Starting phenix.real_space_refine on Fri Oct 23 13:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.cif Found real_map, /net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.map" model { file = "/net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36jl_77611/10_2026/36jl_77611.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Cu 2 5.60 5 P 2 5.49 5 S 56 5.16 5 C 6284 2.51 5 N 1630 2.21 5 O 1769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9744 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9648 Classifications: {'peptide': 1189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1133} Chain breaks: 14 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 96 Unusual residues: {' CA': 1, 'CPS': 1, 'CU1': 2, 'NAG': 2} Inner-chain residues flagged as termini: ['pdbres="SEP A2406 "', 'pdbres="SEP A2407 "'] Classifications: {'peptide': 2, 'undetermined': 6, 'water': 1} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1, None: 7} Not linked: pdbres="NAG A2401 " pdbres="NAG A2402 " Not linked: pdbres="NAG A2402 " pdbres=" CA A2403 " Not linked: pdbres=" CA A2403 " pdbres="CU1 A2404 " Not linked: pdbres="CU1 A2404 " pdbres="CU1 A2405 " Not linked: pdbres="CU1 A2405 " pdbres="SEP A2406 " ... (remaining 2 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6998 SG CYS A2000 50.484 42.176 68.976 1.00115.89 S ATOM 2101 SG CYS A 310 58.957 49.686 85.513 1.00116.04 S Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9744 At special positions: 0 Unit cell: (85.152, 89.587, 136.598, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 2 28.99 Ca 1 19.99 S 56 16.00 P 2 15.00 O 1769 8.00 N 1630 7.00 C 6284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2401 " - " ASN A2118 " " NAG A2402 " - " ASN A 239 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 325.9 milliseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 19 sheets defined 10.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.538A pdb=" N SER A 109 " --> pdb=" O TRP A 106 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 110 " --> pdb=" O LYS A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 106 through 110' Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.739A pdb=" N ASP A 125 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 127 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.968A pdb=" N SER A 241 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 242' Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.742A pdb=" N GLN A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.583A pdb=" N ASP A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 592 removed outlier: 3.508A pdb=" N ASN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.705A pdb=" N ALA A 610 " --> pdb=" O PRO A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 1753 through 1757 removed outlier: 3.863A pdb=" N GLY A1757 " --> pdb=" O GLU A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 removed outlier: 3.902A pdb=" N ALA A1824 " --> pdb=" O HIS A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1844 through 1849 Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1890 through 1899 Processing helix chain 'A' and resid 2002 through 2009 Processing helix chain 'A' and resid 2033 through 2035 No H-bonds generated for 'chain 'A' and resid 2033 through 2035' Processing helix chain 'A' and resid 2047 through 2051 Processing helix chain 'A' and resid 2186 through 2190 removed outlier: 3.848A pdb=" N ILE A2190 " --> pdb=" O ASP A2187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 removed outlier: 3.784A pdb=" N ASP A 82 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 78 removed outlier: 4.617A pdb=" N ALA A 175 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR A 75 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 177 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN A 77 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYS A 179 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 234 removed outlier: 6.752A pdb=" N PHE A 195 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 258 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 197 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET A 260 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 199 " --> pdb=" O MET A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.396A