Starting phenix.real_space_refine on Wed Mar 4 08:06:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuq_32838/03_2026/7wuq_32838.map" } resolution = 2.9 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5293 atoms to isotropic. 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 49 5.16 5 C 5090 2.51 5 N 1383 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1795 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 208} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2564 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 421 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2226 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7973 At special positions: 0 Unit cell: (93, 113, 87, 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 49 16.00 O 1451 8.00 N 1383 7.00 C 5090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.61 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.39 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.20 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: 0.59 Conformation dependent library (CDL) restraints added in 256.1 milliseconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 39.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.841A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.014A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.541A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.564A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.201A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.703A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.506A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.674A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.545A pdb=" N ALA N 56 " --> pdb=" O GLN N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'R' and resid 600 through 605 removed outlier: 3.532A pdb=" N ILE R 603 " --> pdb=" O SER R 600 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 645 removed outlier: 3.703A pdb=" N MET R 618 " --> pdb=" O PRO R 614 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 619 " --> pdb=" O SER R 615 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU R 630 " --> pdb=" O ILE R 626 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA R 644 " --> pdb=" O VAL R 640 " (cutoff:3.500A) Processing helix chain 'R' and resid 646 through 649 Processing helix chain 'R' and resid 651 through 676 removed outlier: 3.690A pdb=" N LYS R 655 " --> pdb=" O ASP R 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP R 674 " --> pdb=" O ILE R 670 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 716 removed outlier: 3.585A pdb=" N MET R 704 " --> pdb=" O SER R 700 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU R 707 " --> pdb=" O TRP R 703 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 716 " --> pdb=" O TYR R 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 725 through 735 removed outlier: 3.626A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 735 through 749 Processing helix chain 'R' and resid 750 through 753 removed outlier: 4.184A pdb=" N TYR R 753 " --> pdb=" O PRO R 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 750 through 753' Processing helix chain 'R' and resid 774 through 782 Processing helix chain 'R' and resid 782 through 795 removed outlier: 3.839A pdb=" N LEU R 792 " --> pdb=" O VAL R 788 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 810 removed outlier: 4.303A pdb=" N ILE R 807 " --> pdb=" O GLN R 803 " (cutoff:3.500A) Processing helix chain 'R' and resid 820 through 835 Processing helix chain 'R' and resid 836 through 842 removed outlier: 3.577A pdb=" N ALA R 841 " --> pdb=" O TRP R 838 " (cutoff:3.500A) Processing helix chain 'R' and resid 848 through 860 removed outlier: 3.509A pdb=" N MET R 853 " --> pdb=" O ASN R 849 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR R 854 " --> pdb=" O VAL R 850 " (cutoff:3.500A) Processing helix chain 'R' and resid 862 through 872 Processing helix chain 'R' and resid 875 through 885 removed outlier: 3.616A pdb=" N GLN R 881 " --> pdb=" O ASN R 877 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP R 882 " --> pdb=" O VAL R 878 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG R 883 " --> pdb=" O ARG R 879 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG R 884 " --> pdb=" O LYS R 880 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.533A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.662A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113 removed