Starting phenix.real_space_refine on Wed Aug 5 11:20:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czb_46409/08_2026/9czb_46409.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 5897 2.51 5 N 1540 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9246 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 9246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9246 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 1143} Chain breaks: 7 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 4, 'ASN:plan1': 12, 'ASP:plan': 8, 'ARG:plan': 5, 'TYR:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 185 Time building chain proxies: 1.83, per 1000 atoms: 0.20 Number of scatterers: 9246 At special positions: 0 Unit cell: (94.56, 115.048, 124.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1787 8.00 N 1540 7.00 C 5897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 294.4 milliseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 19 sheets defined 34.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.869A pdb=" N HIS B 56 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 96 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 205 through 223 removed outlier: 3.602A pdb=" N THR B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 257 through 263 removed outlier: 3.503A pdb=" N ASN B 261 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 288 removed outlier: 3.823A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 298 through 307 removed outlier: 4.005A pdb=" N VAL B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 377 through 388 removed outlier: 3.723A pdb=" N VAL B 382 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN B 383 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLY B 386 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.880A pdb=" N TYR B 443 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.954A pdb=" N ASN B 447 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.101A pdb=" N TYR B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 571 through 588 Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.549A pdb=" N ALA B 609 " --> pdb=" O TYR B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 660 through 693 removed outlier: 3.660A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 725 removed outlier: 3.542A pdb=" N PHE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 725 " --> pdb=" O SER B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 733 removed outlier: 3.939A pdb=" N GLU B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 781 removed outlier: 3.773A pdb=" N ASN B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 760 " --> pdb=" O ASN B 756 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE B 761 " --> pdb=" O ASN B 757 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 762 " --> pdb=" O ILE B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 800 Processing helix chain 'B' and resid 800 through 805 removed outlier: 3.703A pdb=" N LEU B 804 " --> pdb=" O HIS B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 820 Processing helix chain 'B' and resid 1057 through 1066 Processing helix chain 'B' and resid 1223 through 1226 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 4.291A pdb=" N GLU B 133 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 36 removed outlier: 5.839A pdb=" N ASN B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 41 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP B 40 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE B 149 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.754A pdb=" N SER B 191 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B 356 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 233 Processing sheet with id=AA7, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AA8, first strand: chain 'B' and resid 424 through 430 removed outlier: 8.634A pdb=" N HIS B 512 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG B 410 " --> pdb=" O HIS B 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 536 through 538 Processing sheet with id=AB1, first strand: chain 'B' and resid 591 through 592 removed outlier: 3.526A pdb=" N SER B 591 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 861 through 864 removed outlier: 3.539A pdb=" N ARG B 856 " --> pdb=" O VAL B 863 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B1049 " --> pdb=" O VAL B 852 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN B 854 " --> pdb=" O PHE B1047 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE B1047 " --> pdb=" O ASN B 854 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ARG B 856 " --> pdb=" O ARG B1045 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N ARG B1045 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 