Starting phenix.real_space_refine on Wed Mar 4 16:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lth_0968/03_2026/6lth_0968.map" } resolution = 3.0 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= 0.001 sd= 0.046 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 78 5.16 5 C 9485 2.51 5 N 2636 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14970 Number of models: 1 Model: "" Number of chains: 9 Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1022 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3670 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2070 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 13, 'TRANS': 245} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2120 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 6, 'TRANS': 254} Chain breaks: 3 Chain: "O" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2632 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 19, 'TRANS': 305} Chain breaks: 3 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2015 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 2 Chain: "Q" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 860 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "R" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3342 SG CYS L2094 67.010 67.650 63.954 1.00 48.48 S Time building chain proxies: 3.54, per 1000 atoms: 0.24 Number of scatterers: 14970 At special positions: 0 Unit cell: (148.72, 160.16, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 78 16.00 O 2770 8.00 N 2636 7.00 C 9485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 463.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 8 sheets defined 67.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.565A pdb=" N ASN I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.553A pdb=" N GLN I 415 " --> pdb=" O ASN I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 446 through 475 removed outlier: 3.883A pdb=" N ALA I 450 " --> pdb=" O SER I 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1668 through 1679 removed outlier: 4.055A pdb=" N GLY L1679 " --> pdb=" O SER L1675 " (cutoff:3.500A) Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1698 through 1701 removed outlier: 3.727A pdb=" N ILE L1701 " --> pdb=" O ASP L1698 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1698 through 1701' Processing helix chain 'L' and resid 1705 through 1709 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1840 through 1846 removed outlier: 3.578A pdb=" N TRP L1844 " --> pdb=" O GLY L1840 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE L1846 " --> pdb=" O LEU L1842 " (cutoff:3.500A) Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2002 removed outlier: 4.200A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2016 removed outlier: 4.405A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 removed outlier: 3.643A pdb=" N MET L2055 " --> pdb=" O ASP L2051 " (cutoff:3.500A) Processing helix chain 'L' and resid 2069 through 2071 No H-bonds generated for 'chain 'L' and resid 2069 through 2071' Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2127 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 3.722A pdb=" N LEU L2144 " --> pdb=" O PRO L2140 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 removed outlier: 3.655A pdb=" N ALA L2182 " --> pdb=" O ASP L2178 " (cutoff:3.500A) Processing helix chain 'L' and resid 2190 through 2209 removed outlier: 3.704A pdb=" N GLN L2209 " --> pdb=" O ALA L2205 " (cutoff:3.500A) Processing helix chain 'L' and resid 2228 through 2243 Processing helix chain 'L' and resid 2247 through 2252 removed outlier: 3.552A pdb=" N PHE L2251 " --> pdb=" O ASN L2247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR L2252 " --> pdb=" O HIS L2248 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2247 through 2252' Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 93 through 98 Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 248 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 305 through 324 removed outlier: 4.135A pdb=" N THR M 309 " --> pdb=" O GLY M 305 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 312 " --> pdb=" O VAL M 308 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS M 324 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 