outlier: 6.284A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.568A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.696A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.970A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.574A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.696A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.549A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1020 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: 1.06 Time building geometry restraints manager: 0.85 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: 2448 1.34 - 1.46: 1823 1.46 - 1.58: 3797 1.58 - 1.70: 1 1.70 - 1.82: 68 Bond restraints: 8137 Sorted by residual: bond pdb=" CA ARG A 356 " pdb=" CB ARG A 356 " ideal model delta sigma weight residual 1.526 1.616 -0.090 1.76e-02 3.23e+03 2.59e+01 bond pdb=" CA CYS B 317 " pdb=" C CYS B 317 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.04e-02 9.25e+03 4.84e+00 bond pdb=" CA CYS B 103 " pdb=" C CYS B 103 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.34e-02 5.57e+03 4.71e+00 bond pdb=" CB THR B 243 " pdb=" CG2 THR B 243 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" N ALA B 104 " pdb=" CA ALA B 104 " ideal model delta sigma weight residual 1.456 1.434 0.023 1.21e-02 6.83e+03 3.57e+00 ... (remaining 8132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 10705 2.85 - 5.69: 259 5.69 - 8.54: 43 8.54 - 11.39: 5 11.39 - 14.23: 1 Bond angle restraints: 11013 Sorted by residual: angle pdb=" N ARG R 683 " pdb=" CA ARG R 683 " pdb=" C ARG R 683 " ideal model delta sigma weight residual 111.28 118.02 -6.74 1.09e+00 8.42e-01 3.82e+01 angle pdb=" N THR A 40 " pdb=" CA THR A 40 " pdb=" C THR A 40 " ideal model delta sigma weight residual 111.36 117.34 -5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" C ALA R 844 " pdb=" N TRP R 845 " pdb=" CA TRP R 845 " ideal model delta sigma weight residual 121.70 130.52 -8.82 1.80e+00 3.09e-01 2.40e+01 angle pdb=" CB MET N 34 " pdb=" CG MET N 34 " pdb=" SD MET N 34 " ideal model delta sigma weight residual 112.70 126.93 -14.23 3.00e+00 1.11e-01 2.25e+01 angle pdb=" N SER R 608 " pdb=" CA SER R 608 " pdb=" C SER R 608 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4357 17.82 - 35.64: 372 35.64 - 53.46: 70 53.46 - 71.28: 14 71.28 - 89.10: 8 Dihedral angle restraints: 4821 sinusoidal: 1893 harmonic: 2928 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N LYS A 34 " pdb=" CA LYS A 34 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 4818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1079 0.093 - 0.185: 149 0.185 - 0.278: 11 0.278 - 0.370: 3 0.370 - 0.463: 2 Chirality restraints: 1244 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA TRP R 845 " pdb=" N TRP R 845 " pdb=" C TRP R 845 " pdb=" CB TRP R 845 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CG LEU B 55 " pdb=" CB LEU B 55 " pdb=" CD1 LEU B 55 " pdb=" CD2 LEU B 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1241 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 652 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 653 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 653 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 653 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " -0.299 9.50e-02 1.11e+02 1.34e-01 1.23e+01 pdb=" NE ARG B 314 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 844 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ALA R 844 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA R 844 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP R 845 " -0.020 2.00e-02 2.50e+03 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 737 2.74 - 3.28: 8129 3.28 - 3.82: 14543 3.82 - 4.36: 17975 4.36 - 4.90: 29326 Nonbonded interactions: 70710 Sorted by model distance: nonbonded pdb=" O TRP R 845 " pdb=" N ASN R 849 " model vdw 2.204 3.120 nonbonded pdb=" O GLY R 754 " pdb=" ND2 ASN R 773 " model vdw 2.240 3.120 nonbonded pdb=" C TRP R 845 " pdb=" CD PRO R 847 " model vdw 2.248 3.670 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.256 3.040 nonbonded pdb=" O GLY R 754 " pdb=" OD1 ASN R 773 " model vdw 2.267 3.040 ... (remaining 70705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.010 0.575 8140 Z= 0.480 Angle : 1.078 14.234 11019 Z= 0.602 Chirality : 0.066 0.463 1244 Planarity : 0.009 0.134 1394 Dihedral : 14.173 89.100 2918 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.47 % Allowed : 1.87 % Favored : 97.67 % Cbeta Deviations : 0.11 % 