17.389A pdb=" N LYS B 858 " --> pdb=" O GLY B1043 " (cutoff:3.500A) removed outlier: 20.101A pdb=" N GLY B1043 " --> pdb=" O LYS B 858 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 861 through 864 removed outlier: 3.539A pdb=" N ARG B 856 " --> pdb=" O VAL B 863 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B1049 " --> pdb=" O VAL B 852 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN B 854 " --> pdb=" O PHE B1047 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE B1047 " --> pdb=" O ASN B 854 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ARG B 856 " --> pdb=" O ARG B1045 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N ARG B1045 " --> pdb=" O ARG B 856 " (cutoff:3.500A) removed outlier: 17.389A pdb=" N LYS B 858 " --> pdb=" O GLY B1043 " (cutoff:3.500A) removed outlier: 20.101A pdb=" N GLY B1043 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B1044 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG B 922 " --> pdb=" O ILE B1044 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR B1046 " --> pdb=" O TRP B 920 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP B 920 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 916 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 915 " --> pdb=" O ASN B 997 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER B1003 " --> pdb=" O GLN B1014 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN B1014 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B1005 " --> pdb=" O ILE B1012 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 871 through 876 removed outlier: 3.652A pdb=" N ILE B 900 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B1029 " --> pdb=" O ILE B 900 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 910 Processing sheet with id=AB6, first strand: chain 'B' and resid 937 through 943 removed outlier: 7.230A pdb=" N VAL B 952 " --> pdb=" O ILE B 939 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN B 941 " --> pdb=" O TRP B 950 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TRP B 950 " --> pdb=" O ASN B 941 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 958 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 963 " --> pdb=" O GLN B 971 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1087 through 1090 Processing sheet with id=AB8, first strand: chain 'B' and resid 1099 through 1100 Processing sheet with id=AB9, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AC1, first strand: chain 'B' and resid 1126 through 1130 removed outlier: 4.197A pdb=" N LYS B1126 " --> pdb=" O VAL B1153 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP B1146 " --> pdb=" O MET B1190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B1190 " --> pdb=" O ASP B1146 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B1150 " --> pdb=" O GLN B1186 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N GLN B1186 " --> pdb=" O ILE B1150 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET B1199 " --> pdb=" O LEU B1211 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU B1211 " --> pdb=" O MET B1199 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B1201 " --> pdb=" O ILE B1209 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE B1150 " --> pdb=" O LEU B1162 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N ALA B1164 " --> pdb=" O VAL B1148 " (cutoff:3.500A) removed outlier: 15.122A pdb=" N VAL B1148 " --> pdb=" O ALA B1164 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3027 1.34 - 1.46: 1456 1.46 - 1.57: 4902 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9421 Sorted by residual: bond pdb=" CA MET B 704 " pdb=" CB MET B 704 " ideal model delta sigma weight residual 1.528 1.554 -0.026 1.56e-02 4.11e+03 2.75e+00 bond pdb=" N LYS B 89 " pdb=" CA LYS B 89 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.19e-02 7.06e+03 2.66e+00 bond pdb=" CG LEU B 84 " pdb=" CD2 LEU B 84 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" CB MET B 755 " pdb=" CG MET B 755 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" C GLU B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.359 -0.026 2.34e-02 1.83e+03 1.19e+00 ... (remaining 9416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 12642 1.97 - 3.93: 137 3.93 - 5.90: 11 5.90 - 7.87: 2 7.87 - 9.83: 2 Bond angle restraints: 12794 Sorted by residual: angle pdb=" N ILE B1017 " pdb=" CA ILE B1017 " pdb=" C ILE B1017 " ideal model delta sigma weight residual 113.20 109.36 3.84 9.60e-01 1.09e+00 1.60e+01 angle pdb=" CB MET B 814 " pdb=" CG MET B 814 " pdb=" SD MET B 814 " ideal model delta sigma weight residual 112.70 122.53 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA MET B 814 " pdb=" CB MET B 814 " pdb=" CG MET B 814 " ideal model delta sigma weight residual 114.10 