348 Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 452 removed outlier: 4.693A pdb=" N GLY N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 475 removed outlier: 3.533A pdb=" N LEU N 475 " --> pdb=" O ASP N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 490 removed outlier: 3.676A pdb=" N ASN N 489 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 616 Processing helix chain 'N' and resid 620 through 628 removed outlier: 3.554A pdb=" N SER N 624 " --> pdb=" O TRP N 620 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY N 628 " --> pdb=" O SER N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 702 Processing helix chain 'N' and resid 859 through 949 Processing helix chain 'O' and resid 439 through 446 removed outlier: 3.599A pdb=" N ARG O 443 " --> pdb=" O HIS O 439 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 475 Processing helix chain 'O' and resid 482 through 490 removed outlier: 3.825A pdb=" N CYS O 486 " --> pdb=" O THR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 657 through 661 removed outlier: 4.133A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 3.740A pdb=" N THR O 676 " --> pdb=" O PRO O 672 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL O 684 " --> pdb=" O LEU O 680 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.535A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 711 through 716 Processing helix chain 'O' and resid 868 through 952 removed outlier: 4.277A pdb=" N LYS O 872 " --> pdb=" O ALA O 868 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 132 removed outlier: 3.687A pdb=" N LYS P 131 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 132 " --> pdb=" O ALA P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 128 through 132' Processing helix chain 'P' and resid 134 through 141 Processing helix chain 'P' and resid 143 through 173 removed outlier: 3.604A pdb=" N TYR P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 327 Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 356 through 361 Processing helix chain 'P' and resid 400 through 411 Processing helix chain 'P' and resid 414 through 447 removed outlier: 3.830A pdb=" N ASP P 447 " --> pdb=" O SER P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 468 Processing helix chain 'P' and resid 478 through 484 removed outlier: 3.701A pdb=" N PHE P 483 " --> pdb=" O GLU P 480 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 505 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 276 Processing helix chain 'R' and resid 14 through 38 Processing helix chain 'R' and resid 58 through 62 Processing sheet with id=AA1, first strand: chain 'L' and resid 1814 through 1816 removed outlier: 6.197A pdb=" N LYS L1815 " --> pdb=" O ILE O 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AA4, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AA5, first strand: chain 'N' and resid 424 through 426 removed outlier: 7.440A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.781A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AA8, first strand: chain 'P' and resid 309 through 311 removed outlier: 3.550A pdb=" N MET P 366 " --> pdb=" O LYS P 296 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2691 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: 2.67 Time building geometry restraints manager: 2.02 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: 4993 1.34 - 1.46: 3097 1.46 - 1.58: 7030 1.58 - 1.70: 0 1.70 - 1.81: 129 Bond restraints: 15249 Sorted by residual: bond pdb=" CA SER N 456 " pdb=" CB SER N 456 " ideal model delta sigma weight residual 1.532 1.489 0.043 1.65e-02 3.67e+03 6.65e+00 bond pdb=" N SER Q 208 " pdb=" CA SER Q 208 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" N ASN L1692 " pdb=" CA ASN L1692 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.14e+00 bond pdb=" N ARG I 408 " pdb=" CA ARG I 408 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 5.00e+00 bond pdb=" CA SER Q 210 " pdb=" CB SER Q 210 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.69e-02 3.50e+03 4.98e+00 ... (remaining 15244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 19947 1.79 - 3.59: 549 3.59 - 5.38: 62 5.38 - 7.17: 18 7.17 - 8.96: 5 Bond angle restraints: 20581 Sorted by