Starting phenix.real_space_refine on Tue Jun 10 21:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_32838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_32838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_32838.map" model { file = "/net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_32838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuq_32838/06_2025/7wuq_32838.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 4.53, per 1000 atoms: 0.57 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.89 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: 2.26 Time building geometry restraints manager: 2.23 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- 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 : 23.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.004 TRP B 339 HIS 0.021 0.004 HIS A 357 PHE 0.038 0.003 PHE R 730 TYR 0.021 0.002 TYR N 115 ARG 0.020 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.25418 ( 363) hydrogen bonds : angle 9.92899 ( 1020) SS BOND : bond 0.40255 ( 3) SS BOND : angle 8.24799 ( 6) covalent geometry : bond 0.00589 ( 8137) covalent geometry : angle 1.06095 (11013) *********************** 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 : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 VAL cc_start: 0.4845 (p) cc_final: 0.4604 (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: 0.7919 time to fit residues: 156.3587 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 : 0.809 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 76 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 88 optimal weight: 0.0980 overall best weight: 0.2236 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.210232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182589 restraints weight = 9035.470| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.02 r_work: 0.3946 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2082 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= 0.135 Angle : 0.611 7.402 11019 Z= 0.329 Chirality : 0.043 0.143 1244 Planarity : 0.005 0.071 1394 Dihedral : 5.361 27.299 1102 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.40 % Allowed : 12.25 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.25), residues: 987 helix: -0.18 (0.26), residues: 334 sheet: -2.23 (0.36), residues: 177 loop : -1.26 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.007 0.002 HIS A 41 PHE 0.015 0.002 PHE R 730 TYR 0.013 0.001 TYR R 726 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 363) hydrogen bonds : angle 6.14424 ( 1020) SS BOND : bond 0.00508 ( 3) SS BOND : angle 1.00642 ( 6) covalent geometry : bond 0.00288 ( 8137) covalent geometry : angle 0.61064 (11013) *********************** 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 188 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6825 (tp30) cc_final: 0.6007 (tt0) REVERT: B 46 ARG cc_start: 0.7011 (mmm160) cc_final: 0.6633 (mmm-85) REVERT: B 186 ASP cc_start: 0.7655 (p0) cc_final: 0.7448 (p0) REVERT: G 16 VAL cc_start: 0.8052 (t) cc_final: 0.7520 (m) REVERT: R 617 MET cc_start: 0.7614 (tpt) cc_final: 0.7326 (tpt) REVERT: R 682 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7712 (p) outliers start: 12 outliers final: 3 residues processed: 182 average time/residue: 0.9303 time to fit residues: 182.1583 Evaluate side-chains 152 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 687 ILE 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 32 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 88 ASN B 155 ASN B 259 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 668 ASN R 849 ASN R 860 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169061 restraints weight = 9035.655| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.03 r_work: 0.3787 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8140 Z= 0.158 Angle : 0.592 7.485 11019 Z= 0.314 Chirality : 0.043 0.175 1244 Planarity : 0.004 0.061 1394 Dihedral : 4.969 23.092 1099 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.45 % Allowed : 15.87 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.26), residues: 987 helix: 0.57 (0.27), residues: 337 sheet: -1.96 (0.35), residues: 189 loop : -1.16 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.010 0.002 HIS A 357 PHE 0.019 0.002 PHE R 730 TYR 0.013 0.001 TYR R 785 ARG 0.009 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 363) hydrogen bonds : angle 5.72195 ( 1020) SS BOND : bond 0.00097 ( 3) SS BOND : angle 0.92194 ( 