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: -3.00 (0.24), residues: 987 helix: -2.27 (0.21), residues: 347 sheet: -2.06 (0.38), residues: 157 loop : -1.62 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 314 TYR 0.021 0.002 TYR N 115 PHE 0.038 0.003 PHE R 730 TRP 0.031 0.004 TRP B 339 HIS 0.021 0.004 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 8137) covalent geometry : angle 1.06095 (11013) SS BOND : bond 0.40255 ( 3) SS BOND : angle 8.24799 ( 6) hydrogen bonds : bond 0.25418 ( 363) hydrogen bonds : angle 9.92899 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 VAL cc_start: 0.4845 (p) cc_final: 0.4606 (p) REVERT: B 314 ARG cc_start: 0.7910 (tmm-80) cc_final: 0.7646 (ptm160) REVERT: G 38 MET cc_start: 0.5765 (mtp) cc_final: 0.5322 (mtm) REVERT: R 646 GLU cc_start: 0.7088 (tp30) cc_final: 0.6817 (tp30) outliers start: 4 outliers final: 1 residues processed: 181 average time/residue: 0.3676 time to fit residues: 72.3335 Evaluate side-chains 143 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 618 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 41 HIS B 155 ASN B 259 GLN B 295 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 803 GLN R 849 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.202772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174421 restraints weight = 9158.715| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.98 r_work: 0.3890 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8140 Z= 0.154 Angle : 0.622 7.278 11019 Z= 0.334 Chirality : 0.043 0.140 1244 Planarity : 0.005 0.071 1394 Dihedral : 5.399 26.954 1102 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.52 % Allowed : 12.49 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.25), residues: 987 helix: -0.27 (0.26), residues: 344 sheet: -2.13 (0.37), residues: 172 loop : -1.33 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.011 0.001 TYR R 726 PHE 0.018 0.002 PHE R 730 TRP 0.017 0.002 TRP B 211 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8137) covalent geometry : angle 0.62159 (11013) SS BOND : bond 0.00795 ( 3) SS BOND : angle 0.96197 ( 6) hydrogen bonds : bond 0.05117 ( 363) hydrogen bonds : angle 6.16830 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6946 (tp30) cc_final: 0.6189 (tt0) REVERT: B 46 ARG cc_start: 0.7379 (mmm160) cc_final: 0.7061 (mmm-85) REVERT: R 617 MET cc_start: 0.7747 (tpt) cc_final: 0.7434 (tpt) REVERT: R 682 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7681 (p) outliers start: 13 outliers final: 2 residues processed: 181 average time/residue: 0.4229 time to fit residues: 82.2593 Evaluate side-chains 148 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 792 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 41 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 88 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 668 ASN R 849 ASN R 860 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164021 restraints weight = 8912.227| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.03 r_work: 0.3747 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8140 Z= 0.172 Angle : 0.605 7.512 11019 Z= 0.320 Chirality : 0.043 0.171 1244 Planarity : 0.004 0.060 1394 Dihedral : 5.076 23.896 1099 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.92 % Allowed : 15.87 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 987 helix: 0.58 (0.27), residues: 337 sheet: -1.89 (0.36), residues: 188 loop : -1.15 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 105 TYR 0.014 0.002 TYR R 785 PHE 0.018 0.002 PHE R 730 TRP 0.015 0.002 TRP B 211 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8137) covalent geometry : angle 0.60496 (11013) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.89140 ( 6) hydrogen bonds : bond 0.04699 ( 363) hydrogen bonds : angle 5.84600 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 317 ARG cc_start: 0.7646 (mpt180) cc_final: 0.7422 (mpt180) REVERT: A 356 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.6796 (ptm-80) REVERT: A 370 GLU cc_start: 0.6855 (tp30) cc_final: 0.5864 (tt0) REVERT: B 17 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 46 ARG cc_start: 0.7185 (mmm160) cc_final: 0.6803 (mmm-85) REVERT: B 171 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6074 (mp) REVERT: B 266 HIS cc_start: 0.7698 (t-90) cc_final: 0.7465 (t-90) REVERT: B 325 MET cc_start: 0.7101 (mmp) cc_final: 0.5825 (mmp) REVERT: G 42 GLU cc_start: 0.7578 (mp0) cc_final: 0.7341 (mp0) REVERT: R 617 MET cc_start: 0.7528 (tpt) cc_final: 0.7291 (tpt) REVERT: R 646 GLU cc_start: 0.7833 (tt0) cc_final: 0.7617 (tm-30) outliers start: 25 outliers final: 7 residues processed: 196 average time/residue: 0.3997 time to fit residues: 84.6783 Evaluate side-chains 169 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 682 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS N 82 GLN R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.191512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160457 restraints weight = 9050.503| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.03 r_work: 0.3687 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8140 Z= 0.164 Angle : 0.580 8.117 11019 Z= 0.307 Chirality : 0.043 0.240 1244 Planarity : 0.004 0.055 1394 Dihedral : 4.935 21.739 1099 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.85 % Allowed : 18.20 % Favored : 77.95 % 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: -0.89 (0.26), residues: 987 helix: 0.83 (0.28), residues: 341 sheet: -1.87 (0.35), residues: 192 loop : -1.02 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.011 0.001 TYR A 339 PHE 0.014 0.002 PHE B 235 TRP 0.013 0.002 TRP B 211 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8137) covalent geometry : angle 0.57995 (11013) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.84848 ( 6) hydrogen bonds : bond 0.04334 ( 363) hydrogen bonds : angle 5.64041 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7360 (tp30) cc_final: 0.6591 (mt-10) REVERT: A 317 ARG cc_start: 0.7695 (mpt180) cc_final: 0.7448 (mpt180) REVERT: A 356 ARG cc_start: 0.7424 (ptp-110) cc_final: 0.6746 (ptm-80) REVERT: A 370 GLU cc_start: 0.6920 (tp30) cc_final: 0.5985 (tt0) REVERT: B 42 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6321 (tpp-160) REVERT: B 46 ARG cc_start: 0.7277 (mmm160) cc_final: 0.6919 (ttm-80) REVERT: B 171 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6088 (mp) REVERT: B 196 THR cc_start: 0.7077 (OUTLIER) cc_final: 0.6484 (p) REVERT: G 42 GLU cc_start: 0.7691 (mp0) cc_final: 0.7249 (mp0) REVERT: R 753 TYR cc_start: 0.8769 (m-80) cc_final: 0.8200 (m-80) REVERT: R 832 PHE cc_start: 0.8237 (m-80) cc_final: 0.7977 (m-80) outliers start: 33 outliers final: 14 residues processed: 190 average time/residue: 0.3474 time to fit residues: 72.0971 Evaluate side-chains 174 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.189799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158606 restraints weight = 8959.069| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.03 r_work: 0.3701 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8140 Z= 0.163 Angle : 0.580 7.510 11019 Z= 0.304 Chirality : 0.043 0.202 1244 Planarity : 0.004 0.053 1394 Dihedral : 4.858 21.186 1099 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.85 % Allowed : 19.60 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 987 helix: 0.98 (0.28), residues: 342 sheet: -1.83 (0.36), residues: 185 loop : -1.06 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.014 0.001 TYR R 785 PHE 0.017 0.002 PHE R 852 TRP 0.015 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8137) covalent geometry : angle 0.57988 (11013) SS BOND : bond 0.00214 ( 3) SS BOND : angle 0.92284 ( 6) hydrogen bonds : bond 0.04257 ( 363) hydrogen bonds : angle 5.62857 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.7445 (ptp-110) cc_final: 0.6719 (ptm-80) REVERT: A 370 GLU cc_start: 0.7025 (tp30) cc_final: 0.6611 (mt-10) REVERT: B 42 ARG cc_start: 0.6839 (tpt170) cc_final: 0.6207 (tpp-160) REVERT: B 46 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7010 (ttm-80) REVERT: B 155 ASN cc_start: 0.7241 (t0) cc_final: 0.6280 (p0) REVERT: B 171 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6443 (mp) REVERT: B 266 HIS cc_start: 0.7903 (t-90) cc_final: 0.7661 (t-90) REVERT: G 42 GLU cc_start: 0.7708 (mp0) cc_final: 0.7227 (mp0) REVERT: N 90 ASP cc_start: 0.7349 (p0) cc_final: 0.7122 (p0) REVERT: R 682 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7684 (p) REVERT: R 711 MET cc_start: 0.8547 (mtt) cc_final: 0.8321 (mtp) REVERT: R 831 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8823 (t) REVERT: R 832 PHE cc_start: 0.8280 (m-80) cc_final: 0.8060 (m-80) outliers start: 33 outliers final: 14 residues processed: 189 average time/residue: 0.3487 time to fit residues: 71.5765 Evaluate side-chains 179 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 799 VAL Chi-restraints excluded: chain R residue 831 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 