Starting phenix.real_space_refine on Mon Dec 30 03:06:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wuq_32838/12_2024/7wuq_32838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuq_32838/12_2024/7wuq_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_32838/12_2024/7wuq_32838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuq_32838/12_2024/7wuq_32838.map" model { file = "/net/cci-nas-00/data/ceres_data/7wuq_32838/12_2024/7wuq_32838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuq_32838/12_2024/7wuq_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-5532/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: 4.86, per 1000 atoms: 0.61 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: 2.08 Conformation dependent library (CDL) restraints added in 991.4 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: 0.78 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: 2.22 Time building geometry restraints manager: 2.38 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.870 Find NCS groups from input model: 0.060 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- 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 : 0.006 0.090 8137 Z= 0.381 Angle : 1.061 14.234 11013 Z= 0.595 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 *********************** 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 : 0.880 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: 0.8268 time to fit residues: 162.9812 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 : 0.929 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 8137 Z= 0.186 Angle : 0.611 7.402 11013 Z= 0.328 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 *********************** 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 : 0.903 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6547 (tp30) cc_final: 0.6268 (tt0) REVERT: G 16 VAL cc_start: 0.8170 (t) cc_final: 0.7677 (m) REVERT: R 682 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7493 (p) outliers start: 12 outliers final: 3 residues processed: 182 average time/residue: 0.9933 time to fit residues: 194.6442 Evaluate side-chains 151 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 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 23 ASN A 41 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8137 Z= 0.243 Angle : 0.600 7.502 11013 Z= 0.318 Chirality : 0.043 0.177 1244 Planarity : 0.005 0.061 1394 Dihedral : 4.993 23.581 1099 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.36 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: -1.14 (0.26), residues: 987 helix: 0.57 (0.27), residues: 337 sheet: -1.96 (0.35), residues: 189 loop : -1.15 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.011 0.002 HIS A 357 PHE 0.020 0.002 PHE R 730 TYR 0.013 0.002 TYR R 785 ARG 0.008 0.001 ARG N 105 *********************** 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 : 0.880 Fit side-chains revert: symmetry clash REVERT: A 356 ARG cc_start: 0.6986 (ptp-110) cc_final: 0.6776 (ptp-170) REVERT: A 370 GLU cc_start: 0.6291 (tp30) cc_final: 0.5946 (tt0) REVERT: B 171 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6112 (mp) REVERT: B 325 MET cc_start: 0.5937 (mmp) cc_final: 0.4599 (mmp) outliers start: 21 outliers final: 6 residues processed: 181 average time/residue: 0.9242 time to fit residues: 181.3241 Evaluate side-chains 160 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 0.0170 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8137 Z= 0.216 Angle : 0.571 7.240 11013 Z= 0.302 Chirality : 0.042 0.223 1244 Planarity : 0.004 0.056 1394 Dihedral : 4.849 21.778 1099 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.03 % Allowed : 18.79 % Favored : 78.18 % 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: -0.86 (0.26), residues: 987 helix: 0.85 (0.27), residues: 341 sheet: -1.83 (0.36), residues: 188 loop : -1.04 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE R 852 TYR 0.009 0.001 TYR N 117 ARG 0.008 0.001 ARG N 105 *********************** 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 199 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.6205 (tp30) cc_final: 0.5875 (tt0) REVERT: B 42 ARG cc_start: 0.6244 (tpt170) cc_final: 0.6034 (tpp-160) REVERT: B 171 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.5955 (mp) REVERT: B 325 MET cc_start: 0.6117 (mmp) cc_final: 0.4825 (mmp) REVERT: R 753 TYR cc_start: 0.8495 (m-80) cc_final: 0.8126 (m-80) outliers start: 26 outliers final: 10 residues processed: 184 average time/residue: 0.8708 time to fit residues: 173.6687 Evaluate side-chains 171 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 160 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain N residue 2 VAL 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 878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN G 18 GLN N 31 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8137 