residual: angle pdb=" C GLY M 304 " pdb=" N GLY M 305 " pdb=" CA GLY M 305 " ideal model delta sigma weight residual 121.32 112.36 8.96 1.79e+00 3.12e-01 2.51e+01 angle pdb=" N ASP M 345 " pdb=" CA ASP M 345 " pdb=" C ASP M 345 " ideal model delta sigma weight residual 111.11 105.49 5.62 1.20e+00 6.94e-01 2.20e+01 angle pdb=" N VAL O 707 " pdb=" CA VAL O 707 " pdb=" C VAL O 707 " ideal model delta sigma weight residual 109.02 104.88 4.14 9.30e-01 1.16e+00 1.98e+01 angle pdb=" C ASN N 511 " pdb=" CA ASN N 511 " pdb=" CB ASN N 511 " ideal model delta sigma weight residual 111.73 117.49 -5.76 1.42e+00 4.96e-01 1.64e+01 angle pdb=" C LYS L1662 " pdb=" N ASP L1663 " pdb=" CA ASP L1663 " ideal model delta sigma weight residual 125.66 132.45 -6.79 1.85e+00 2.92e-01 1.35e+01 ... (remaining 20576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8300 17.85 - 35.70: 916 35.70 - 53.54: 153 53.54 - 71.39: 32 71.39 - 89.24: 11 Dihedral angle restraints: 9412 sinusoidal: 3968 harmonic: 5444 Sorted by residual: dihedral pdb=" CA MET M 38 " pdb=" C MET M 38 " pdb=" N PHE M 39 " pdb=" CA PHE M 39 " ideal model delta harmonic sigma weight residual -180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN M 342 " pdb=" C ASN M 342 " pdb=" N THR M 343 " pdb=" CA THR M 343 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ARG R 38 " pdb=" C ARG R 38 " pdb=" N LEU R 39 " pdb=" CA LEU R 39 " ideal model delta harmonic sigma weight residual -180.00 -155.21 -24.79 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1928 0.061 - 0.121: 351 0.121 - 0.182: 18 0.182 - 0.242: 0 0.242 - 0.303: 3 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA ASN N 511 " pdb=" N ASN N 511 " pdb=" C ASN N 511 " pdb=" CB ASN N 511 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU N 505 " pdb=" N GLU N 505 " pdb=" C GLU N 505 " pdb=" CB GLU N 505 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA GLU Q 209 " pdb=" N GLU Q 209 " pdb=" C GLU Q 209 " pdb=" CB GLU Q 209 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2297 not shown) Planarity restraints: 2650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR O 458 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO O 459 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO O 459 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO O 459 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS M 350 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO M 351 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO M 351 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 351 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 537 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO O 538 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO O 538 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 538 " 0.034 5.00e-02 4.00e+02 ... (remaining 2647 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 876 2.72 - 3.26: 16043 3.26 - 3.81: 25396 3.81 - 4.35: 31645 4.35 - 4.90: 52289 Nonbonded interactions: 126249 Sorted by model distance: nonbonded pdb=" OD1 ASP L2157 " pdb=" N ARG L2158 " model vdw 2.174 3.120 nonbonded pdb=" OG SER L1645 " pdb=" OG SER O 669 " model vdw 2.203 3.040 nonbonded pdb=" O SER P 410 " pdb=" OG SER P 413 " model vdw 2.212 3.040 nonbonded pdb=" O LEU L2017 " pdb=" NH2 ARG L2057 " model vdw 2.213 3.120 nonbonded pdb=" OD1 ASP N 471 " pdb=" OG1 THR O 528 " model vdw 2.215 3.040 ... (remaining 126244 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=0.21 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: 12.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 0.086 15253 Z= 0.255 Angle : 0.725 10.065 20584 Z= 0.422 Chirality : 0.045 0.303 2300 Planarity : 0.005 0.067 2650 Dihedral : 15.071 89.242 5840 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.16), residues: 1795 helix: -1.79 (0.12), residues: 1156 sheet: -3.03 (0.62), residues: 46 loop : -2.97 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 441 TYR 0.018 0.002 TYR M 26 PHE 0.019 0.002 PHE N 906 TRP 0.016 0.002 TRP N 507 HIS 0.007 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00554 (15249) covalent geometry : angle 0.72027 (20581) hydrogen bonds : bond 0.10887 ( 918) hydrogen bonds : angle 5.98150 ( 2691) metal coordination : bond 