20.0000 chunk 86 optimal weight: 0.0030 chunk 67 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160184 restraints weight = 8927.368| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.02 r_work: 0.3725 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8140 Z= 0.146 Angle : 0.572 8.143 11019 Z= 0.300 Chirality : 0.042 0.222 1244 Planarity : 0.004 0.052 1394 Dihedral : 4.779 20.917 1099 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.20 % Allowed : 19.49 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.27), residues: 987 helix: 1.06 (0.28), residues: 342 sheet: -1.88 (0.36), residues: 191 loop : -0.97 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 105 TYR 0.025 0.001 TYR R 753 PHE 0.015 0.001 PHE R 852 TRP 0.013 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8137) covalent geometry : angle 0.57208 (11013) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.88844 ( 6) hydrogen bonds : bond 0.04088 ( 363) hydrogen bonds : angle 5.57054 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7325 (tp30) cc_final: 0.6607 (mt-10) REVERT: A 216 LYS cc_start: 0.8245 (pttm) cc_final: 0.7855 (ptmt) REVERT: A 356 ARG cc_start: 0.7419 (ptp-110) cc_final: 0.6712 (ptm-80) REVERT: B 46 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6951 (ttm-80) REVERT: B 134 ARG cc_start: 0.7105 (ptm-80) cc_final: 0.6881 (ptm-80) REVERT: B 155 ASN cc_start: 0.7336 (t0) cc_final: 0.6381 (p0) REVERT: B 171 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6481 (mp) REVERT: B 196 THR cc_start: 0.6448 (OUTLIER) cc_final: 0.6076 (p) REVERT: B 266 HIS cc_start: 0.7945 (t-90) cc_final: 0.7675 (t-90) REVERT: G 42 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: R 682 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7650 (p) REVERT: R 711 MET cc_start: 0.8538 (mtt) cc_final: 0.8288 (mtp) REVERT: R 753 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: R 801 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8058 (mt) REVERT: R 832 PHE cc_start: 0.8306 (m-80) cc_final: 0.8104 (m-80) outliers start: 36 outliers final: 17 residues processed: 190 average time/residue: 0.3556 time to fit residues: 73.5600 Evaluate side-chains 182 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 799 VAL Chi-restraints excluded: chain R residue 801 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.0010 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.193422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163502 restraints weight = 8960.399| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.99 r_work: 0.3747 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8140 Z= 0.135 Angle : 0.569 7.902 11019 Z= 0.298 Chirality : 0.042 0.241 1244 Planarity : 0.004 0.051 1394 Dihedral : 4.652 20.542 1099 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.08 % Allowed : 20.89 % Favored : 75.03 % 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: -0.64 (0.27), residues: 987 helix: 1.14 (0.28), residues: 342 sheet: -1.94 (0.36), residues: 198 loop : -0.85 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 105 TYR 0.023 0.001 TYR R 753 PHE 0.014 0.001 PHE R 601 TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8137) covalent geometry : angle 0.56888 (11013) SS BOND : bond 0.00031 ( 3) SS BOND : angle 1.20723 ( 6) hydrogen bonds : bond 0.03954 ( 363) hydrogen bonds : angle 5.49523 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6978 (tt0) cc_final: 0.6260 (mt-10) REVERT: A 16 GLU cc_start: 0.7290 (tp30) cc_final: 0.6561 (mt-10) REVERT: A 356 ARG cc_start: 0.7221 (ptp-110) cc_final: 0.6518 (ptm-80) REVERT: B 42 ARG cc_start: 0.6699 (tpt170) cc_final: 0.6233 (tpp-160) REVERT: B 46 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6870 (ttm-80) REVERT: B 134 ARG cc_start: 0.7089 (ptm-80) cc_final: 0.6861 (ptm-80) REVERT: B 155 ASN cc_start: 0.7019 (t0) cc_final: 0.6286 (p0) REVERT: B 171 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6432 (mp) REVERT: B 196 THR cc_start: 0.6322 (OUTLIER) cc_final: 0.6006 (p) REVERT: B 266 HIS cc_start: 0.7906 (t-90) cc_final: 0.7636 (t-90) REVERT: B 331 SER cc_start: 0.9385 (t) cc_final: 0.9150 (p) REVERT: G 42 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: N 67 ARG cc_start: 0.7062 (ptt-90) cc_final: 0.6640 (ptt-90) REVERT: R 618 MET cc_start: 0.7112 (tpt) cc_final: 0.6359 (pp-130) REVERT: R 682 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7819 (p) REVERT: R 711 MET cc_start: 0.8476 (mtt) cc_final: 0.8264 (mtp) REVERT: R 753 