb=" C ASP A 345 " pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " ideal model delta sigma weight residual 116.54 110.53 6.01 1.15e+00 7.56e-01 2.73e+01 angle pdb=" C1' C B -14 " pdb=" N1 C B -14 " pdb=" C2 C B -14 " ideal model delta sigma weight residual 118.80 123.89 -5.09 1.10e+00 8.26e-01 2.14e+01 angle pdb=" N ASP A 345 " pdb=" CA ASP A 345 " pdb=" C ASP A 345 " ideal model delta sigma weight residual 108.31 115.13 -6.82 1.52e+00 4.33e-01 2.01e+01 angle pdb=" C2' A B 3 " pdb=" C1' A B 3 " pdb=" N9 A B 3 " ideal model delta sigma weight residual 112.00 116.67 -4.67 1.10e+00 8.26e-01 1.80e+01 angle pdb=" C1' C B 7 " pdb=" N1 C B 7 " pdb=" C2 C B 7 " ideal model delta sigma weight residual 118.80 123.39 -4.59 1.10e+00 8.26e-01 1.74e+01 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 6566 32.04 - 64.09: 203 64.09 - 96.13: 27 96.13 - 128.17: 0 128.17 - 160.22: 1 Dihedral angle restraints: 6797 sinusoidal: 3112 harmonic: 3685 Sorted by residual: dihedral pdb=" O4' C B 7 " pdb=" C1' C B 7 " pdb=" N1 C B 7 " pdb=" C2 C B 7 " ideal model delta sinusoidal sigma weight residual 200.00 39.78 160.22 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" CA ASP A 345 " pdb=" C ASP A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" O4' G B -9 " pdb=" C1' G B -9 " pdb=" N9 G B -9 " pdb=" C4 G B -9 " ideal model delta sinusoidal sigma weight residual -106.00 -167.29 61.29 1 1.70e+01 3.46e-03 1.73e+01 ... (remaining 6794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1350 0.056 - 0.111: 252 0.111 - 0.167: 42 0.167 - 0.223: 0 0.223 - 0.278: 1 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C1' A B 3 " pdb=" O4' A B 3 " pdb=" C2' A B 3 " pdb=" N9 A B 3 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' U B 6 " pdb=" C3' U B 6 " pdb=" O2' U B 6 " pdb=" C1' U B 6 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CG LEU A 923 " pdb=" CB LEU A 923 " pdb=" CD1 LEU A 923 " pdb=" CD2 LEU A 923 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1642 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1096 " 0.058 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A1097 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A1097 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1097 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 3 " -0.035 2.00e-02 2.50e+03 1.60e-02 7.03e+00 pdb=" N9 A B 3 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 3 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A B 3 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 3 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 3 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A B 3 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 4 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" N9 A B 4 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A B 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 4 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 4 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 4 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B 4 " -0.006 2.00e-02 2.50e+03 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2051 2.77 - 3.30: 10716 3.30 - 3.84: 17217 3.84 - 4.37: 20136 4.37 - 4.90: 33383 Nonbonded interactions: 83503 Sorted by model distance: nonbonded pdb=" O LEU A 127 " pdb=" OG SER A 136 " model vdw 2.238 3.040 nonbonded pdb=" O LEU A 529 " pdb=" NE2 GLN A 532 " model vdw 2.248 3.120 nonbonded pdb=" O ILE A1085 " pdb=" ND2 ASN A1257 " model vdw 2.278 3.120 nonbonded pdb=" NH1 ARG A 918 " pdb=" OE2 GLU A1006 " model vdw 2.278 3.120 nonbonded pdb=" O SER A 116 " pdb=" NZ LYS A 120 " model vdw 2.285 3.120 ... (remaining 83498 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: 1.420 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 0.022 11138 Z= 0.126 Angle : 0.569 8.339 15096 Z= 0.364 Chirality : 0.044 0.278 1645 Planarity : 0.004 0.090 1829 Dihedral : 15.730 160.218 4411 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.23), residues: 1226 helix: 0.68 (0.24), residues: 528 sheet: -1.47 (0.46), residues: 120 loop : -1.74 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 921 TYR 0.026 0.001 TYR A 724 PHE 0.020 0.001 PHE A 720 TRP 0.013 0.001 TRP A1142 HIS 0.015 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (11138) covalent geometry : angle 0.56855 / 0.36 (15096) hydrogen bonds : bond 0.15324 / 10.26 ( 428) hydrogen bonds : angle 5.56620 / 3.93 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 ASP cc_start: 0.6991 (m-30) cc_final: 0.6270 (m-30) REVERT: A 740 ARG cc_start: 0.7434 (mmt180) cc_final: 0.7076 (tpm170) REVERT: A 747 TYR cc_start: 0.5030 (m-10) cc_final: 0.4332 (m-80) REVERT: A 1014 ARG cc_start: 0.6941 (mmt180) cc_final: 0.6725 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1168 time to fit residues: 21.1925 Evaluate side-chains 52 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 270 ASN A 580 ASN A 851 ASN A1296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.094422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.073439 restraints weight = 