120.09 -5.99 2.00e+00 2.50e-01 8.97e+00 angle pdb=" CA ILE B 408 " pdb=" CB ILE B 408 " pdb=" CG1 ILE B 408 " ideal model delta sigma weight residual 110.40 115.40 -5.00 1.70e+00 3.46e-01 8.64e+00 angle pdb=" CB MET B 755 " pdb=" CG MET B 755 " pdb=" SD MET B 755 " ideal model delta sigma weight residual 112.70 104.75 7.95 3.00e+00 1.11e-01 7.02e+00 ... (remaining 12789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4773 17.74 - 35.48: 642 35.48 - 53.22: 182 53.22 - 70.96: 31 70.96 - 88.70: 11 Dihedral angle restraints: 5639 sinusoidal: 2166 harmonic: 3473 Sorted by residual: dihedral pdb=" CA LYS B 356 " pdb=" C LYS B 356 " pdb=" N TYR B 357 " pdb=" CA TYR B 357 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASN B 698 " pdb=" CB ASN B 698 " pdb=" CG ASN B 698 " pdb=" OD1 ASN B 698 " ideal model delta sinusoidal sigma weight residual -90.00 -163.96 73.96 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASN B 884 " pdb=" CB ASN B 884 " pdb=" CG ASN B 884 " pdb=" OD1 ASN B 884 " ideal model delta sinusoidal sigma weight residual -90.00 -159.91 69.91 2 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 861 0.031 - 0.061: 363 0.061 - 0.092: 133 0.092 - 0.122: 91 0.122 - 0.153: 7 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CB THR B 273 " pdb=" CA THR B 273 " pdb=" OG1 THR B 273 " pdb=" CG2 THR B 273 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CB ILE B1059 " pdb=" CA ILE B1059 " pdb=" CG1 ILE B1059 " pdb=" CG2 ILE B1059 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE B1071 " pdb=" N ILE B1071 " pdb=" C ILE B1071 " pdb=" CB ILE B1071 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1452 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 705 " 0.017 2.00e-02 2.50e+03 2.06e-02 8.50e+00 pdb=" CG TYR B 705 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 705 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 705 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 705 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 705 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 705 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 705 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 154 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 155 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 57 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 58 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " 0.027 5.00e-02 4.00e+02 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 802 2.74 - 3.28: 9487 3.28 - 3.82: 15712 3.82 - 4.36: 18657 4.36 - 4.90: 32385 Nonbonded interactions: 77043 Sorted by model distance: nonbonded pdb=" O LYS B 225 " pdb=" OG1 THR B 229 " model vdw 2.199 3.040 nonbonded pdb=" O ALA B 587 " pdb=" OH TYR B 605 " model vdw 2.208 3.040 nonbonded pdb=" O ILE B 448 " pdb=" NZ LYS B 677 " model vdw 2.211 3.120 nonbonded pdb=" O PHE B 684 " pdb=" ND2 ASN B 688 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS B1004 " pdb=" OE2 GLU B1053 " model vdw 2.236 3.120 ... (remaining 77038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 2.370 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9422 Z= 0.144 Angle : 0.527 9.834 12796 Z= 0.286 Chirality : 0.044 0.153 1455 Planarity : 0.004 0.049 1659 Dihedral : 17.586 88.700 3392 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.79 % Allowed : 29.94 % Favored : 64.27 % 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: -0.50 (0.25), residues: 1161 helix: 0.94 (0.27), residues: 363 sheet: -0.75 (0.41), residues: 174 loop : -0.96 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 45 TYR 0.050 0.001 TYR B 705 PHE 0.029 0.002 PHE B 975 TRP 0.023 0.002 TRP B 990 HIS 0.002 0.000 HIS B1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9421) covalent geometry : angle 0.52715 / 0.29 (12794) SS BOND : bond 0.00127 / 0.08 ( 1) SS BOND : angle 0.32003 / 0.17 ( 2) hydrogen bonds : bond 0.18891 / 13.32 ( 379) hydrogen bonds : angle 7.42403 / 5.31 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 98 time to evaluate : 0.359 Fit side-chains REVERT: B 29 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: B 124 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: B 349 GLN cc_start: 0.6167 (OUTLIER) cc_final: 0.5862 (pt0) REVERT: B 526 GLN cc_start: 0.6202 (mp10) cc_final: 0.5428 (mt0) REVERT: B 799 GLN cc_start: 0.7581 (mm110) cc_final: 0.7107 (mm-40) REVERT: B 911 LYS cc_start: 0.6928 (tppt) cc_final: 0.6573 (mmmt) outliers start: 58 outliers final: 52 residues processed: 149 average time/residue: 0.0743 time to fit residues: 16.8165 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 527 LYS Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 850 SER Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 916 SER Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain B residue 1017 ILE Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1055 ASP Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1113 SER Chi-restraints excluded: chain B residue 1151 ASN Chi-restraints excluded: chain B residue 1187 VAL Chi-restraints excluded: chain B residue 1190 MET Chi-restraints excluded: chain B residue 1244 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN B 195 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN B 925 ASN B 957 ASN ** B 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1196 ASN B1241 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.222268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.213281 restraints weight = 9858.