pdb=" N LEU A 245 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP A 327 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY A 247 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.561A pdb=" N THR A 514 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP A 482 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 390 through 394 Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 456 removed outlier: 6.454A pdb=" N LEU A 453 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS A 554 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY A 455 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 549 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A 532 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.728A pdb=" N ASN A 572 " --> pdb=" O TYR A 636 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 633 " --> pdb=" O MET A 682 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 622 through 629 removed outlier: 5.031A pdb=" N LEU A 705 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 625 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 707 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 627 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AB3, first strand: chain 'A' and resid 658 through 660 Processing sheet with id=AB4, first strand: chain 'A' and resid 1730 through 1738 removed outlier: 4.419A pdb=" N PHE A1699 " --> pdb=" O PHE A1738 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1763 through 1766 removed outlier: 6.052A pdb=" N ILE A1763 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N CYS A1858 " --> pdb=" O ILE A1763 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A1765 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1917 through 1921 removed outlier: 6.990A pdb=" N THR A1985 " --> pdb=" O ARG A1966 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG A1966 " --> pdb=" O THR A1985 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1933 through 1935 Processing sheet with id=AB8, first strand: chain 'A' and resid 2023 through 2024 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2023 through 2024 current: chain 'A' and resid 2113 through 2114 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 2272 through 2273 removed outlier: 11.464A pdb=" N LEU A2297 " --> pdb=" O THR A2244 " (cutoff:3.500A) removed outlier: 11.363A pdb=" N THR A2244 " --> pdb=" O LEU A2297 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLY A2242 " --> pdb=" O PRO A2299 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR A2305 " --> pdb=" O LYS A2236 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N LYS A2236 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 12.456A pdb=" N ARG A2307 " --> pdb=" O PHE A2234 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N PHE A2234 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 11.475A pdb=" N HIS A2309 " --> pdb=" O VAL A2232 " (cutoff:3.500A) removed outlier: 12.917A pdb=" N VAL A2232 " --> pdb=" O HIS A2309 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2248 through 2250 227 hydrogen bonds defined for protein. 561 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: 2.34 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1584 1.32 - 1.44: 2899 1.44 - 1.57: 5427 1.57 - 1.69: 9 1.69 - 1.81: 93 Bond restraints: 10012 Sorted by residual: bond pdb=" C GLN A 592 " pdb=" O GLN A 592 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.30e-02 5.92e+03 7.53e+00 bond pdb=" CA ARG A 593 " pdb=" CB ARG A 593 " ideal model delta sigma weight residual 1.541 1.515 0.026 1.20e-02 6.94e+03 4.56e+00 bond pdb=" CB PRO A 606 " pdb=" CG PRO A 606 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.18e+00 bond pdb=" N ARG A 593 " pdb=" CA ARG A 593 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.23e-02 6.61e+03 3.60e+00 bond pdb=" CG PRO A 606 " pdb=" CD PRO A 606 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.39e+00 ... (remaining 10007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 13093 1.67 - 3.34: 385 3.34 - 5.00: 77 5.00 - 6.67: 11 6.67 - 8.34: 5 Bond angle restraints: 13571 Sorted by residual: angle pdb=" N THR A 292 " pdb=" CA THR A 292 " pdb=" C THR A 292 " ideal model delta sigma weight residual 110.24 118.58 -8.34 1.30e+00 5.92e-01 4.11e+01 angle pdb=" CA PRO A 606 " pdb=" N PRO A 