48031.585| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.27 r_work: 0.3535 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11138 Z= 0.235 Angle : 0.666 11.096 15096 Z= 0.365 Chirality : 0.045 0.181 1645 Planarity : 0.004 0.055 1829 Dihedral : 13.144 158.806 1752 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % Rotamer: Outliers : 1.06 % Allowed : 9.09 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.09 (0.23), residues: 1226 helix: 0.53 (0.23), residues: 540 sheet: -1.56 (0.46), residues: 120 loop : -1.79 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 921 TYR 0.033 0.002 TYR A 190 PHE 0.018 0.002 PHE A 879 TRP 0.011 0.002 TRP A1142 HIS 0.006 0.002 HIS A1187 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (11138) covalent geometry : angle 0.66610 / 0.36 (15096) hydrogen bonds : bond 0.06271 / 4.26 ( 428) hydrogen bonds : angle 5.33279 / 3.78 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7675 (tt) REVERT: A 740 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6882 (tpm170) REVERT: A 756 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6362 (pt0) outliers start: 12 outliers final: 7 residues processed: 71 average time/residue: 0.0902 time to fit residues: 9.7194 Evaluate side-chains 55 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 115 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN A1261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.093882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.073103 restraints weight = 48457.392| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.15 r_work: 0.3526 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11138 Z= 0.204 Angle : 0.612 10.488 15096 Z= 0.339 Chirality : 0.044 0.192 1645 Planarity : 0.004 0.044 1829 Dihedral : 13.180 158.115 1752 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.49 % Favored : 95.35 % Rotamer: Outliers : 1.85 % Allowed : 12.09 % Favored : 86.05 % 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 are not related in a simple way. whole: -1.17 (0.23), residues: 1226 helix: 0.37 (0.22), residues: 546 sheet: -1.20 (0.48), residues: 111 loop : -1.85 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 921 TYR 0.016 0.002 TYR A1055 PHE 0.022 0.002 PHE A 723 TRP 0.013 0.002 TRP A1142 HIS 0.005 0.002 HIS A1187 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (11138) covalent geometry : angle 0.61230 / 0.34 (15096) hydrogen bonds : bond 0.05902 / 4.04 ( 428) hydrogen bonds : angle 5.20673 / 3.69 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 572 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 626 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7457 (t0) REVERT: A 740 ARG cc_start: 0.7234 (mmt180) cc_final: 0.6941 (tpm170) REVERT: A 1061 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.6363 (p90) outliers start: 21 outliers final: 9 residues processed: 68 average time/residue: 0.0834 time to fit residues: 9.1994 Evaluate side-chains 59 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS A1056 GLN A1216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.073766 restraints weight = 48469.868| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 4.09 r_work: 0.3540 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11138 Z= 0.152 Angle : 0.558 9.982 15096 Z= 0.311 Chirality : 0.042 0.195 1645 Planarity : 0.003 0.039 1829 Dihedral : 13.143 157.279 1752 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.94 % Rotamer: Outliers : 1.50 % Allowed : 14.12 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.07 (0.23), residues: 1226 helix: 0.49 (0.23), residues: 546 sheet: -1.17 (0.48), residues: 111 loop : -1.83 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 921 TYR 0.016 0.002 TYR A1130 PHE 0.024 0.002 PHE A 753 TRP 0.013 0.001 TRP A1142 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11138) covalent geometry : angle 0.55836 / 0.31 (15096) hydrogen bonds : bond 0.05090 / 3.50 ( 428) hydrogen bonds : angle 4.98427 / 3.54 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7733 (tt) REVERT: A 572 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9068 (tt) REVERT: A 740 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6919 (tpm170) REVERT: A 1061 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.6316 (p90) outliers start: 17 outliers final: 9 residues processed: 65 average time/residue: 0.0768 time to fit residues: 7.8063 Evaluate side-chains 59 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 0.0670 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.092350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.071559 restraints weight = 48560.196| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.14 r_work: 0.3509 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11138 Z= 0.219 Angle : 0.616 9.775 15096 Z= 0.338 Chirality : 0.044 0.206 1645 Planarity : 0.004 0.036 1829 Dihedral : 13.188 156.707 1752 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 3.00 % Allowed : 14.56 % Favored : 82.44 % 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 are not related in a simple way. whole: -1.20 (0.23), residues: 1226 