0.04596 ( 4) metal coordination : angle 6.76327 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8694 (mttt) cc_final: 0.8262 (tmmt) REVERT: I 449 GLU cc_start: 0.6571 (pt0) cc_final: 0.6181 (pt0) REVERT: I 453 THR cc_start: 0.7723 (m) cc_final: 0.6962 (m) REVERT: I 457 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8196 (mt-10) REVERT: M 178 GLU cc_start: 0.7996 (tp30) cc_final: 0.7622 (tp30) REVERT: O 616 TYR cc_start: 0.8152 (m-80) cc_final: 0.7933 (m-80) REVERT: P 154 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7175 (tm-30) REVERT: P 158 ASP cc_start: 0.8056 (p0) cc_final: 0.7474 (p0) REVERT: P 162 MET cc_start: 0.7669 (tpt) cc_final: 0.7357 (tpp) REVERT: P 339 CYS cc_start: 0.6624 (m) cc_final: 0.4789 (m) REVERT: P 359 GLN cc_start: 0.7436 (pt0) cc_final: 0.6724 (tp40) REVERT: Q 223 ARG cc_start: 0.6949 (ttt-90) cc_final: 0.6743 (mmm-85) REVERT: Q 249 GLU cc_start: 0.7768 (tp30) cc_final: 0.7567 (tm-30) outliers start: 2 outliers final: 1 residues processed: 366 average time/residue: 0.7332 time to fit residues: 290.0246 Evaluate side-chains 248 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 167 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L1997 ASN L2268 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN M 322 HIS N 451 ASN N 489 ASN N 511 ASN N 513 GLN N 638 HIS N 938 GLN N 948 GLN O 439 HIS O 501 HIS ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 632 GLN O 925 GLN P 432 ASN P 484 GLN Q 190 HIS Q 253 GLN Q 267 ASN ** Q 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS R 70 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091777 restraints weight = 29178.102| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.97 r_work: 0.3152 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15253 Z= 0.190 Angle : 0.648 7.957 20584 Z= 0.336 Chirality : 0.042 0.160 2300 Planarity : 0.005 0.049 2650 Dihedral : 5.071 29.596 2005 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.41 % Allowed : 14.80 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1795 helix: 0.19 (0.14), residues: 1167 sheet: -2.26 (0.76), residues: 40 loop : -2.13 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 687 TYR 0.021 0.002 TYR O 941 PHE 0.021 0.002 PHE N 906 TRP 0.013 0.001 TRP N 507 HIS 0.005 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00443 (15249) covalent geometry : angle 0.64757 (20581) hydrogen bonds : bond 0.04480 ( 918) hydrogen bonds : angle 4.61871 ( 2691) metal coordination : bond 0.01111 ( 4) metal coordination : angle 2.09141 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8873 (mttt) cc_final: 0.8144 (tmmt) REVERT: I 449 GLU cc_start: 0.6940 (pt0) cc_final: 0.6539 (pt0) REVERT: I 457 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8160 (mt-10) REVERT: L 1705 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8579 (t0) REVERT: L 2098 GLU cc_start: 0.8206 (tt0) cc_final: 0.7773 (mm-30) REVERT: M 26 TYR cc_start: 0.7900 (m-80) cc_final: 0.7659 (m-80) REVERT: M 178 GLU cc_start: 0.8910 (tp30) cc_final: 0.8412 (tp30) REVERT: N 698 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: N 913 MET cc_start: 0.8270 (tmm) cc_final: 0.7597 (tmm) REVERT: O 687 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7731 (mtm110) REVERT: O 930 ASP cc_start: 0.7821 (m-30) cc_final: 0.7291 (OUTLIER) REVERT: O 944 MET cc_start: 0.6765 (mmm) cc_final: 0.6493 (tpt) REVERT: P 154 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7729 (tm-30) REVERT: P 158 ASP cc_start: 0.8734 (p0) cc_final: 0.8158 (p0) REVERT: P 167 ASP cc_start: 0.8510 (t0) cc_final: 0.8308 (OUTLIER) REVERT: P 330 ASP cc_start: 0.7864 (t0) cc_final: 0.7574 (t70) REVERT: Q 209 GLU cc_start: 0.8198 (pm20) cc_final: 0.7912 (pm20) REVERT: Q 223 ARG cc_start: 0.7006 (ttt-90) cc_final: 0.6668 (mmm-85) REVERT: Q 249 GLU cc_start: 0.8139 (tp30) cc_final: 0.7403 (tm-30) REVERT: Q 250 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7730 (tm-30) REVERT: Q 253 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7576 (mp-120) outliers start: 56 outliers final: 20 residues processed: 306 average time/residue: 0.6513 time to fit residues: 217.1855 Evaluate side-chains 276 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain L residue 1705 