6) covalent geometry : bond 0.00356 ( 8137) covalent geometry : angle 0.59148 (11013) *********************** 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 192 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.7586 (mtmm) cc_final: 0.7338 (mtmm) REVERT: A 317 ARG cc_start: 0.7601 (mpt180) cc_final: 0.7377 (mpt180) REVERT: A 356 ARG cc_start: 0.7427 (ptp-110) cc_final: 0.6758 (ptp-170) REVERT: A 370 GLU cc_start: 0.6653 (tp30) cc_final: 0.5643 (tt0) REVERT: B 46 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6845 (ttm-80) REVERT: B 134 ARG cc_start: 0.6918 (ppt90) cc_final: 0.6630 (ptm-80) REVERT: B 155 ASN cc_start: 0.7412 (t0) cc_final: 0.7108 (t0) REVERT: B 171 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5903 (mp) REVERT: B 186 ASP cc_start: 0.7973 (p0) cc_final: 0.7570 (p0) REVERT: B 254 ASP cc_start: 0.7569 (t70) cc_final: 0.7317 (t0) REVERT: B 266 HIS cc_start: 0.7545 (t-90) cc_final: 0.7327 (t-90) REVERT: B 277 SER cc_start: 0.8843 (p) cc_final: 0.8488 (m) REVERT: B 325 MET cc_start: 0.6937 (mmp) cc_final: 0.5616 (mmp) REVERT: G 42 GLU cc_start: 0.7617 (mp0) cc_final: 0.7202 (mp0) REVERT: R 617 MET cc_start: 0.7415 (tpt) cc_final: 0.7215 (tpt) REVERT: R 646 GLU cc_start: 0.7913 (tt0) cc_final: 0.7669 (tm-30) outliers start: 21 outliers final: 7 residues processed: 182 average time/residue: 0.8759 time to fit residues: 172.9920 Evaluate side-chains 159 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain R residue 687 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 62 HIS ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4174 r_free = 0.4174 target = 0.195260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164547 restraints weight = 8933.737| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.03 r_work: 0.3759 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3230 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= 0.159 Angle : 0.570 7.247 11019 Z= 0.304 Chirality : 0.043 0.243 1244 Planarity : 0.004 0.055 1394 Dihedral : 4.877 21.745 1099 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 18.90 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 987 helix: 0.84 (0.27), residues: 342 sheet: -1.88 (0.35), residues: 195 loop : -1.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.010 0.001 HIS A 357 PHE 0.014 0.002 PHE A 212 TYR 0.021 0.001 TYR R 753 ARG 0.005 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 363) hydrogen bonds : angle 5.59023 ( 1020) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.87110 ( 6) covalent geometry : bond 0.00362 ( 8137) covalent geometry : angle 0.56946 (11013) *********************** 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 193 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7351 (tp30) cc_final: 0.6567 (mt-10) REVERT: A 210 THR cc_start: 0.7482 (p) cc_final: 0.7161 (p) REVERT: A 216 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7482 (mtmm) REVERT: A 317 ARG cc_start: 0.7688 (mpt180) cc_final: 0.7417 (mpt180) REVERT: A 370 GLU cc_start: 0.6722 (tp30) cc_final: 0.5757 (tt0) REVERT: B 42 ARG cc_start: 0.6910 (tpt170) cc_final: 0.6307 (tpp-160) REVERT: B 46 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6767 (ttm-80) REVERT: B 134 ARG cc_start: 0.7003 (ppt90) cc_final: 0.6743 (ppt90) REVERT: B 171 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.5814 (mp) REVERT: B 186 ASP cc_start: 0.7773 (p0) cc_final: 0.7503 (p0) REVERT: B 325 MET cc_start: 0.6905 (mmp) cc_final: 0.5643 (mmp) REVERT: G 42 GLU cc_start: 0.7486 (mp0) cc_final: 0.7227 (mp0) REVERT: R 617 MET cc_start: 0.7409 (tpt) cc_final: 0.7208 (tpt) outliers start: 24 outliers final: 10 residues processed: 183 average time/residue: 0.8482 time to fit residues: 168.4513 Evaluate side-chains 165 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain N residue 2 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 792 LEU Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN G 18 GLN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149099 restraints weight = 8822.089| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.05 r_work: 0.3586 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8140 Z= 0.243 Angle : 0.655 8.165 11019 Z= 0.342 Chirality : 0.045 0.211 1244 Planarity : 0.005 0.053 1394 Dihedral : 5.117 23.987 1099 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.50 % Allowed : 19.25 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 987 helix: 0.85 (0.28), residues: 342 sheet: -1.92 (0.36), residues: 189 loop : -1.14 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.013 0.002 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.014 0.002 TYR A 339 ARG 0.011 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 363) hydrogen bonds : angle 5.89145 ( 1020) SS BOND : bond 0.00366 ( 3) SS BOND : angle 0.88901 ( 6) covalent geometry : bond 0.00560 ( 8137) covalent geometry : angle 0.65478 (11013) *********************** 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 210 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7863 (mtmm) REVERT: A 317 ARG cc_start: 0.7664 (mpt180) cc_final: 0.7400 (mpt180) REVERT: A 343 ASP cc_start: 0.8490 (m-30) cc_final: 0.8154 (m-30) REVERT: A 356 ARG cc_start: 0.7565 (ptp-110) cc_final: 0.6831 (ptm-80) REVERT: A 378 ASP cc_start: 0.7929 (m-30) cc_final: 0.7712 (m-30) REVERT: B 46 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7108 (ttm-80) REVERT: B 66 ASP cc_start: 0.8383 (p0) cc_final: 0.8181 (p0) REVERT: B 171 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6576 (mp) REVERT: B 186 ASP cc_start: 0.8182 (p0) cc_final: 0.7688 (p0) REVERT: B 196 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6446 (p) REVERT: B 266 HIS cc_start: 0.8026 (t-90) cc_final: 0.7757 (t-90) REVERT: B 340 ASN cc_start: 0.7917 (m110) cc_final: 0.7310 (m110) REVERT: G 42 GLU cc_start: 0.7794 (mp0) cc_final: 0.7257 (mp0) REVERT: N 83 MET cc_start: 0.7443 (mtt) cc_final: 0.7208 (mtt) REVERT: R 711 MET cc_start: 0.8828 (mtt) cc_final: 0.8581 (mtp) REVERT: R 743 SER cc_start: 0.8712 (m) cc_final: 0.8482 (m) REVERT: R 753 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: R 832 PHE cc_start: 0.8527 (m-80) cc_final: 0.8128 (m-80) outliers start: 30 outliers final: 15 residues processed: 198 average time/residue: 0.8229 time to fit residues: 177.3539 Evaluate side-chains 182 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU 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 196 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 91 THR 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 733 VAL Chi-restraints excluded: chain R residue 753 TYR Chi-restraints excluded: chain R residue 801 LEU Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN 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 = 0.4090 r_free = 0.4090 target = 0.186616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155252 restraints weight = 8737.847| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.01 r_work: 0.3621 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3981 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= 0.165 Angle : 0.603 7.952 11019 Z= 0.314 Chirality : 0.042 0.198 1244 Planarity : 0.004 0.051 1394 Dihedral : 4.960 21.208 1099 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.85 % Allowed : 21.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 987 helix: 0.95 (0.28), residues: 344 sheet: -1.84 (0.35), residues: 189 loop : -1.00 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.011 0.001 TYR R 753 ARG 0.010 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 363) hydrogen bonds : angle 5.71963 ( 1020) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.27502 ( 6) covalent geometry : bond 0.00378 ( 8137) covalent geometry : angle 0.60226 (11013) *********************** 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 212 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 317 ARG cc_start: 0.7530 (mpt180) cc_final: 0.7280 (mpt180) REVERT: A 356 ARG cc_start: 0.7471 (ptp-110) cc_final: 0.6672 (ptm-80) REVERT: A 378 ASP cc_start: 0.7678 (m-30) cc_final: 0.7373 (m-30) REVERT: B 46 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6893 (ttm-80) REVERT: B 66 ASP cc_start: 0.8260 (p0) cc_final: 0.8025 (p0) REVERT: B 78 LYS cc_start: 0.8357 (tppp) cc_final: 0.8132 (tppt) REVERT: B 155 ASN cc_start: 0.7335 (t0) cc_final: 0.6340 (p0) REVERT: B 171 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6558 (mp) REVERT: B 186 ASP cc_start: 0.8020 (p0) cc_final: 0.7549 (p0) REVERT: B 196 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.6253 (p) REVERT: B 266 HIS cc_start: 0.8011 (t-90) cc_final: 0.7700 (t-90) REVERT: G 42 GLU cc_start: 0.7743 (mp0) cc_final: 0.7242 (mp0) REVERT: N 67 ARG cc_start: 0.7127 (ptt-90) cc_final: 0.6813 (ptt-90) REVERT: R 682 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (p) REVERT: R 711 MET cc_start: 0.8662 (mtt) cc_final: 0.8391 (mtp) REVERT: R 743 SER cc_start: 0.8667 (m) cc_final: 0.8433 (m) REVERT: R 753 