helix: 0.37 (0.23), residues: 544 sheet: -1.22 (0.48), residues: 111 loop : -1.88 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.026 0.002 TYR A1055 PHE 0.018 0.002 PHE A 880 TRP 0.012 0.002 TRP A1142 HIS 0.005 0.002 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (11138) covalent geometry : angle 0.61597 / 0.34 (15096) hydrogen bonds : bond 0.05771 / 3.96 ( 428) hydrogen bonds : angle 5.13950 / 3.63 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 46 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 572 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9099 (tt) REVERT: A 626 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7477 (t0) REVERT: A 740 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6963 (tpm170) REVERT: A 1061 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.6473 (p90) outliers start: 34 outliers final: 11 residues processed: 75 average time/residue: 0.0666 time to fit residues: 8.0610 Evaluate side-chains 63 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1177 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.091993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.071140 restraints weight = 48620.097| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.16 r_work: 0.3499 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11138 Z= 0.215 Angle : 0.616 9.575 15096 Z= 0.340 Chirality : 0.044 0.211 1645 Planarity : 0.004 0.034 1829 Dihedral : 13.221 156.479 1752 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.71 % Favored : 94.13 % Rotamer: Outliers : 2.91 % Allowed : 16.50 % Favored : 80.58 % 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 are not related in a simple way. whole: -1.24 (0.23), residues: 1226 helix: 0.38 (0.23), residues: 544 sheet: -1.25 (0.48), residues: 111 loop : -1.95 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.025 0.002 TYR A1055 PHE 0.019 0.002 PHE A 880 TRP 0.014 0.002 TRP A1142 HIS 0.006 0.002 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 (11138) covalent geometry : angle 0.61611 / 0.34 (15096) hydrogen bonds : bond 0.05747 / 3.96 ( 428) hydrogen bonds : angle 5.14621 / 3.64 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7765 (tt) REVERT: A 572 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9124 (tt) REVERT: A 626 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7466 (t0) REVERT: A 740 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6813 (tpm170) REVERT: A 1061 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6447 (p90) outliers start: 33 outliers final: 19 residues processed: 81 average time/residue: 0.0699 time to fit residues: 8.8804 Evaluate side-chains 72 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.091681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.070583 restraints weight = 48472.499| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.17 r_work: 0.3476 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11138 Z= 0.241 Angle : 0.658 9.624 15096 Z= 0.360 Chirality : 0.046 0.223 1645 Planarity : 0.004 0.034 1829 Dihedral : 13.311 156.026 1752 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.28 % Favored : 93.56 % Rotamer: Outliers : 3.09 % Allowed : 17.30 % Favored : 79.61 % 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 are not related in a simple way. whole: -1.39 (0.23), residues: 1226 helix: 0.29 (0.22), residues: 543 sheet: -1.39 (0.47), residues: 112 loop : -2.06 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 921 TYR 0.025 0.002 TYR A1055 PHE 0.020 0.002 PHE A 880 TRP 0.014 0.002 TRP A1142 HIS 0.006 0.002 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.24 (11138) covalent geometry : angle 0.65782 / 0.36 (15096) hydrogen bonds : bond 0.06119 / 4.23 ( 428) hydrogen bonds : angle 5.27177 / 3.72 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7806 (tt) REVERT: A 572 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9142 (tt) REVERT: A 626 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7438 (t0) REVERT: A 740 ARG cc_start: 0.7005 (mmt180) cc_final: 0.6789 (tpm170) REVERT: A 1055 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.8137 (p90) REVERT: A 1061 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.6677 (p90) outliers start: 35 outliers final: 22 residues processed: 82 average time/residue: 0.0921 time to fit residues: 11.5807 Evaluate side-chains 77 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.093183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072321 restraints weight = 47458.609| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 4.18 r_work: 0.3512 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11138 Z= 0.146 Angle : 0.564 9.443 15096 Z= 0.313 Chirality : 0.042 0.211 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.226 155.784 1752 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 2.21 % Allowed : 18.62 % Favored : 79.17 % 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 are not related in a simple way. whole: -1.20 (0.23), residues: 1226 helix: 0.50 (0.23), residues: 536 sheet: -1.26 (0.48), residues: 111 loop : -1.99 