606 " pdb=" CD PRO A 606 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" N GLN A 592 " pdb=" CA GLN A 592 " pdb=" C GLN A 592 " ideal model delta sigma weight residual 110.46 103.56 6.90 1.48e+00 4.57e-01 2.17e+01 angle pdb=" CA ILE A 591 " pdb=" C ILE A 591 " pdb=" N GLN A 592 " ideal model delta sigma weight residual 117.53 113.26 4.27 1.19e+00 7.06e-01 1.29e+01 angle pdb=" N ARG A 121 " pdb=" CA ARG A 121 " pdb=" C ARG A 121 " ideal model delta sigma weight residual 111.28 107.43 3.85 1.09e+00 8.42e-01 1.25e+01 ... (remaining 13566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 5444 23.62 - 47.24: 437 47.24 - 70.86: 62 70.86 - 94.48: 16 94.48 - 118.10: 1 Dihedral angle restraints: 5960 sinusoidal: 2492 harmonic: 3468 Sorted by residual: dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual -86.00 -146.16 60.16 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA ASN A2141 " pdb=" C ASN A2141 " pdb=" N PRO A2142 " pdb=" CA PRO A2142 " ideal model delta harmonic sigma weight residual 180.00 154.50 25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR A1911 " pdb=" C THR A1911 " pdb=" N PHE A1912 " pdb=" CA PHE A1912 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 974 0.040 - 0.080: 344 0.080 - 0.121: 114 0.121 - 0.161: 28 0.161 - 0.201: 1 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C1 NAG A2402 " pdb=" ND2 ASN A 239 " pdb=" C2 NAG A2402 " pdb=" O5 NAG A2402 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE A 617 " pdb=" N ILE A 617 " pdb=" C ILE A 617 " pdb=" CB ILE A 617 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE A1921 " pdb=" N ILE A1921 " pdb=" C ILE A1921 " pdb=" CB ILE A1921 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 1458 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 591 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C ILE A 591 " 0.083 2.00e-02 2.50e+03 pdb=" O ILE A 591 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN A 592 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 605 " -0.061 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 606 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A2141 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A2142 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2142 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2142 " 0.027 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 118 2.62 - 3.19: 8222 3.19 - 3.76: 14727 3.76 - 4.33: 22307 4.33 - 4.90: 36859 Nonbonded interactions: 82233 Sorted by model distance: nonbonded pdb=" OH TYR A 16 " pdb=" OE2 GLU A 204 " model vdw 2.047 3.040 nonbonded pdb=" OE2 GLU A 110 " pdb=" OH TYR A 114 " model vdw 2.068 3.040 nonbonded pdb=" ND1 HIS A2005 " pdb="CU CU1 A2404 " model vdw 2.089 3.060 nonbonded pdb=" OG1 THR A 516 " pdb=" OD1 ASP A 519 " model vdw 2.132 3.040 nonbonded pdb=" ND1 HIS A1954 " pdb="CU CU1 A2404 " model vdw 2.152 3.060 ... (remaining 82228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.300 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 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 : 0.004 0.102 10021 Z= 0.172 Angle : 0.711 8.339 13591 Z= 0.384 Chirality : 0.047 0.201 1461 Planarity : 0.005 0.088 1696 Dihedral : 16.892 118.102 3705 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.09 % Allowed : 17.96 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.23), residues: 1159 helix: -2.68 (0.50), residues: 81 sheet: -1.23 (0.26), residues: 401 loop : -1.96 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1781 TYR 0.021 0.001 TYR A 586 PHE 0.029 0.001 PHE A 652 TRP 0.012 0.001 TRP A1942 HIS 0.007 0.001 HIS A1822 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (10012) covalent geometry : angle 0.70994 / 0.38 (13571) SS BOND : bond 0.00132 / 0.07 ( 7) SS BOND : angle 0.65130 / 0.37 ( 14) hydrogen bonds : bond 0.16667 / 10.48 ( 227) hydrogen bonds : angle 8.33035 / 5.47 ( 561) link_NAG-ASN : bond 0.00416 / 0.22 ( 2) link_NAG-ASN : angle 2.23944 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 SER cc_start: 0.6579 (t) cc_final: 0.6236 (p) REVERT: A 1766 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 1805 ASN cc_start: 0.7139 (p0) cc_final: 0.6859 (p0) REVERT: A 1896 GLU cc_start: 0.7026 (tt0) cc_final: 0.6807 (pt0) REVERT: A 2010 MET cc_start: 0.7870 (ttm) cc_final: 0.7430 (ttm) REVERT: A 2229 