Starting phenix.real_space_refine on Wed Mar 4 05:40:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mkt_48337/03_2026/9mkt_48337.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mkt_48337/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mkt_48337/03_2026/9mkt_48337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mkt_48337/03_2026/9mkt_48337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mkt_48337/03_2026/9mkt_48337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mkt_48337/03_2026/9mkt_48337.map" } 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-dev-5986/lib/python3.9/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: 2.34, per 1000 atoms: 0.22 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: 0.87 Conformation dependent library (CDL) restraints added in 455.4 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: 0.94 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: 2.12 Time building geometry restraints manager: 1.09 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=" 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 bond pdb=" CA ILE A1085 " pdb=" CB ILE A1085 " ideal model delta sigma weight residual 1.550 1.542 0.009 1.03e-02 9.43e+03 7.08e-01 ... (remaining 11133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 14836 1.67 - 3.34: 217 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=" 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=" C SER A 67 " pdb=" N SER A 68 " pdb=" CA SER A 68 " ideal model delta sigma weight residual 122.56 116.52 6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C ASN A 156 " pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA ASP A 345 " pdb=" C ASP A 345 " pdb=" N SER A 346 " ideal model delta sigma weight residual 119.52 116.66 2.86 7.90e-01 1.60e+00 1.31e+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 - 0.053: 1353 0.053 - 0.106: 262 0.106 - 0.159: 29 0.159 - 0.212: 0 0.212 - 0.265: 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 2.46 2.19 0.27 2.00e-01 2.50e+01 1.76e+00 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 chirality pdb=" CB ILE A 469 " pdb=" CA ILE A 469 " pdb=" CG1 ILE A 469 " pdb=" CG2 ILE A 469 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-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: 1.720 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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= 0.115 Angle : 0.542 8.339 15096 Z= 0.307 Chirality : 0.041 0.265 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 covalent geometry : bond 0.00224 (11138) covalent geometry : angle 0.54246 (15096) hydrogen bonds : bond 0.15324 ( 428) hydrogen bonds : angle 5.56620 ( 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 : 0.334 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: 0.1167 time to fit residues: 21.0200 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 : 0.401 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 580 ASN A 851 ASN A1296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.093465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.072478 restraints weight = 48260.608| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.26 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11138 Z= 0.243 Angle : 0.685 11.280 15096 Z= 0.370 Chirality : 0.046 0.318 1645 Planarity : 0.004 0.059 1829 Dihedral : 13.240 159.221 1752 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.94 % Rotamer: Outliers : 1.50 % Allowed : 9.71 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.10 (0.23), residues: 1226 helix: 0.50 (0.23), residues: 545 sheet: -1.47 (0.46), residues: 120 loop : -1.82 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 921 TYR 0.022 0.002 TYR A1055 PHE 0.023 0.002 PHE A 723 TRP 0.012 0.002 TRP A1142 HIS 0.007 0.002 HIS A1187 Details of bonding type rmsd covalent geometry : bond 0.00539 (11138) covalent geometry : angle 0.68470 (15096) hydrogen bonds : bond 0.06081 ( 428) hydrogen bonds : angle 5.29556 ( 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 77 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 572 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9040 (tt) REVERT: A 626 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 740 ARG cc_start: 0.7184 (mmt180) cc_final: 0.6883 (tpm170) REVERT: A 1014 ARG cc_start: 0.7210 (mmt180) cc_final: 0.6969 (tpp-160) REVERT: A 1061 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6371 (p90) outliers start: 17 outliers final: 6 residues processed: 73 average time/residue: 0.0815 time to fit residues: 9.3118 Evaluate side-chains 59 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 626 ASP Chi-restraints excluded: chain A residue 756 GLU Chi-restraints excluded: chain A residue 1061 PHE 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: 1.9990 chunk 23 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 92 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 538 HIS A1216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.096097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.075560 restraints weight = 47935.025| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.19 r_work: 0.3585 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11138 Z= 0.106 Angle : 0.526 10.092 15096 Z= 0.289 Chirality : 0.041 0.332 1645 Planarity : 0.003 0.044 1829 Dihedral : 13.041 158.136 1752 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.84 % Rotamer: Outliers : 1.59 % Allowed : 11.92 % Favored : 86.50 % 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: -0.83 (0.23), residues: 1226 helix: 0.66 (0.23), residues: 553 sheet: -1.08 (0.48), residues: 111 loop : -1.69 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 921 TYR 0.018 0.001 TYR A 925 PHE 0.026 0.001 PHE A 753 TRP 0.013 0.001 TRP A1142 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00212 (11138) covalent geometry : angle 0.52604 (15096) hydrogen bonds : bond 0.04154 ( 428) hydrogen bonds : angle 4.73519 ( 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 76 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7623 (p0) REVERT: A 374 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7679 (tt) REVERT: A 740 ARG cc_start: 0.7319 (mmt180) cc_final: 0.7003 (tpm170) REVERT: A 1014 ARG cc_start: 0.7360 (mmt180) cc_final: 0.7130 (tpp-160) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 0.0943 time to fit residues: 10.1023 Evaluate side-chains 59 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 633 MET Chi-restraints excluded: chain A residue 778 VAL 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: 8.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN A1257 ASN A1261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.091477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.070621 restraints weight = 49396.887| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.20 r_work: 0.3479 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11138 Z= 0.281 Angle : 0.700 9.476 15096 Z= 0.378 Chirality : 0.047 0.372 1645 Planarity : 0.004 0.052 1829 Dihedral : 13.323 158.113 1752 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 2.47 % Allowed : 14.92 % Favored : 82.61 % 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: -1.21 (0.23), residues: 1226 helix: 0.38 (0.23), residues: 544 sheet: -1.31 (0.48), residues: 112 loop : -1.89 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 872 TYR 0.030 0.002 TYR A1055 PHE 0.026 0.002 PHE A 723 TRP 0.013 0.002 TRP A1142 HIS 0.007 0.002 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00625 (11138) covalent geometry : angle 0.70020 (15096) hydrogen bonds : bond 0.06386 ( 428) hydrogen bonds : angle 5.33435 ( 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 81 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8348 (mm) cc_final: 0.8057 (tp) REVERT: A 374 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 572 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9164 (tt) REVERT: A 740 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6900 (tpm170) REVERT: A 1014 ARG cc_start: 0.7492 (mmt180) cc_final: 0.7233 (tpp-160) REVERT: A 1055 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.8004 (p90) REVERT: A 1061 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6750 (p90) outliers start: 28 outliers final: 15 residues processed: 78 average time/residue: 0.0855 time to fit residues: 10.2360 Evaluate side-chains 68 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 206 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 572 LEU 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 1006 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1214 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.092070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.071162 restraints weight = 49167.996| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.28 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11138 Z= 0.204 Angle : 0.613 9.289 15096 Z= 0.335 Chirality : 0.044 0.386 1645 Planarity : 0.003 0.035 1829 Dihedral : 13.264 157.365 1752 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 2.65 % Allowed : 16.86 % Favored : 80.49 % 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: -1.22 (0.23), residues: 1226 helix: 0.40 (0.23), residues: 545 sheet: -1.38 (0.48), residues: 112 loop : -1.91 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.017 0.002 TYR A 659 PHE 0.019 0.002 PHE A 880 TRP 0.014 0.002 TRP A1142 HIS 0.008 0.002 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00452 (11138) covalent geometry : angle 0.61279 (15096) hydrogen bonds : bond 0.05571 ( 428) hydrogen bonds : angle 5.16882 ( 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 81 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8419 (mm) cc_final: 0.8068 (tp) REVERT: A 374 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7830 (tt) REVERT: A 626 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7372 (t0) REVERT: A 740 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6942 (tpm170) REVERT: A 1014 ARG cc_start: 0.7390 (mmt180) cc_final: 0.7126 (tpp-160) REVERT: A 1061 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6703 (p90) outliers start: 30 outliers final: 16 residues processed: 77 average time/residue: 0.0941 time to fit residues: 10.9630 Evaluate side-chains 70 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 543 PHE 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 1056 GLN 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 1214 ILE Chi-restraints excluded: chain A residue 1269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 466 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.092384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.071541 restraints weight = 49001.745| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 4.23 r_work: 0.3499 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11138 Z= 0.172 Angle : 0.584 9.075 15096 Z= 0.317 Chirality : 0.043 