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8306 (m-80) outliers start: 33 outliers final: 16 residues processed: 194 average time/residue: 0.7875 time to fit residues: 166.3111 Evaluate side-chains 191 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 314 GLU 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 296 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 91 THR 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 799 VAL Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 278 ASN A 371 ASN 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 = 0.4082 r_free = 0.4082 target = 0.186385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154918 restraints weight = 8884.477| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.03 r_work: 0.3639 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4130 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= 0.172 Angle : 0.601 8.039 11019 Z= 0.314 Chirality : 0.043 0.209 1244 Planarity : 0.004 0.053 1394 Dihedral : 4.890 20.946 1099 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.62 % Allowed : 22.05 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 987 helix: 0.98 (0.28), residues: 345 sheet: -1.94 (0.35), residues: 189 loop : -0.95 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.002 HIS A 362 PHE 0.017 0.002 PHE A 212 TYR 0.015 0.002 TYR R 785 ARG 0.012 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 363) hydrogen bonds : angle 5.66837 ( 1020) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.48067 ( 6) covalent geometry : bond 0.00397 ( 8137) covalent geometry : angle 0.60014 (11013) *********************** 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 205 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7824 (mtmm) REVERT: A 317 ARG cc_start: 0.7558 (mpt180) cc_final: 0.7334 (mpt180) REVERT: A 356 ARG cc_start: 0.7473 (ptp-110) cc_final: 0.6679 (ptm-80) REVERT: B 46 ARG cc_start: 0.7297 (mmm160) cc_final: 0.6924 (ttm-80) REVERT: B 66 ASP cc_start: 0.8262 (p0) cc_final: 0.8031 (p0) REVERT: B 137 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.6168 (mtp180) REVERT: B 155 ASN cc_start: 0.7345 (t0) cc_final: 0.6364 (p0) REVERT: B 171 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6562 (mp) REVERT: B 186 ASP cc_start: 0.7980 (p0) cc_final: 0.7511 (p0) REVERT: B 196 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6265 (p) REVERT: B 266 HIS cc_start: 0.8065 (t-90) cc_final: 0.7787 (t-90) REVERT: G 42 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: N 90 ASP cc_start: 0.7503 (p0) cc_final: 0.7160 (p0) REVERT: R 682 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7701 (p) REVERT: R 711 MET cc_start: 0.8691 (mtt) cc_final: 0.8447 (mtp) REVERT: R 743 SER cc_start: 0.8641 (m) cc_final: 0.8421 (m) REVERT: R 753 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: R 832 PHE cc_start: 0.8494 (m-80) cc_final: 0.8258 (m-80) outliers start: 31 outliers final: 16 residues processed: 190 average time/residue: 0.7908 time to fit residues: 163.7992 Evaluate side-chains 187 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 286 SER 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 157 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 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 91 THR 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 799 VAL Chi-restraints excluded: chain R residue 878 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 0.0570 chunk 36 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 278 ASN A 294 GLN A 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN N 31 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.188079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157154 restraints weight = 8966.040| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.03 r_work: 0.3686 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8140 Z= 0.156 Angle : 0.594 8.350 11019 Z= 0.308 Chirality : 0.042 0.229 1244 Planarity : 0.004 0.051 1394 Dihedral : 4.827 20.883 1099 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.55 % Allowed : 22.05 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 987 helix: 1.01 (0.28), residues: 343 sheet: -1.84 (0.36), residues: 191 loop : -0.91 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.009 0.002 HIS A 220 PHE 0.017 0.002 PHE A 212 TYR 0.012 0.001 TYR R 722 ARG 0.011 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 363) hydrogen bonds : angle 5.62150 ( 1020) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.35774 ( 6) covalent