TRP cc_start: 0.6854 (p-90) cc_final: 0.6087 (p-90) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.0903 time to fit residues: 19.9239 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 384 HIS A1954 HIS A2246 GLN A2311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126630 restraints weight = 11566.281| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.72 r_work: 0.3290 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10021 Z= 0.178 Angle : 0.636 9.959 13591 Z= 0.329 Chirality : 0.047 0.264 1461 Planarity : 0.004 0.054 1696 Dihedral : 7.879 108.422 1421 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.84 % Allowed : 17.96 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.23), residues: 1159 helix: -2.62 (0.47), residues: 82 sheet: -0.98 (0.26), residues: 396 loop : -1.93 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.016 0.002 TYR A2043 PHE 0.021 0.002 PHE A1983 TRP 0.012 0.001 TRP A1942 HIS 0.002 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10012) covalent geometry : angle 0.63434 / 0.33 (13571) SS BOND : bond 0.00180 / 0.07 ( 7) SS BOND : angle 0.88589 / 0.54 ( 14) hydrogen bonds : bond 0.03500 / 2.22 ( 227) hydrogen bonds : angle 6.88243 / 4.55 ( 561) link_NAG-ASN : bond 0.00434 / 0.23 ( 2) link_NAG-ASN : angle 1.95569 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.382 Fit side-chains REVERT: A 1805 ASN cc_start: 0.7336 (p0) cc_final: 0.7088 (p0) REVERT: A 2229 TRP cc_start: 0.7558 (p-90) cc_final: 0.7153 (p-90) REVERT: A 2311 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7467 (pp30) outliers start: 30 outliers final: 17 residues processed: 174 average time/residue: 0.0881 time to fit residues: 22.1775 Evaluate side-chains 168 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2154 THR Chi-restraints excluded: chain A residue 2311 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 39, 84, 22, 115, 26, 2, 68, 83, 89, 100] chunk 108 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1950 ASN A2311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.129529 restraints weight = 11480.107| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.68 r_work: 0.3285 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10021 Z= 0.108 Angle : 0.565 10.550 13591 Z= 0.290 Chirality : 0.045 0.230 1461 Planarity : 0.004 0.051 1696 Dihedral : 7.591 105.663 1421 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.65 % Allowed : 19.19 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1159 helix: -2.20 (0.50), residues: 81 sheet: -0.88 (0.28), residues: 373 loop : -1.79 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 282 TYR 0.017 0.001 TYR A2043 PHE 0.018 0.001 PHE A1983 TRP 0.011 0.001 TRP A1942 HIS 0.003 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10012) covalent geometry : angle 0.56380 / 0.29 (13571) SS BOND : bond 0.00136 / 0.07 ( 7) SS BOND : angle 0.64607 / 0.39 ( 14) hydrogen bonds : bond 0.02764 / 1.76 ( 227) hydrogen bonds : angle 6.44364 / 4.25 ( 561) link_NAG-ASN : bond 0.00469 / 0.25 ( 2) link_NAG-ASN : angle 1.74819 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.322 Fit side-chains REVERT: A 69 MET cc_start: 0.8795 (mmm) cc_final: 0.8461 (mmt) REVERT: A 1748 TYR cc_start: 0.7083 (t80) cc_final: 0.6788 (t80) REVERT: A 1768 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6037 (pp20) REVERT: A 1805 ASN cc_start: 0.7155 (p0) cc_final: 0.6911 (p0) REVERT: A 1934 MET cc_start: 0.8702 (ptp) cc_final: 0.8444 (ptp) REVERT: A 2229 TRP cc_start: 0.7501 (p-90) cc_final: 0.7126 (p-90) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.0841 time to fit residues: 20.9703 Evaluate side-chains 170 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2020 LYS Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2311 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [77, 31, 84, 60, 89, 116, 20, 28, 107, 78, 46] chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS A1919 HIS A2129 ASN A2155 HIS A2311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122893 restraints weight = 11832.914| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3233 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10021 Z= 0.265 Angle : 0.677 10.052 13591 Z= 0.352 Chirality : 0.048 0.252 1461 Planarity : 0.004 0.059 1696 Dihedral : 8.028 106.976 1421 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.44 % Allowed : 18.53 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.23), residues: 1159 helix: -2.41 (0.48), residues: 80 sheet: -0.74 (0.28), residues: 357 loop : -1.94 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 531 TYR 0.017 0.002 TYR A2043 PHE 0.041 0.002 PHE A 679 TRP 0.009 0.002 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (10012) covalent geometry : angle 0.67522 / 0.35 (13571) SS BOND : bond 0.00236 / 0.11 ( 7) SS BOND : angle 1.04119 / 0.63 ( 14) hydrogen bonds : bond 0.03645 / 2.32 ( 227) hydrogen bonds : angle 6.76580 / 4.48 ( 561) link_NAG-ASN : bond 0.00436 / 0.23 ( 2) link_NAG-ASN : angle 2.00463 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.331 Fit side-chains REVERT: A 512 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.4846 (ttmt) REVERT: A 614 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.6011 (mtp) REVERT: A 1768 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: A 1805 ASN cc_start: 0.7233 (p0) cc_final: 0.6867 (p0) REVERT: A 2097 TYR cc_start: 0.8540 (p90) cc_final: 0.8322 (p90) REVERT: A 2229 TRP cc_start: 0.7588 (p-90) cc_final: 0.7144 (p-90) REVERT: A 2302 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8045 (mt) REVERT: A 2309 HIS cc_start: 0.7124 (m170) cc_final: 0.6818 (m170) outliers start: 47 outliers final: 27 residues processed: 186 average time/residue: 0.0803 time to fit residues: 21.8703 Evaluate side-chains 183 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1896 GLU Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2273 LEU Chi-restraints excluded: chain A residue 2302 LEU Chi-restraints excluded: chain A residue 2311 GLN Chi-restraints excluded: chain A residue 2319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [49, 40, 13, 86, 42, 56, 91, 89, 96, 117, 51] chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125449 restraints weight = 11610.074| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.77 r_work: 0.3229 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10021 Z= 0.158 Angle : 0.601 9.823 13591 Z= 0.309 Chirality : 0.046 0.237 1461 Planarity : 0.004 0.054 1696 Dihedral : 7.807 107.061 1421 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.88 % Allowed : 19.47 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.23), residues: 1159 helix: -2.26 (0.50), residues: 80 sheet: -0.80 (0.27), residues: 384 loop : -1.85 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.014 0.001 TYR A1976 PHE 0.041 0.002 PHE A 679 TRP 0.011 0.001 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10012) covalent geometry : angle 0.59924 / 0.31 (13571) SS BOND : bond 0.00157 / 0.08 ( 7) SS BOND : angle 0.80337 / 0.49 ( 14) hydrogen bonds : bond 0.02970 / 1.87 ( 227) hydrogen bonds : angle 6.50073 / 4.28 ( 561) link_NAG-ASN : bond 0.00470 / 0.25 ( 2) link_NAG-ASN : angle 1.80125 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.335 Fit side-chains REVERT: A 327 ASP cc_start: 0.7863 (t0) cc_final: 0.7649 (p0) REVERT: A 1768 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6178 (pp20) REVERT: A 1805 ASN cc_start: 0.7223 (p0) cc_final: 0.6879 (p0) REVERT: A 1911 THR cc_start: 0.6511 (OUTLIER) cc_final: 0.6179 (m) REVERT: A 2229 TRP cc_start: 0.7568 (p-90) cc_final: 0.7126 (p-90) REVERT: A 2236 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7149 (tppt) REVERT: A 2309 HIS cc_start: 0.7151 (m170) cc_final: 0.6884 (m170) outliers start: 41 outliers final: 26 residues processed: 185 average time/residue: 0.0822 time to fit residues: 22.4388 Evaluate side-chains 178 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2020 LYS Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2107 LEU Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2311 GLN Chi-restraints excluded: chain A residue 2312 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [89, 88, 97, 70, 11, 23, 79, 16, 51, 100, 32] chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123774 restraints weight = 11817.818| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.71 r_work: 0.3227 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10021 Z= 0.215 Angle : 0.646 10.936 13591 Z= 0.330 Chirality : 0.047 0.246 1461 Planarity : 0.004 0.068 1696 Dihedral : 7.916 108.276 1421 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.54 % Allowed : 