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.197057 restraints weight = 16928.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.195624 restraints weight = 13882.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.196342 restraints weight = 12844.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.196923 restraints weight = 10700.715| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9422 Z= 0.269 Angle : 0.639 9.417 12796 Z= 0.344 Chirality : 0.048 0.154 1455 Planarity : 0.004 0.051 1659 Dihedral : 8.785 59.075 1342 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 9.48 % Allowed : 25.55 % Favored : 64.97 % 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: -0.99 (0.24), residues: 1161 helix: 0.19 (0.26), residues: 376 sheet: -1.23 (0.37), residues: 198 loop : -0.94 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 45 TYR 0.024 0.002 TYR B 69 PHE 0.027 0.003 PHE B 554 TRP 0.016 0.002 TRP B 689 HIS 0.002 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 ( 9421) covalent geometry : angle 0.63930 / 0.34 (12794) SS BOND : bond 0.00124 / 0.08 ( 1) SS BOND : angle 0.13962 / 0.07 ( 2) hydrogen bonds : bond 0.04713 / 3.32 ( 379) hydrogen bonds : angle 5.79928 / 4.08 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 112 time to evaluate : 0.255 Fit side-chains REVERT: B 29 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: B 82 ARG cc_start: 0.4564 (OUTLIER) cc_final: 0.4323 (ptt-90) REVERT: B 124 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: B 250 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6205 (tp30) REVERT: B 526 GLN cc_start: 0.5902 (mp10) cc_final: 0.5271 (mt0) REVERT: B 799 GLN cc_start: 0.7520 (mm110) cc_final: 0.6735 (mm-40) REVERT: B 1020 LEU cc_start: 0.3919 (OUTLIER) cc_final: 0.3604 (mp) REVERT: B 1073 LYS cc_start: 0.4948 (OUTLIER) cc_final: 0.4228 (mmtm) outliers start: 95 outliers final: 53 residues processed: 189 average time/residue: 0.0731 time to fit residues: 20.3568 Evaluate side-chains 169 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 110 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 758 ILE Chi-restraints excluded: chain B residue 765 SER Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 921 VAL Chi-restraints excluded: chain B residue 925 ASN Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1017 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1190 MET Chi-restraints excluded: chain B residue 1199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN B 694 ASN B 854 ASN B 910 ASN B 957 ASN ** B1096 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.229100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.220306 restraints weight = 9651.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.206831 restraints weight = 14720.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.205032 restraints weight = 13490.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.205266 restraints weight = 13267.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.205591 restraints weight = 10704.942| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9422 Z= 0.119 Angle : 0.504 8.849 12796 Z= 0.269 Chirality : 0.044 0.141 1455 Planarity : 0.003 0.050 1659 Dihedral : 7.453 59.184 1309 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.89 % Allowed : 28.84 % Favored : 66.27 % 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: -0.43 (0.25), residues: 1161 helix: 0.87 (0.27), residues: 369 sheet: -0.62 (0.41), residues: 162 loop : -0.87 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 700 TYR 0.011 0.001 TYR B 796 PHE 0.019 0.001 PHE B 975 TRP 0.018 0.002 TRP B 990 HIS 0.001 0.000 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9421) covalent geometry : angle 0.50360 / 0.27 (12794) SS BOND : bond 0.00098 / 0.07 ( 1) SS BOND : angle 0.17007 / 0.09 ( 2) hydrogen bonds : bond 0.03591 / 2.54 ( 379) hydrogen bonds : angle 5.05753 / 3.56 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: B 124 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6782 (m-10) REVERT: B 375 