0.388 1645 Planarity : 0.003 0.034 1829 Dihedral : 13.215 157.039 1752 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 2.91 % Allowed : 17.12 % Favored : 79.96 % 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: -1.11 (0.23), residues: 1226 helix: 0.54 (0.23), residues: 542 sheet: -1.32 (0.48), residues: 111 loop : -1.90 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.015 0.002 TYR A 659 PHE 0.019 0.002 PHE A 880 TRP 0.014 0.002 TRP A1142 HIS 0.007 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00379 (11138) covalent geometry : angle 0.58391 (15096) hydrogen bonds : bond 0.05154 ( 428) hydrogen bonds : angle 5.01640 ( 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 82 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 49 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8398 (mm) cc_final: 0.8033 (tp) REVERT: A 178 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: A 374 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7764 (tt) REVERT: A 626 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 740 ARG cc_start: 0.7232 (mmt180) cc_final: 0.6954 (tpm170) REVERT: A 1014 ARG cc_start: 0.7490 (mmt180) cc_final: 0.7213 (tpp-160) REVERT: A 1055 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7974 (p90) REVERT: A 1061 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6590 (p90) outliers start: 33 outliers final: 21 residues processed: 78 average time/residue: 0.0786 time to fit residues: 9.5069 Evaluate side-chains 72 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 543 PHE 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 1006 GLU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1081 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1217 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** A 466 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.090081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.069063 restraints weight = 48516.916| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.19 r_work: 0.3446 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11138 Z= 0.284 Angle : 0.703 9.073 15096 Z= 0.378 Chirality : 0.047 0.413 1645 Planarity : 0.004 0.041 1829 Dihedral : 13.415 156.846 1752 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.18 % Favored : 92.66 % Rotamer: Outliers : 3.09 % Allowed : 17.83 % Favored : 79.08 % 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: -1.44 (0.23), residues: 1226 helix: 0.30 (0.23), residues: 530 sheet: -1.61 (0.47), residues: 115 loop : -2.05 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.025 0.002 TYR A1055 PHE 0.029 0.002 PHE A 723 TRP 0.014 0.002 TRP A1142 HIS 0.007 0.002 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00633 (11138) covalent geometry : angle 0.70326 (15096) hydrogen bonds : bond 0.06357 ( 428) hydrogen bonds : angle 5.39520 ( 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 78 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 43 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: A 374 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 626 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7403 (t0) REVERT: A 740 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6982 (tpm170) REVERT: A 1061 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.6768 (p90) outliers start: 35 outliers final: 25 residues processed: 75 average time/residue: 0.0818 time to fit residues: 9.5222 Evaluate side-chains 71 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 42 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 206 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 543 PHE 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 874 THR Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1081 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1217 MET 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: 2.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.093027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.072433 restraints weight = 47465.064| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 4.16 r_work: 0.3529 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11138 Z= 0.117 Angle : 0.544 9.282 15096 Z= 0.294 Chirality : 0.042 0.385 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.200 156.346 1752 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.11 % Rotamer: Outliers : 2.47 % Allowed : 18.62 % Favored : 78.91 % 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: -1.08 (0.23), residues: 1226 helix: 0.68 (0.23), residues: 537 sheet: -1.38 (0.47), residues: 115 loop : -1.97 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.012 0.001 TYR A 659 PHE 0.020 0.001 PHE A 723 TRP 0.016 0.001 TRP A1142 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00248 (11138) covalent geometry : angle 0.54442 (15096) hydrogen bonds : bond 0.04353 ( 428) hydrogen bonds : angle 4.82882 ( 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 75 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8388 (mm) cc_final: 0.8003 (tp) REVERT: A 178 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7869 (m-80) REVERT: A 374 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7716 (tt) REVERT: A 740 ARG cc_start: 0.7208 (mmt180) cc_final: 0.6984 (tpm170) REVERT: A 1061 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6515 (p90) outliers start: 28 outliers final: 18 residues processed: 71 average time/residue: 0.0766 time to fit residues: 8.6480 Evaluate side-chains 63 