Z= 0.446 Angle : 0.716 9.163 11013 Z= 0.373 Chirality : 0.047 0.212 1244 Planarity : 0.005 0.054 1394 Dihedral : 5.356 26.555 1099 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.08 % Allowed : 19.02 % Favored : 76.90 % 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: -1.03 (0.26), residues: 987 helix: 0.70 (0.28), residues: 342 sheet: -1.89 (0.35), residues: 191 loop : -1.13 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 99 HIS 0.015 0.002 HIS A 357 PHE 0.019 0.002 PHE R 786 TYR 0.017 0.002 TYR A 339 ARG 0.009 0.001 ARG A 356 *********************** 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 222 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7366 (m-30) cc_final: 0.7117 (m-30) REVERT: B 171 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6819 (mp) REVERT: B 186 ASP cc_start: 0.7678 (p0) cc_final: 0.7472 (p0) REVERT: B 251 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7875 (mtt90) REVERT: N 82 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7526 (mm-40) REVERT: N 90 ASP cc_start: 0.7635 (p0) cc_final: 0.7379 (p0) REVERT: R 753 TYR cc_start: 0.8777 (m-80) cc_final: 0.8358 (m-80) REVERT: R 832 PHE cc_start: 0.8340 (m-80) cc_final: 0.8090 (m-80) outliers start: 35 outliers final: 18 residues processed: 211 average time/residue: 0.8828 time to fit residues: 201.7209 Evaluate side-chains 185 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 372 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 B residue 178 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 91 THR 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 733 VAL 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 85 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.004 0.044 8137 Z= 0.252 Angle : 0.622 8.454 11013 Z= 0.325 Chirality : 0.042 0.187 1244 Planarity : 0.004 0.050 1394 Dihedral : 5.077 21.254 1099 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.20 % Allowed : 21.70 % Favored : 74.10 % 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: -0.93 (0.27), residues: 987 helix: 0.79 (0.28), residues: 345 sheet: -1.99 (0.35), residues: 191 loop : -1.02 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.009 0.001 TYR N 32 ARG 0.010 0.001 ARG N 105 *********************** 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 222 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7199 (m-30) cc_final: 0.6839 (m-30) REVERT: B 171 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6752 (mp) REVERT: N 20 LEU cc_start: 0.8169 (mt) cc_final: 0.7814 (mt) REVERT: R 682 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7412 (p) REVERT: R 753 TYR cc_start: 0.8667 (m-80) cc_final: 0.8305 (m-80) outliers start: 36 outliers final: 14 residues processed: 203 average time/residue: 0.7692 time to fit residues: 170.8596 Evaluate side-chains 188 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 B residue 160 SER Chi-restraints excluded: chain B residue 171 ILE 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 831 THR 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 10 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 0.0000 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8137 Z= 0.236 Angle : 0.624 8.278 11013 Z= 0.323 Chirality : 0.043 0.225 1244 Planarity : 0.004 0.047 1394 Dihedral : 4.948 21.250 1099 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.38 % Allowed : 23.22 % 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: -0.83 (0.27), residues: 987 helix: 0.89 (0.28), residues: 343 sheet: -1.92 (0.35), residues: 189 loop : -0.97 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.002 HIS B 62 PHE 0.017 0.002 PHE A 212 TYR 0.013 0.001 TYR R 785 ARG 0.012 0.001 ARG N 105 *********************** 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 217 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7223 (t0) cc_final: 0.6706 (p0) REVERT: B 171 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6675 (mp) REVERT: B 262 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5461 (ppp) REVERT: B 325 MET cc_start: 0.7524 (tpp) cc_final: 0.7212 (tpp) REVERT: B 340 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6895 (m110) REVERT: N 67 ARG cc_start: 0.7250 (ptt-90) cc_final: 0.6874 (ptt-90) REVERT: R 753 TYR cc_start: 0.8631 (m-80) cc_final: 0.8254 (m-80) REVERT: R 832 PHE cc_start: 0.8249 (m-80) cc_final: 0.8011 (m-80) outliers start: 29 outliers final: 11 residues processed: 200 average time/residue: 0.8508 time to fit residues: 184.9317 Evaluate side-chains 182 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 733 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 37 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 294 GLN A 371 ASN B 220 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8137 Z= 0.277 Angle : 0.644 8.131 11013 Z= 0.333 Chirality : 0.043 0.223 1244 Planarity : 0.004 0.064 1394 Dihedral : 4.946 20.673 1099 