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: B 522 TYR cc_start: 0.3919 (m-80) cc_final: 0.3553 (m-80) REVERT: B 526 GLN cc_start: 0.5666 (mp10) cc_final: 0.5294 (mt0) REVERT: B 799 GLN cc_start: 0.7286 (mm110) cc_final: 0.6453 (mm-40) REVERT: B 930 ILE cc_start: 0.7982 (tt) cc_final: 0.7617 (tt) REVERT: B 1011 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6822 (tt) REVERT: B 1073 LYS cc_start: 0.4391 (OUTLIER) cc_final: 0.3657 (mmtm) outliers start: 49 outliers final: 28 residues processed: 149 average time/residue: 0.0861 time to fit residues: 18.8307 Evaluate side-chains 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 933 VAL Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1110 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN B 711 GLN B 910 ASN ** B 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1096 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.227239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.218369 restraints weight = 9789.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206235 restraints weight = 18628.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.203717 restraints weight = 15726.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.204285 restraints weight = 13660.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.204617 restraints weight = 11297.336| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9422 Z= 0.155 Angle : 0.520 9.918 12796 Z= 0.278 Chirality : 0.045 0.142 1455 Planarity : 0.004 0.051 1659 Dihedral : 6.664 57.931 1288 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.09 % Allowed : 28.34 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1161 helix: 0.80 (0.27), residues: 369 sheet: -0.56 (0.41), residues: 162 loop : -0.88 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.025 0.001 TYR B 705 PHE 0.016 0.002 PHE B 554 TRP 0.021 0.002 TRP B 990 HIS 0.001 0.000 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 9421) covalent geometry : angle 0.51988 / 0.28 (12794) SS BOND : bond 0.00069 / 0.05 ( 1) SS BOND : angle 0.18508 / 0.10 ( 2) hydrogen bonds : bond 0.03656 / 2.56 ( 379) hydrogen bonds : angle 5.00744 / 3.53 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 110 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: B 124 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: B 526 GLN cc_start: 0.5913 (mp10) cc_final: 0.5588 (mt0) REVERT: B 799 GLN cc_start: 0.7272 (mm110) cc_final: 0.6522 (mm-40) REVERT: B 855 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7573 (ttp) REVERT: B 930 ILE cc_start: 0.7967 (tt) cc_final: 0.7579 (tt) REVERT: B 1020 LEU cc_start: 0.3727 (OUTLIER) cc_final: 0.3414 (mp) REVERT: B 1073 LYS cc_start: 0.4538 (OUTLIER) cc_final: 0.3704 (mmtm) outliers start: 51 outliers final: 35 residues processed: 151 average time/residue: 0.0873 time to fit residues: 18.9966 Evaluate side-chains 144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 680 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1092 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 0.0060 chunk 112 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 114 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN B 988 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.231747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.223255 restraints weight = 9690.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.208553 restraints weight = 14836.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.207318 restraints weight = 12828.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.208099 restraints weight = 11568.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.208147 restraints weight = 9905.316| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9422 Z= 0.103 Angle : 0.476 10.258 12796 Z= 0.252 Chirality : 0.043 0.150 1455 Planarity : 0.003 0.051 1659 Dihedral : 6.184 59.036 1283 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.19 % Allowed : 29.14 % Favored : 66.67 % 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: -0.18 (0.25), residues: 1161 helix: 1.10 (0.27), residues: 370 sheet: -0.45 (0.41), residues: 160 loop : -0.75 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.016 0.001 TYR B 705 PHE 0.015 0.001 PHE B 975 TRP 0.018 0.001 TRP B 990 HIS 0.002 0.000 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9421) covalent geometry : angle 0.47575 / 0.25 (12794) SS BOND : bond 0.00084 / 0.06 ( 1) SS BOND : angle 0.19606 / 0.13 ( 2) hydrogen bonds : bond 0.03198 / 2.23 ( 379) hydrogen bonds : angle 4.65157 / 3.27 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: B 124 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: B 205 ASP cc_start: 0.7206 (m-30) cc_final: 0.6672 (m-30) REVERT: B 250 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6256 (tp30) REVERT: B 522 TYR cc_start: 0.4004 (m-80) cc_final: 0.3683 (m-80) REVERT: B 523 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2093 (tp) REVERT: B 526 GLN cc_start: 0.5690 (mp10) cc_final: 0.5490 (mt0) REVERT: B 799 GLN cc_start: 0.7501 (mm110) cc_final: 0.6867 (mm-40) REVERT: B 855 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7433 (ttp) REVERT: B 930 ILE cc_start: 0.7799 (tt) cc_final: 0.7446 (tt) REVERT: B 1073 LYS cc_start: 0.4163 (OUTLIER) cc_final: 0.3351 (mmtm) outliers start: 42 outliers final: 17 residues processed: 142 average time/residue: 0.0827 time to fit residues: 17.2245 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1073 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.224448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215486 restraints weight = 9797.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.200120 restraints weight = 16045.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.199316 restraints weight = 12737.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.200414 restraints weight = 11169.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.200517 restraints weight = 9742.262| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9422 Z= 0.210 Angle : 0.579 10.564 12796 Z= 0.308 Chirality : 0.046 0.188 1455 Planarity : 0.004 0.050 1659 Dihedral : 6.048 57.629 1271 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.49 % Allowed : 28.54 % Favored : 65.97 % 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: -0.59 (0.25), residues: 1161 helix: 0.58 (0.27), residues: 375 sheet: -0.60 (0.41), residues: 172 loop : -0.91 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 45 TYR 0.021 0.002 TYR B 705 PHE 0.022 0.002 PHE B 975 TRP 0.018 0.002 TRP B 990 HIS 0.002 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 9421) covalent geometry : angle 0.57873 / 0.31 (12794) SS BOND : bond 0.00066 / 0.04 ( 1) SS BOND : angle 0.23549 / 0.13 ( 2) hydrogen bonds : bond 0.03896 / 2.70 ( 379) hydrogen bonds : angle 5.03671 / 3.54 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 105 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 124 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6779 (m-10) REVERT: B 250 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6236 (tp30) REVERT: B 357 TYR cc_start: 0.6249 (m-80) cc_final: 0.4867 (m-80) REVERT: B 402 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5628 (ttt90) REVERT: B 799 GLN cc_start: 0.7653 (mm110) cc_final: 0.7076 (mm-40) REVERT: B 855 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7695 (ttp) REVERT: B 930 ILE cc_start: 0.7760 (tt) cc_final: 0.7423 (tt) REVERT: B 959 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5933 (mp) REVERT: B 1011 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6692 (tt) REVERT: B 1020 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3498 (mp) REVERT: B 1073 LYS cc_start: 0.4558 (OUTLIER) cc_final: 0.3700 (mmtm) outliers start: 55 outliers final: 31 residues processed: 147 average time/residue: 0.0753 time to fit residues: 16.7969 Evaluate side-chains 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 852 VAL Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1011 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1110 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.231180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.223029 restraints weight = 9704.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.207021 restraints weight = 13665.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.207993 restraints weight = 12860.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.208113 restraints weight = 11246.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.208507 restraints weight = 9355.802| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9422 Z= 0.106 Angle : 0.495 11.902 12796 Z= 0.259 Chirality : 0.044 0.199 1455 Planarity : 0.003 0.051 1659 Dihedral : 5.707 59.545 1271 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.19 % Allowed : 30.94 % Favored : 65.87 % 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: -0.21 (0.25), residues: 1161 helix: 1.09 (0.27), residues: 370 sheet: -0.43 (0.41), residues: 165 loop : -0.78 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 999 TYR 0.016 0.001 TYR B 705 PHE 0.018 0.001 PHE B 975 TRP 0.030 0.002 TRP B 990 HIS 0.001 0.000 HIS B1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9421) covalent geometry : angle 0.49538 / 0.26 (12794) SS BOND : bond 0.00096 / 0.06 ( 1) SS BOND : angle 0.18028 / 0.10 ( 2) hydrogen bonds : bond 0.03182 / 2.20 ( 379) hydrogen bonds : angle 4.56104 / 3.20 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: B 124 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: B 250 