ASN Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain N residue 515 ASP Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain O residue 510 ILE Chi-restraints excluded: chain O residue 631 THR Chi-restraints excluded: chain O residue 637 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 253 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 79 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 58 optimal weight: 0.0050 chunk 151 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN M 179 ASN M 244 GLN N 451 ASN N 511 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN O 935 HIS R 15 GLN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094881 restraints weight = 29243.267| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.99 r_work: 0.3203 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15253 Z= 0.121 Angle : 0.587 8.391 20584 Z= 0.301 Chirality : 0.040 0.148 2300 Planarity : 0.005 0.052 2650 Dihedral : 4.457 25.203 2003 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.41 % Allowed : 16.32 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1795 helix: 1.24 (0.15), residues: 1167 sheet: -1.04 (0.79), residues: 40 loop : -1.62 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 478 TYR 0.022 0.002 TYR O 941 PHE 0.019 0.001 PHE N 906 TRP 0.012 0.001 TRP N 507 HIS 0.004 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00265 (15249) covalent geometry : angle 0.58740 (20581) hydrogen bonds : bond 0.03837 ( 918) hydrogen bonds : angle 4.14926 ( 2691) metal coordination : bond 0.00449 ( 4) metal coordination : angle 0.85347 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 295 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8842 (mttt) cc_final: 0.8072 (tmmt) REVERT: I 424 MET cc_start: 0.9338 (tpt) cc_final: 0.9129 (tpt) REVERT: I 449 GLU cc_start: 0.6710 (pt0) cc_final: 0.6351 (pt0) REVERT: I 457 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8200 (mt-10) REVERT: M 38 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8612 (mtm) REVERT: N 674 MET cc_start: 0.6492 (mmt) cc_final: 0.5198 (mtp) REVERT: N 698 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: N 913 MET cc_start: 0.8177 (tmm) cc_final: 0.7401 (tmm) REVERT: O 619 ASP cc_start: 0.8286 (t0) cc_final: 0.7904 (t0) REVERT: O 913 MET cc_start: 0.8954 (tmm) cc_final: 0.8354 (tpp) REVERT: O 930 ASP cc_start: 0.7853 (m-30) cc_final: 0.7434 (t0) REVERT: O 944 MET cc_start: 0.6749 (mmm) cc_final: 0.6512 (tpt) REVERT: P 154 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7632 (tm-30) REVERT: P 158 ASP cc_start: 0.8738 (p0) cc_final: 0.8306 (p0) REVERT: P 162 MET cc_start: 0.8548 (tpp) cc_final: 0.8293 (tpp) REVERT: P 167 ASP cc_start: 0.8494 (t0) cc_final: 0.8290 (OUTLIER) REVERT: P 330 ASP cc_start: 0.7771 (t0) cc_final: 0.7465 (t70) REVERT: P 366 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6448 (ptp) REVERT: P 502 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7196 (mmm-85) REVERT: Q 209 GLU cc_start: 0.8244 (pm20) cc_final: 0.8041 (pm20) REVERT: Q 249 GLU cc_start: 0.8060 (tp30) cc_final: 0.7727 (tm-30) REVERT: Q 250 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8027 (tm-30) REVERT: Q 267 ASN cc_start: 0.7742 (m-40) cc_final: 0.7280 (t0) REVERT: R 44 SER cc_start: 0.7591 (m) cc_final: 0.7210 (m) outliers start: 56 outliers final: 14 residues processed: 323 average time/residue: 0.6400 time to fit residues: 225.4637 Evaluate side-chains 264 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 253 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 68 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 0.0010 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 511 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN O 925 GLN P 310 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.114123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.093227 restraints weight = 29281.215| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.00 r_work: 0.3176 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15253 Z= 0.145 Angle : 0.596 7.620 20584 Z= 0.303 Chirality : 0.041 0.164 2300 Planarity : 0.004 0.047 2650 Dihedral : 4.318 24.759 2003 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.65 % Allowed : 18.21 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1795 