geometry : bond 0.00359 ( 8137) covalent geometry : angle 0.59358 (11013) *********************** 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 211 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8286 (t70) cc_final: 0.8048 (t0) REVERT: A 356 ARG cc_start: 0.7417 (ptp-110) cc_final: 0.6692 (ptm-80) REVERT: B 46 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6891 (ttm-80) REVERT: B 66 ASP cc_start: 0.8200 (p0) cc_final: 0.7998 (p0) REVERT: B 134 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.7027 (ptm-80) REVERT: B 155 ASN cc_start: 0.7395 (t0) cc_final: 0.6492 (p0) REVERT: B 171 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6638 (mp) REVERT: B 186 ASP cc_start: 0.7960 (p0) cc_final: 0.7470 (p0) REVERT: B 196 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.6055 (p) REVERT: B 266 HIS cc_start: 0.8066 (t-90) cc_final: 0.7786 (t-90) REVERT: G 42 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: N 67 ARG cc_start: 0.6905 (ptt-90) cc_final: 0.6463 (ptt180) REVERT: R 618 MET cc_start: 0.7279 (tpt) cc_final: 0.6487 (pp-130) REVERT: R 682 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7788 (p) REVERT: R 711 MET cc_start: 0.8658 (mtt) cc_final: 0.8446 (mtp) REVERT: R 753 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: R 755 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7820 (pt) REVERT: R 832 PHE cc_start: 0.8474 (m-80) cc_final: 0.8237 (m-80) REVERT: R 858 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mp) outliers start: 39 outliers final: 15 residues processed: 192 average time/residue: 0.7763 time to fit residues: 162.7146 Evaluate side-chains 184 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR 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 755 ILE Chi-restraints excluded: chain R residue 799 VAL Chi-restraints excluded: chain R residue 858 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN N 31 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156484 restraints weight = 9007.586| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.03 r_work: 0.3681 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4262 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= 0.166 Angle : 0.611 7.946 11019 Z= 0.316 Chirality : 0.043 0.231 1244 Planarity : 0.004 0.053 1394 Dihedral : 4.823 20.600 1099 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 24.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 987 helix: 1.03 (0.28), residues: 343 sheet: -1.90 (0.35), residues: 191 loop : -0.91 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.008 0.002 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.015 0.001 TYR R 785 ARG 0.012 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 363) hydrogen bonds : angle 5.59235 ( 1020) SS BOND : bond 0.00273 ( 3) SS BOND : angle 1.35283 ( 6) covalent geometry : bond 0.00384 ( 8137) covalent geometry : angle 0.61064 (11013) *********************** 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 194 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 274 ASP cc_start: 0.8318 (t70) cc_final: 0.8059 (t0) REVERT: A 356 ARG cc_start: 0.7447 (ptp-110) cc_final: 0.6730 (ptm-80) REVERT: B 46 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6948 (ttm-80) REVERT: B 155 ASN cc_start: 0.7374 (t0) cc_final: 0.6509 (p0) REVERT: B 171 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6784 (mp) REVERT: B 186 ASP cc_start: 0.7928 (p0) cc_final: 0.7510 (p0) REVERT: B 196 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.6005 (p) REVERT: B 266 HIS cc_start: 0.8085 (t-90) cc_final: 0.7788 (t-90) REVERT: G 42 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: N 31 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7703 (m110) REVERT: N 67 ARG cc_start: 0.6933 (ptt-90) cc_final: 0.6587 (ptt-90) REVERT: R 618 MET cc_start: 0.7207 (tpt) cc_final: 0.6495 (pp-130) REVERT: R 682 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7879 (p) REVERT: R 711 MET cc_start: 0.8664 (mtt) cc_final: 0.8423 (mtp) REVERT: R 753 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: R 755 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7791 (pt) REVERT: R 832 PHE cc_start: 0.8515 (m-80) cc_final: 0.8283 (m-80) REVERT: R 854 TYR cc_start: 0.8204 (m-80) cc_final: 0.7768 (m-80) REVERT: R 858 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8265 (mp) outliers start: 28 outliers final: 14 residues processed: 179 average time/residue: 0.7467 time to fit residues: 146.8996 Evaluate side-chains 184 