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6329 (tp30) REVERT: B 357 TYR cc_start: 0.6133 (m-80) cc_final: 0.4589 (m-80) REVERT: B 522 TYR cc_start: 0.3951 (m-80) cc_final: 0.3651 (m-80) REVERT: B 523 LEU cc_start: 0.2977 (OUTLIER) cc_final: 0.2369 (tp) REVERT: B 799 GLN cc_start: 0.7406 (mm110) cc_final: 0.6894 (mm-40) REVERT: B 816 THR cc_start: 0.7680 (m) cc_final: 0.6859 (m) REVERT: B 855 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7441 (ttp) REVERT: B 930 ILE cc_start: 0.7728 (tt) cc_final: 0.7395 (tt) REVERT: B 1073 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3296 (mmtm) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.0719 time to fit residues: 13.8760 Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 855 MET Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1110 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 115 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN B 934 ASN ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.230357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.221610 restraints weight = 9656.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.206923 restraints weight = 14147.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.207424 restraints weight = 12786.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.207308 restraints weight = 10985.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.207408 restraints weight = 10006.105| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9422 Z= 0.118 Angle : 0.498 11.854 12796 Z= 0.263 Chirality : 0.044 0.166 1455 Planarity : 0.003 0.051 1659 Dihedral : 5.708 59.582 1271 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.69 % Allowed : 30.44 % Favored : 65.87 % 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: -0.12 (0.25), residues: 1161 helix: 1.21 (0.27), residues: 369 sheet: -0.34 (0.41), residues: 165 loop : -0.77 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.017 0.001 TYR B 705 PHE 0.033 0.001 PHE B 975 TRP 0.036 0.002 TRP B 990 HIS 0.001 0.000 HIS B1228 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9421) covalent geometry : angle 0.49755 / 0.26 (12794) SS BOND : bond 0.00039 / 0.03 ( 1) SS BOND : angle 0.10633 / 0.06 ( 2) hydrogen bonds : bond 0.03278 / 2.27 ( 379) hydrogen bonds : angle 4.57059 / 3.21 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.350 Fit side-chains REVERT: B 29 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: B 124 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 250 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6233 (tp30) REVERT: B 357 TYR cc_start: 0.6128 (m-80) cc_final: 0.4477 (m-80) REVERT: B 434 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7038 (mt) REVERT: B 513 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5862 (m-30) REVERT: B 799 GLN cc_start: 0.7393 (mm110) cc_final: 0.6890 (mm-40) REVERT: B 930 ILE cc_start: 0.7687 (tt) cc_final: 0.7395 (tt) REVERT: B 959 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.5901 (mp) outliers start: 37 outliers final: 26 residues processed: 130 average time/residue: 0.0702 time to fit residues: 14.0400 Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 934 ASN Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1071 ILE Chi-restraints excluded: chain B residue 1110 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 934 ASN ** B1028 ASN ** 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 = 0.4433 r_free = 0.4433 target = 0.222416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.213401 restraints weight = 9731.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.195829 restraints weight = 16648.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.197133 restraints weight = 13470.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197763 restraints weight = 10906.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.197924 restraints weight = 10396.565| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9422 Z= 0.260 Angle : 0.654 12.174 12796 Z= 0.347 Chirality : 0.048 0.183 1455 Planarity : 0.004 0.052 1659 Dihedral : 6.095 57.754 1269 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.79 % Allowed : 29.74 % Favored : 66.47 % 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 (0.24), residues: 1161 helix: 0.38 (0.26), residues: 375 sheet: -0.91 (0.38), residues: 187 loop : -0.99 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 944 TYR 0.024 0.002 TYR B 912 PHE 0.036 0.003 PHE B 975 TRP 0.050 0.003 TRP B 990 HIS 0.008 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 ( 9421) covalent geometry : angle 0.65369 / 0.35 (12794) SS BOND : bond 0.00046 / 0.03 ( 1) SS BOND : angle 0.21540 / 0.13 ( 2) hydrogen bonds : bond 0.04239 / 2.92 ( 379) hydrogen bonds : angle 5.14310 / 3.61 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.218 