19.75 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.23), residues: 1159 helix: -2.38 (0.49), residues: 80 sheet: -0.80 (0.27), residues: 383 loop : -1.90 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.018 0.002 TYR A2043 PHE 0.035 0.002 PHE A 679 TRP 0.011 0.001 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (10012) covalent geometry : angle 0.64431 / 0.33 (13571) SS BOND : bond 0.00197 / 0.09 ( 7) SS BOND : angle 0.88477 / 0.54 ( 14) hydrogen bonds : bond 0.03259 / 2.06 ( 227) hydrogen bonds : angle 6.55211 / 4.32 ( 561) link_NAG-ASN : bond 0.00441 / 0.23 ( 2) link_NAG-ASN : angle 1.82334 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 512 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4804 (ttmt) REVERT: A 1768 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6176 (pp20) REVERT: A 1793 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: A 1805 ASN cc_start: 0.7189 (p0) cc_final: 0.6806 (p0) REVERT: A 1911 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6079 (m) REVERT: A 2229 TRP cc_start: 0.7591 (p-90) cc_final: 0.7125 (p-90) REVERT: A 2309 HIS cc_start: 0.7107 (m170) cc_final: 0.6814 (m170) REVERT: A 2324 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8439 (mt) outliers start: 48 outliers final: 34 residues processed: 184 average time/residue: 0.0817 time to fit residues: 21.9656 Evaluate side-chains 186 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1793 GLU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1896 GLU Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2107 LEU Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2207 LYS Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2273 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2311 GLN Chi-restraints excluded: chain A residue 2312 SER Chi-restraints excluded: chain A residue 2324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [86, 36, 25, 92, 35, 112, 47, 14, 109, 73, 41] chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124155 restraints weight = 11773.406| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.71 r_work: 0.3223 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10021 Z= 0.186 Angle : 0.628 12.078 13591 Z= 0.320 Chirality : 0.046 0.242 1461 Planarity : 0.004 0.053 1696 Dihedral : 7.844 108.717 1421 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.25 % Allowed : 19.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.23), residues: 1159 helix: -2.42 (0.48), residues: 80 sheet: -0.78 (0.27), residues: 391 loop : -1.86 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 531 TYR 0.019 0.002 TYR A2043 PHE 0.033 0.002 PHE A 679 TRP 0.012 0.001 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10012) covalent geometry : angle 0.62686 / 0.32 (13571) SS BOND : bond 0.00167 / 0.07 ( 7) SS BOND : angle 0.80859 / 0.50 ( 14) hydrogen bonds : bond 0.03098 / 1.97 ( 227) hydrogen bonds : angle 6.45063 / 4.25 ( 561) link_NAG-ASN : bond 0.00462 / 0.24 ( 2) link_NAG-ASN : angle 1.81945 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 512 LYS cc_start: 0.5239 (OUTLIER) cc_final: 0.4772 (ttmt) REVERT: A 1768 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6186 (pp20) REVERT: A 1793 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: A 1805 ASN cc_start: 0.7147 (p0) cc_final: 0.6770 (p0) REVERT: A 1911 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.6111 (m) REVERT: A 2229 TRP cc_start: 0.7583 (p-90) cc_final: 0.7137 (p-90) outliers start: 45 outliers final: 33 residues processed: 184 average time/residue: 0.0841 time to fit residues: 22.7190 Evaluate side-chains 187 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1793 GLU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1896 GLU Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2107 LEU Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2207 LYS Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2273 LEU Chi-restraints excluded: chain A residue 2282 VAL Chi-restraints excluded: chain A residue 2288 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [5, 107, 99, 114, 46, 45, 35, 90, 116, 62, 115] chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 HIS A 602 GLN A 618 ASN A2087 GLN A2311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122832 restraints weight = 11773.421| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.71 