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.27 % Allowed : 24.50 % Favored : 72.23 % 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: -0.80 (0.27), residues: 987 helix: 0.87 (0.28), residues: 336 sheet: -1.82 (0.35), residues: 185 loop : -0.95 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.008 0.002 HIS A 220 PHE 0.018 0.002 PHE A 212 TYR 0.011 0.001 TYR R 722 ARG 0.013 0.001 ARG N 105 *********************** 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 205 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7224 (t0) cc_final: 0.6732 (p0) REVERT: B 171 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6781 (mp) REVERT: N 67 ARG cc_start: 0.7218 (ptt-90) cc_final: 0.6989 (ptt-90) REVERT: N 90 ASP cc_start: 0.7094 (p0) cc_final: 0.6778 (p0) REVERT: R 753 TYR cc_start: 0.8647 (m-80) cc_final: 0.8255 (m-80) REVERT: R 832 PHE cc_start: 0.8289 (m-80) cc_final: 0.8079 (m-80) outliers start: 28 outliers final: 14 residues processed: 191 average time/residue: 0.7360 time to fit residues: 154.7498 Evaluate side-chains 184 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 598 LEU 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 799 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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 236 GLN A 278 ASN A 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8137 Z= 0.188 Angle : 0.615 7.924 11013 Z= 0.316 Chirality : 0.043 0.240 1244 Planarity : 0.004 0.058 1394 Dihedral : 4.755 20.562 1099 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.33 % Allowed : 25.44 % Favored : 72.23 % 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: -0.68 (0.27), residues: 987 helix: 0.99 (0.28), residues: 339 sheet: -1.86 (0.35), residues: 200 loop : -0.79 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.006 0.001 HIS B 62 PHE 0.017 0.001 PHE A 212 TYR 0.014 0.001 TYR R 785 ARG 0.014 0.001 ARG N 105 *********************** 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 198 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: B 171 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6584 (mp) REVERT: N 67 ARG cc_start: 0.7075 (ptt-90) cc_final: 0.6856 (ptt-90) REVERT: N 90 ASP cc_start: 0.6903 (p0) cc_final: 0.6634 (p0) REVERT: R 753 TYR cc_start: 0.8550 (m-80) cc_final: 0.8174 (m-80) REVERT: R 801 LEU cc_start: 0.8505 (mt) cc_final: 0.8105 (mt) REVERT: R 832 PHE cc_start: 0.8173 (m-80) cc_final: 0.7965 (m-80) outliers start: 20 outliers final: 11 residues processed: 187 average time/residue: 0.7747 time to fit residues: 158.9416 Evaluate side-chains 171 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 93 VAL 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 776 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 220 GLN R 849 ASN ** R 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8137 Z= 0.250 Angle : 0.649 8.462 11013 Z= 0.330 Chirality : 0.044 0.275 1244 Planarity : 0.004 0.054 1394 Dihedral : 4.828 20.571 1099 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.98 % Allowed : 27.42 % Favored : 70.60 % 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: -0.64 (0.27), residues: 987 helix: 1.07 (0.28), residues: 338 sheet: -1.96 (0.35), residues: 196 loop : -0.76 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.011 0.002 HIS A 220 PHE 0.014 0.002 PHE B 235 TYR 0.013 0.001 TYR A 360 ARG 0.014 0.001 ARG B 150 ********************** 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 175 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7616 (mtm-85) cc_final: 0.6988 (mtt-85) REVERT: N 67 ARG cc_start: 0.7063 (ptt-90) cc_final: 0.6714 (ptt-90) REVERT: R 753 TYR cc_start: 0.8598 (m-80) cc_final: 0.8264 (m-80) REVERT: R 832 PHE cc_start: 0.8248 (m-80) cc_final: 0.8039 (m-80) outliers start: 17 outliers final: 8 residues processed: 167 average time/residue: 0.7927 time to fit residues: 144.8010 Evaluate side-chains 163 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.3980 chunk 23 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.191256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160659 restraints weight = 8884.768| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.98 r_work: 0.3724 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8137 Z= 0.228 Angle : 0.647 7.897 11013 Z= 0.329 Chirality : 0.044 0.274 1244 Planarity : 0.005 0.057 1394 Dihedral : 4.796 20.232 1099 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.10 % Allowed : 27.54 % Favored : 70.36 % 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: -0.63 (0.27), residues: 987 helix: 1.05 (0.28), residues: 338 sheet: -1.99 (0.35), residues: 192 loop : -0.72 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.009 0.002 HIS A 362 PHE 0.014 0.002 PHE B 235 TYR 0.016 0.002 TYR R 785 ARG 0.012 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.52 seconds wall clock time: 60 minutes 41.34 seconds (3641.34 seconds total)