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.014 0.001 TYR A 659 PHE 0.020 0.001 PHE A 880 TRP 0.016 0.002 TRP A1142 HIS 0.008 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (11138) covalent geometry : angle 0.56423 / 0.31 (15096) hydrogen bonds : bond 0.05072 / 3.51 ( 428) hydrogen bonds : angle 5.01426 / 3.56 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8349 (mm) cc_final: 0.8009 (tp) REVERT: A 374 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 740 ARG cc_start: 0.6985 (mmt180) cc_final: 0.6758 (tpm170) REVERT: A 1061 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6599 (p90) REVERT: A 1195 ILE cc_start: 0.6938 (mm) cc_final: 0.6723 (mm) outliers start: 25 outliers final: 21 residues processed: 74 average time/residue: 0.0869 time to fit residues: 9.8421 Evaluate side-chains 72 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.092089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.071113 restraints weight = 48357.335| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.18 r_work: 0.3483 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11138 Z= 0.213 Angle : 0.625 9.345 15096 Z= 0.341 Chirality : 0.044 0.223 1645 Planarity : 0.004 0.033 1829 Dihedral : 13.272 155.327 1752 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 2.38 % Allowed : 18.89 % Favored : 78.73 % 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 are not related in a simple way. whole: -1.30 (0.23), residues: 1226 helix: 0.36 (0.22), residues: 549 sheet: -1.31 (0.48), residues: 111 loop : -2.05 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.020 0.002 TYR A1055 PHE 0.021 0.002 PHE A 723 TRP 0.012 0.002 TRP A1142 HIS 0.009 0.002 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (11138) covalent geometry : angle 0.62512 / 0.34 (15096) hydrogen bonds : bond 0.05752 / 3.98 ( 428) hydrogen bonds : angle 5.13815 / 3.63 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8337 (mm) cc_final: 0.8004 (tp) REVERT: A 178 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: A 374 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 740 ARG cc_start: 0.7083 (mmt180) cc_final: 0.6836 (tpm170) REVERT: A 1061 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6664 (p90) REVERT: A 1195 ILE cc_start: 0.7093 (mm) cc_final: 0.6892 (mm) outliers start: 27 outliers final: 19 residues processed: 72 average time/residue: 0.0920 time to fit residues: 10.0455 Evaluate side-chains 69 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.093328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.072734 restraints weight = 46952.430| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.11 r_work: 0.3541 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11138 Z= 0.113 Angle : 0.542 9.319 15096 Z= 0.299 Chirality : 0.041 0.204 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.162 155.247 1752 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 1.85 % Allowed : 19.68 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.07 (0.24), residues: 1226 helix: 0.52 (0.23), residues: 555 sheet: -1.22 (0.47), residues: 115 loop : -1.89 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.012 0.001 TYR A 659 PHE 0.021 0.001 PHE A 880 TRP 0.019 0.002 TRP A1142 HIS 0.009 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (11138) covalent geometry : angle 0.54199 / 0.30 (15096) hydrogen bonds : bond 0.04379 / 3.03 ( 428) hydrogen bonds : angle 4.81871 / 3.43 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8372 (mm) cc_final: 0.8049 (tp) REVERT: A 178 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: A 374 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 740 ARG cc_start: 0.7120 (mmt180) cc_final: 0.6875 (tpm170) REVERT: A 1061 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6557 (p90) outliers start: 21 outliers final: 14 residues processed: 70 average time/residue: 0.0747 time to fit residues: 8.0023 Evaluate side-chains 66 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 532 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.093501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.072670 restraints weight = 48062.959| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.28 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11138 Z= 0.134 Angle : 0.545 9.245 15096 Z= 0.298 Chirality : 0.041 0.211 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.134 154.836 1752 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 1.85 % Allowed : 19.68 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.03 (0.24), residues: 1226 helix: 0.56 (0.23), residues: 557 sheet: -1.06 (0.49), residues: 111 loop : -1.92 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.014 0.001 TYR A 450 PHE 0.020 0.001 PHE A 723 TRP 0.013 0.002 TRP A1142 HIS 0.008 0.001 HIS A 922 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (11138) covalent geometry : angle 0.54477 / 0.30 (15096) hydrogen bonds : bond 0.04616 / 3.20 ( 428) hydrogen bonds : angle 4.79233 / 3.41 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.65 seconds wall clock time: 48 minutes 49.96 seconds (2929.96 seconds total)