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: R 801 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8037 (mt) REVERT: R 832 PHE cc_start: 0.8311 (m-80) cc_final: 0.8074 (m-80) outliers start: 35 outliers final: 15 residues processed: 186 average time/residue: 0.3607 time to fit residues: 73.1942 Evaluate side-chains 174 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 799 VAL Chi-restraints excluded: chain R residue 801 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 773 ASN R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.193844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163633 restraints weight = 8995.847| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.03 r_work: 0.3757 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8140 Z= 0.136 Angle : 0.574 8.169 11019 Z= 0.297 Chirality : 0.042 0.248 1244 Planarity : 0.004 0.057 1394 Dihedral : 4.625 20.358 1099 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.62 % Allowed : 21.94 % Favored : 74.45 % 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: -0.58 (0.27), residues: 987 helix: 1.21 (0.28), residues: 342 sheet: -1.90 (0.36), residues: 193 loop : -0.85 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.022 0.001 TYR R 753 PHE 0.014 0.001 PHE R 601 TRP 0.012 0.002 TRP B 211 HIS 0.008 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8137) covalent geometry : angle 0.57367 (11013) SS BOND : bond 0.00199 ( 3) SS BOND : angle 1.17637 ( 6) hydrogen bonds : bond 0.03902 ( 363) hydrogen bonds : angle 5.46719 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7317 (tp30) cc_final: 0.6524 (pt0) REVERT: A 33 ASP cc_start: 0.7112 (p0) cc_final: 0.6682 (p0) REVERT: A 216 LYS cc_start: 0.8114 (pttm) cc_final: 0.7715 (ptmt) REVERT: A 356 ARG cc_start: 0.7346 (ptp-110) cc_final: 0.6673 (ptm-80) REVERT: B 42 ARG cc_start: 0.6716 (tpt170) cc_final: 0.6327 (tpp-160) REVERT: B 46 ARG cc_start: 0.7283 (mmm160) cc_final: 0.6918 (ttm-80) REVERT: B 134 ARG cc_start: 0.7057 (ptm-80) cc_final: 0.6840 (ptm-80) REVERT: B 150 ARG cc_start: 0.8317 (mmt-90) cc_final: 0.8030 (mmp-170) REVERT: B 155 ASN cc_start: 0.6882 (t0) cc_final: 0.6246 (p0) REVERT: B 171 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6333 (mp) REVERT: B 196 THR cc_start: 0.6405 (OUTLIER) cc_final: 0.6138 (p) REVERT: B 266 HIS cc_start: 0.7915 (t-90) cc_final: 0.7661 (t-90) REVERT: G 42 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: N 67 ARG cc_start: 0.7033 (ptt-90) cc_final: 0.6569 (ptt-90) REVERT: R 618 MET cc_start: 0.7252 (tpt) cc_final: 0.6448 (pp-130) REVERT: R 682 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7752 (p) REVERT: R 753 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: R 832 PHE cc_start: 0.8327 (m-80) cc_final: 0.8111 (m-80) outliers start: 31 outliers final: 15 residues processed: 179 average time/residue: 0.3617 time to fit residues: 70.3804 Evaluate side-chains 177 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 220 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.187834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.156598 restraints weight = 8853.381| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.00 r_work: 0.3678 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8140 Z= 0.177 Angle : 0.607 7.931 11019 Z= 0.312 Chirality : 0.043 0.235 1244 Planarity : 0.004 0.048 1394 Dihedral : 4.733 19.797 1099 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 22.52 % Favored : 73.63 % 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: -0.65 (0.27), residues: 987 helix: 1.24 (0.28), residues: 340 sheet: -2.03 (0.35), residues: 193 loop : -0.91 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.023 0.002 TYR R 753 PHE 0.015 0.002 PHE B 235 TRP 0.016 0.002 TRP A 234 HIS 0.010 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8137) covalent geometry : angle 0.60521 (11013) SS BOND : bond 0.00212 ( 3) SS BOND : angle 1.89256 ( 6) hydrogen bonds : bond 0.04185 ( 363) hydrogen bonds : angle 5.59316 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7342 (tp30) cc_final: 0.6740 (pt0) REVERT: A 33 ASP cc_start: 0.7126 (p0) cc_final: 0.6833 (p0) REVERT: A 356 ARG cc_start: 0.7453 (ptp-110) cc_final: 0.6762 (ptm-80) REVERT: B 46 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7051 (ttm-80) REVERT: B 155 ASN cc_start: 0.6928 (t0) cc_final: 0.6405 (p0) REVERT: B 171 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6609 (mp) REVERT: B 196 THR cc_start: 0.6534 (OUTLIER) cc_final: 0.6256 (p) REVERT: B 262 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.4856 (ppp) REVERT: B 266 HIS cc_start: 0.8046 (t-90) cc_final: 0.7774 (t-90) REVERT: B 277 SER cc_start: 0.8655 (p) cc_final: 0.8378 (m) REVERT: G 42 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: R 682 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7746 (p) REVERT: R 753 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: R 832 PHE cc_start: 0.8422 (m-80) cc_final: 0.8095 (m-80) REVERT: R 858 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7889 (mt) outliers start: 33 outliers final: 17 residues processed: 185 average time/residue: 0.3456 time to fit residues: 69.6657 Evaluate side-chains 182 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.191469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160694 restraints weight = 8904.025| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.02 r_work: 0.3728 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8140 Z= 0.144 Angle : 0.609 9.298 11019 Z= 0.311 Chirality : 0.044 0.307 1244 Planarity : 0.004 0.055 1394 Dihedral : 4.692 19.682 1099 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.15 % Allowed : 23.92 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 987 helix: 1.15 (0.28), residues: 343 sheet: -2.09 (0.34), residues: 200 loop : -0.80 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.023 0.001 TYR R 753 PHE 0.015 0.001 PHE R 601 TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8137) covalent geometry : angle 0.60795 (11013) SS BOND : bond 0.00219 ( 3) SS BOND : angle 1.70533 ( 6) hydrogen bonds : bond 0.03994 ( 363) hydrogen bonds : angle 5.55639 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7373 (tp30) cc_final: 0.6760 (pt0) REVERT: A 33 ASP cc_start: 0.7193 (p0) cc_final: 0.6831 (p0) REVERT: A 356 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.6662 (ptm-80) REVERT: B 46 ARG cc_start: 0.7343 (mmm160) cc_final: 0.6998 (ttm-80) REVERT: B 100 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 155 ASN cc_start: 0.6718 (t0) cc_final: 0.6347 (p0) REVERT: B 196 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.6207 (p) REVERT: B 262 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.4662 (ppp) REVERT: B 266 HIS cc_start: 0.8024 (t-90) cc_final: 0.7759 (t-90) REVERT: B 331 SER cc_start: 0.9400 (t) cc_final: 0.9176 (p) REVERT: G 42 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: N 67 ARG cc_start: 0.6853 (ptt-90) cc_final: 0.6423 (ptt-90) REVERT: R 618 MET cc_start: 0.7064 (tpt) cc_final: 0.6359 (pp-130) REVERT: R 682 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7795 (p) REVERT: R 711 MET cc_start: 0.8649 (mtt) cc_final: 0.8370 (mtt) REVERT: R 753 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: R 832 PHE cc_start: 0.8441 (m-80) cc_final: 0.8114 (m-80) REVERT: R 858 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7768 (mt) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.3629 time to fit residues: 70.5376 Evaluate side-chains 181 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 723 ILE Chi-restraints excluded: chain R residue 730 PHE Chi-restraints excluded: chain R residue 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 858 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 362 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 877 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 = 0.4118 r_free = 0.4118 target = 0.188754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157654 restraints weight = 8910.987| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.98 r_work: 0.3682 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8140 Z= 0.168 Angle : 0.624 9.269 11019 Z= 0.318 Chirality : 0.043 0.216 1244 Planarity : 0.005 0.064 1394 Dihedral : 4.767 19.548 1099 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.15 % Allowed : 24.27 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.27), residues: 987 helix: 1.23 (0.28), residues: 339 sheet: -2.09 (0.34), residues: 195 loop : -0.85 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 105 TYR 0.023 0.002 TYR R 753 PHE 0.016 0.002 PHE R 601 TRP 0.016 0.002 TRP R 838 HIS 0.010 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8137) covalent geometry : angle 0.62290 (11013) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.66442 ( 6) hydrogen bonds : bond 0.04103 ( 363) hydrogen bonds : angle 5.60577 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.04 seconds wall clock time: 48 minutes 36.44 seconds (2916.44 seconds total)