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 598 LEU 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 755 ILE Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 799 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 35 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 268 ASN N 31 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.187320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156104 restraints weight = 8871.146| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.02 r_work: 0.3674 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4291 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= 0.168 Angle : 0.622 8.221 11019 Z= 0.321 Chirality : 0.043 0.244 1244 Planarity : 0.004 0.054 1394 Dihedral : 4.828 20.607 1099 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.73 % Allowed : 23.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 987 helix: 1.01 (0.28), residues: 343 sheet: -1.98 (0.34), residues: 192 loop : -0.86 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.008 0.002 HIS A 357 PHE 0.018 0.002 PHE A 212 TYR 0.011 0.001 TYR R 722 ARG 0.013 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 363) hydrogen bonds : angle 5.60958 ( 1020) SS BOND : bond 0.00226 ( 3) SS BOND : angle 1.27598 ( 6) covalent geometry : bond 0.00390 ( 8137) covalent geometry : angle 0.62132 (11013) ********************** 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 199 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7046 (p0) cc_final: 0.6830 (p0) REVERT: A 356 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.6662 (ptm-80) REVERT: B 46 ARG cc_start: 0.7271 (mmm160) cc_final: 0.6918 (ttm-80) REVERT: B 134 ARG cc_start: 0.7323 (ptm-80) cc_final: 0.7106 (ptm-80) REVERT: B 155 ASN cc_start: 0.7174 (t0) cc_final: 0.6602 (p0) REVERT: B 186 ASP cc_start: 0.7926 (p0) cc_final: 0.7441 (p0) REVERT: B 196 THR cc_start: 0.6285 (OUTLIER) cc_final: 0.5984 (p) REVERT: B 239 ASN cc_start: 0.7488 (m-40) cc_final: 0.7269 (m-40) REVERT: B 266 HIS cc_start: 0.8082 (t-90) cc_final: 0.7775 (t-90) REVERT: G 42 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: N 67 ARG cc_start: 0.7016 (ptt-90) cc_final: 0.6583 (ptt180) REVERT: N 83 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7572 (mtt) REVERT: R 618 MET cc_start: 0.7219 (tpt) cc_final: 0.6432 (pp-130) REVERT: R 682 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7925 (p) REVERT: R 753 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: R 755 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7722 (pt) REVERT: R 832 PHE cc_start: 0.8501 (m-80) cc_final: 0.8293 (m-80) REVERT: R 854 TYR cc_start: 0.8230 (m-80) cc_final: 0.7766 (m-80) REVERT: R 858 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8185 (mp) outliers start: 32 outliers final: 14 residues processed: 182 average time/residue: 0.7646 time to fit residues: 152.6243 Evaluate side-chains 180 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 112 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 83 MET 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 755 ILE Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 799 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 13 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 278 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** 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 31 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.187377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156817 restraints weight = 8983.368| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.00 r_work: 0.3691 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 0.038 8140 Z= 0.162 Angle : 0.614 7.933 11019 Z= 0.318 Chirality : 0.043 0.250 1244 Planarity : 0.004 0.058 1394 Dihedral : 4.778 20.528 1099 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.50 % Allowed : 24.15 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 987 helix: 1.03 (0.28), residues: 343 sheet: -1.96 (0.35), residues: 188 loop : -0.82 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.011 0.002 HIS A 362 PHE 0.017 0.002 PHE A 212 TYR 0.016 0.002 TYR R 785 ARG 0.013 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 363) hydrogen bonds : angle 5.59693 ( 1020) SS BOND : bond 0.00086 ( 3) SS BOND : angle 1.90927 ( 6) covalent geometry : bond 0.00373 ( 8137) covalent geometry : angle 0.61297 (11013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6202.55 seconds wall clock time: 106 minutes 48.20 seconds (6408.20 seconds total)