r_work: 0.3211 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10021 Z= 0.236 Angle : 0.669 12.750 13591 Z= 0.342 Chirality : 0.048 0.247 1461 Planarity : 0.004 0.054 1696 Dihedral : 7.978 110.001 1421 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.54 % Allowed : 20.04 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.23), residues: 1159 helix: -2.54 (0.47), residues: 82 sheet: -0.85 (0.27), residues: 384 loop : -1.94 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.019 0.002 TYR A2043 PHE 0.026 0.002 PHE A1983 TRP 0.011 0.002 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (10012) covalent geometry : angle 0.66726 / 0.34 (13571) SS BOND : bond 0.00206 / 0.09 ( 7) SS BOND : angle 0.90706 / 0.56 ( 14) hydrogen bonds : bond 0.03377 / 2.15 ( 227) hydrogen bonds : angle 6.53981 / 4.33 ( 561) link_NAG-ASN : bond 0.00456 / 0.24 ( 2) link_NAG-ASN : angle 1.89318 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 512 LYS cc_start: 0.5250 (OUTLIER) cc_final: 0.4817 (ttmt) REVERT: A 1768 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6244 (pp20) REVERT: A 1793 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: A 1805 ASN cc_start: 0.7206 (p0) cc_final: 0.6777 (p0) REVERT: A 1911 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.6188 (m) REVERT: A 2229 TRP cc_start: 0.7612 (p-90) cc_final: 0.7130 (p-90) REVERT: A 2309 HIS cc_start: 0.7155 (m170) cc_final: 0.6906 (m170) outliers start: 48 outliers final: 36 residues processed: 183 average time/residue: 0.0846 time to fit residues: 22.7599 Evaluate side-chains 188 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1793 GLU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1896 GLU Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2107 LEU Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2207 LYS Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2273 LEU Chi-restraints excluded: chain A residue 2288 ASP Chi-restraints excluded: chain A residue 2311 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [6, 106, 1, 36, 74, 71, 40, 110, 2, 68, 112] chunk 6 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 ASN A2087 GLN A2311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122717 restraints weight = 11722.184| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.70 r_work: 0.3211 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10021 Z= 0.235 Angle : 0.675 13.466 13591 Z= 0.345 Chirality : 0.048 0.248 1461 Planarity : 0.004 0.055 1696 Dihedral : 8.016 110.631 1421 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.44 % Allowed : 20.23 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.23), residues: 1159 helix: -2.47 (0.48), residues: 80 sheet: -0.87 (0.27), residues: 384 loop : -1.94 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.020 0.002 TYR A2043 PHE 0.026 0.002 PHE A1983 TRP 0.012 0.002 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (10012) covalent geometry : angle 0.67306 / 0.34 (13571) SS BOND : bond 0.00227 / 0.10 ( 7) SS BOND : angle 1.45067 / 0.98 ( 14) hydrogen bonds : bond 0.03367 / 2.15 ( 227) hydrogen bonds : angle 6.56108 / 4.35 ( 561) link_NAG-ASN : bond 0.00446 / 0.23 ( 2) link_NAG-ASN : angle 1.91011 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 512 LYS cc_start: 0.5241 (OUTLIER) cc_final: 0.4810 (ttmt) REVERT: A 1768 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: A 1793 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: A 1805 ASN cc_start: 0.7249 (p0) cc_final: 0.6814 (p0) REVERT: A 1911 THR cc_start: 0.6502 (OUTLIER) cc_final: 0.6233 (m) REVERT: A 2229 TRP cc_start: 0.7624 (p-90) cc_final: 0.7124 (p-90) outliers start: 47 outliers final: 37 residues processed: 183 average time/residue: 0.0824 time to fit residues: 22.1390 Evaluate side-chains 186 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1747 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1793 GLU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1896 GLU Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1964 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2069 SER Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2107 LEU Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2122 THR Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2207 LYS Chi-restraints excluded: chain A residue 