Fit side-chains REVERT: B 124 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: B 250 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6196 (tp30) REVERT: B 357 TYR cc_start: 0.6125 (m-80) cc_final: 0.4337 (m-80) REVERT: B 402 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.5613 (ttt90) REVERT: B 799 GLN cc_start: 0.7552 (mm110) cc_final: 0.7079 (mm-40) REVERT: B 930 ILE cc_start: 0.7732 (tt) cc_final: 0.7399 (tt) REVERT: B 959 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.5874 (mt) outliers start: 38 outliers final: 29 residues processed: 137 average time/residue: 0.0674 time to fit residues: 14.1799 Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 934 ASN Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN B 934 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.228547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.207255 restraints weight = 9679.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207092 restraints weight = 9208.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207091 restraints weight = 8556.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207091 restraints weight = 8554.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207091 restraints weight = 8553.000| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9422 Z= 0.120 Angle : 0.533 12.235 12796 Z= 0.280 Chirality : 0.044 0.166 1455 Planarity : 0.003 0.051 1659 Dihedral : 5.748 59.657 1269 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.49 % Allowed : 30.24 % Favored : 66.27 % 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: -0.33 (0.25), residues: 1161 helix: 0.95 (0.27), residues: 369 sheet: -0.49 (0.40), residues: 175 loop : -0.84 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.017 0.001 TYR B 705 PHE 0.027 0.001 PHE B 975 TRP 0.056 0.002 TRP B 990 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9421) covalent geometry : angle 0.53308 / 0.28 (12794) SS BOND : bond 0.00100 / 0.07 ( 1) SS BOND : angle 0.28160 / 0.15 ( 2) hydrogen bonds : bond 0.03357 / 2.35 ( 379) hydrogen bonds : angle 4.68412 / 3.29 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: B 124 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: B 250 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: B 357 TYR cc_start: 0.6100 (m-80) cc_final: 0.4373 (m-80) REVERT: B 799 GLN cc_start: 0.7177 (mm110) cc_final: 0.6691 (mm-40) REVERT: B 897 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6730 (pt0) REVERT: B 930 ILE cc_start: 0.7661 (tt) cc_final: 0.7332 (tt) REVERT: B 959 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5813 (mp) REVERT: B 971 GLN cc_start: 0.6146 (tp-100) cc_final: 0.5676 (tp-100) outliers start: 35 outliers final: 26 residues processed: 134 average time/residue: 0.0717 time to fit residues: 14.5189 Evaluate side-chains 134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 774 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 897 GLU Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 959 ILE Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1110 ASN Chi-restraints excluded: chain B residue 1187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 0.0020 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 ASN ** B1096 ASN ** 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 = 0.4498 r_free = 0.4498 target = 0.229963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.221507 restraints weight = 9671.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.208614 restraints weight = 15600.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.204909 restraints weight = 14057.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.206297 restraints weight = 11673.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.206566 restraints weight = 9479.260| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9422 Z= 0.116 Angle : 0.518 11.788 12796 Z= 0.272 Chirality : 0.044 0.160 1455 Planarity : 0.003 0.051 1659 Dihedral : 5.619 59.552 1269 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.39 % Allowed : 30.54 % Favored : 66.07 % 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: -0.21 (0.25), residues: 1161 helix: 1.10 (0.27), residues: 369 sheet: -0.45 (0.41), residues: 165 loop : -0.79 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.015 0.001 TYR B 705 PHE 0.024 0.001 PHE B 975 TRP 0.052 0.002 TRP B 990 HIS 0.007 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9421) covalent geometry : angle 0.51850 / 0.27 (12794) SS BOND : bond 0.00224 / 0.15 ( 1) SS BOND : angle 0.26769 / 0.16 ( 2) hydrogen bonds : bond 0.03239 / 2.26 ( 379) hydrogen bonds : angle 4.57538 / 3.20 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1504.00 seconds wall clock time: 26 minutes 51.40 seconds (1611.40 seconds total)