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 633 MET 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 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1081 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 0.0770 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 466 HIS ** 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 = 0.4073 r_free = 0.4073 target = 0.092406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071638 restraints weight = 47434.255| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 4.13 r_work: 0.3495 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11138 Z= 0.188 Angle : 0.593 8.802 15096 Z= 0.321 Chirality : 0.044 0.397 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.236 156.231 1752 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 2.74 % Allowed : 18.89 % Favored : 78.38 % 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: -1.11 (0.24), residues: 1226 helix: 0.63 (0.23), residues: 543 sheet: -1.33 (0.49), residues: 111 loop : -2.01 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.016 0.002 TYR A 659 PHE 0.020 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 covalent geometry : bond 0.00419 (11138) covalent geometry : angle 0.59313 (15096) hydrogen bonds : bond 0.05103 ( 428) hydrogen bonds : angle 4.96946 ( 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 74 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8413 (mm) cc_final: 0.8082 (tp) REVERT: A 178 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 374 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 740 ARG cc_start: 0.7225 (mmt180) cc_final: 0.6996 (tpm170) REVERT: A 1061 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6660 (p90) outliers start: 31 outliers final: 23 residues processed: 70 average time/residue: 0.0771 time to fit residues: 8.7227 Evaluate side-chains 69 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain A residue 309 GLN 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 633 MET 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 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1081 PHE Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1217 MET 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 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 ASN A1056 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.093636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.073113 restraints weight = 48429.453| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.26 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11138 Z= 0.105 Angle : 0.530 9.035 15096 Z= 0.285 Chirality : 0.041 0.371 1645 Planarity : 0.003 0.033 1829 Dihedral : 13.151 156.153 1752 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 2.03 % Allowed : 19.51 % 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: -0.93 (0.24), residues: 1226 helix: 0.76 (0.23), residues: 543 sheet: -1.31 (0.47), residues: 115 loop : -1.88 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 921 TYR 0.012 0.001 TYR A 450 PHE 0.019 0.001 PHE A 880 TRP 0.017 0.001 TRP A1142 HIS 0.007 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00213 (11138) covalent geometry : angle 0.52953 (15096) hydrogen bonds : bond 0.03966 ( 428) hydrogen bonds : angle 4.63463 ( 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 69 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8464 (mm) cc_final: 0.8125 (tp) REVERT: A 178 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: A 374 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7727 (tt) REVERT: A 740 ARG cc_start: 0.7172 (mmt180) cc_final: 0.6964 (tpm170) REVERT: A 1061 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.6526 (p90) REVERT: A 1195 ILE cc_start: 0.6856 (mm) cc_final: 0.6644 (mm) outliers start: 23 outliers final: 20 residues processed: 65 average time/residue: 0.0822 time to fit residues: 8.4448 Evaluate side-chains 65 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 242 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 633 MET 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 1043 ASN Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1061 PHE Chi-restraints excluded: chain A residue 1081 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: 5.9990 chunk 11 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 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 = 0.4112 r_free = 0.4112 target = 0.093553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.073045 restraints weight = 49250.389| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.20 r_work: 0.3549 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 11138 Z= 0.183 Angle : 0.822 59.155 15096 Z= 0.497 Chirality : 0.045 0.687 1645 Planarity : 0.004 0.090 1829 Dihedral : 13.170 156.146 1752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 19.68 % Favored : 78.20 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.95 (0.24), residues: 1226 helix: 0.75 (0.23), residues: 543 sheet: -1.29 (0.47), residues: 115 loop : -1.91 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 921 TYR 0.013 0.001 TYR A1228 PHE 0.018 0.001 PHE A 880 TRP 0.015 0.001 TRP A1142 HIS 0.007 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00352 (11138) covalent geometry : angle 0.82231 (15096) hydrogen bonds : bond 0.04022 ( 428) hydrogen bonds : angle 4.65445 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.90 seconds wall clock time: 50 minutes 35.76 seconds (3035.76 seconds total)