2246 GLN Chi-restraints excluded: chain A residue 2272 THR Chi-restraints excluded: chain A residue 2273 LEU Chi-restraints excluded: chain A residue 2288 ASP Chi-restraints excluded: chain A residue 2311 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [7, 83, 15, 105, 2, 30, 95, 73, 32, 31, 97] chunk 7 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 ASN A1729 GLN A2311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129725 restraints weight = 11391.473| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.65 r_work: 0.3319 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10021 Z= 0.110 Angle : 0.595 14.824 13591 Z= 0.300 Chirality : 0.045 0.231 1461 Planarity : 0.004 0.048 1696 Dihedral : 7.560 108.517 1421 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.02 % Allowed : 21.46 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.23), residues: 1159 helix: -2.21 (0.50), residues: 80 sheet: -0.76 (0.27), residues: 386 loop : -1.71 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.021 0.001 TYR A2043 PHE 0.020 0.001 PHE A1983 TRP 0.013 0.001 TRP A1942 HIS 0.006 0.001 HIS A2309 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10012) covalent geometry : angle 0.59361 / 0.30 (13571) SS BOND : bond 0.00109 / 0.04 ( 7) SS BOND : angle 0.88137 / 0.60 ( 14) hydrogen bonds : bond 0.02610 / 1.66 ( 227) hydrogen bonds : angle 6.15976 / 4.06 ( 561) link_NAG-ASN : bond 0.00511 / 0.27 ( 2) link_NAG-ASN : angle 1.72901 / 0.96 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.8812 (mmm) cc_final: 0.8484 (mmt) REVERT: A 424 LYS cc_start: 0.7410 (ptmt) cc_final: 0.7189 (tttp) REVERT: A 512 LYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4723 (ttmt) REVERT: A 1768 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6378 (pp20) REVERT: A 1793 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: A 1805 ASN cc_start: 0.7177 (p0) cc_final: 0.6823 (p0) REVERT: A 1911 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6273 (m) REVERT: A 2073 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8641 (t) REVERT: A 2229 TRP cc_start: 0.7524 (p-90) cc_final: 0.7113 (p-90) outliers start: 32 outliers final: 21 residues processed: 172 average time/residue: 0.0835 time to fit residues: 21.0188 Evaluate side-chains 173 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain A residue 1788 SER Chi-restraints excluded: chain A residue 1793 GLU Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1911 THR Chi-restraints excluded: chain A residue 1983 PHE Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2073 VAL Chi-restraints excluded: chain A residue 2108 ASP Chi-restraints excluded: chain A residue 2182 SER Chi-restraints excluded: chain A residue 2207 LYS Chi-restraints excluded: chain A residue 2288 ASP Chi-restraints excluded: chain A residue 2311 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [3, 108, 27, 40, 75, 41, 0, 39, 73, 97, 66] chunk 3 optimal weight: 0.9990 chunk 108 optimal weight: 0.0370 chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.0000 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN A 609 GLN A 618 ASN A1729 GLN ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127675 restraints weight = 11593.204| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.71 r_work: 0.3333 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10021 Z= 0.116 Angle : 0.595 14.629 13591 Z= 0.297 Chirality : 0.045 0.234 1461 Planarity : 0.004 0.048 1696 Dihedral : 7.420 107.325 1421 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.65 % Allowed : 22.12 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1159 helix: -2.15 (0.50), residues: 80 sheet: -0.70 (0.27), residues: 386 loop : -1.63 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.012 0.001 TYR A1976 PHE 0.020 0.001 PHE A1983 TRP 0.012 0.001 TRP A1942 HIS 0.004 0.001 HIS A1954 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10012) covalent geometry : angle 0.59339 / 0.30 (13571) SS BOND : bond 0.00113 / 0.05 ( 7) SS BOND : angle 0.88345 / 0.61 ( 14) hydrogen bonds : bond 0.02618 / 1.68 ( 227) hydrogen bonds : angle 6.05279 / 4.00 ( 561) link_NAG-ASN : bond 0.00463 / 0.24 ( 2) link_NAG-ASN : angle 1.67518 / 0.91 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.76 seconds wall clock time: 43 minutes 42.72 seconds (2622.72 seconds total)