helix: 1.51 (0.15), residues: 1178 sheet: -0.92 (0.90), residues: 34 loop : -1.43 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 229 TYR 0.026 0.002 TYR M 47 PHE 0.021 0.001 PHE M 17 TRP 0.011 0.001 TRP N 507 HIS 0.007 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00334 (15249) covalent geometry : angle 0.59596 (20581) hydrogen bonds : bond 0.03792 ( 918) hydrogen bonds : angle 4.07002 ( 2691) metal coordination : bond 0.00566 ( 4) metal coordination : angle 1.32406 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 356 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6695 (pp30) REVERT: I 399 LYS cc_start: 0.8872 (mttt) cc_final: 0.8079 (tmmt) REVERT: I 457 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8287 (mt-10) REVERT: I 472 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7335 (m170) REVERT: L 1705 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (t0) REVERT: L 2230 MET cc_start: 0.8910 (tpp) cc_final: 0.8378 (mmp) REVERT: M 272 ASN cc_start: 0.8123 (p0) cc_final: 0.7868 (m-40) REVERT: N 674 MET cc_start: 0.6464 (mmt) cc_final: 0.5161 (mtp) REVERT: N 698 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: N 913 MET cc_start: 0.8184 (tmm) cc_final: 0.7394 (tmm) REVERT: N 914 ASP cc_start: 0.8418 (t0) cc_final: 0.8168 (t0) REVERT: O 913 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8382 (tpp) REVERT: O 921 GLU cc_start: 0.8333 (tp30) cc_final: 0.8118 (tp30) REVERT: O 930 ASP cc_start: 0.7792 (m-30) cc_final: 0.7337 (t0) REVERT: O 944 MET cc_start: 0.6846 (mmm) cc_final: 0.6542 (tpt) REVERT: P 154 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7699 (tm-30) REVERT: P 158 ASP cc_start: 0.8759 (p0) cc_final: 0.8344 (p0) REVERT: P 162 MET cc_start: 0.8612 (tpp) cc_final: 0.8410 (tpp) REVERT: P 330 ASP cc_start: 0.7812 (t0) cc_final: 0.7511 (t70) REVERT: P 366 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6649 (mpt) REVERT: Q 209 GLU cc_start: 0.8266 (pm20) cc_final: 0.8061 (pm20) REVERT: Q 249 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: Q 267 ASN cc_start: 0.7774 (m-40) cc_final: 0.7303 (t0) REVERT: R 44 SER cc_start: 0.7575 (m) cc_final: 0.7266 (m) outliers start: 60 outliers final: 30 residues processed: 295 average time/residue: 0.6104 time to fit residues: 197.5773 Evaluate side-chains 274 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1705 ASN Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2127 ILE Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain M residue 46 ARG Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 246 GLU Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 337 VAL Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 26 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 149 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 451 ASN N 511 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.114434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093356 restraints weight = 29330.902| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.01 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15253 Z= 0.138 Angle : 0.592 8.436 20584 Z= 0.300 Chirality : 0.040 0.176 2300 Planarity : 0.004 0.050 2650 Dihedral : 4.243 24.262 2003 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.29 % Allowed : 20.10 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1795 helix: 1.61 (0.15), residues: 1184 sheet: -0.79 (0.91), residues: 34 loop : -1.32 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 251 TYR 0.023 0.002 TYR M 47 PHE 0.023 0.001 PHE M 17 TRP 0.011 0.001 TRP N 507 HIS 0.005 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00318 (15249) covalent geometry : angle 0.59214 (20581) hydrogen bonds : bond 0.03702 ( 918) hydrogen bonds : angle 4.00167 ( 2691) metal coordination : bond 0.00428 ( 4) metal coordination : angle 1.24820 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8869 (mttt) cc_final: 0.8074 (tmmt) REVERT: I 457 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8319 (mt-10) REVERT: I 468 ARG cc_start: 0.7627 (tmm-80) cc_final: 0.7406 (tmm-80) REVERT: I 472 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7257 (m170) REVERT: L 1956 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8515 (mm-30) REVERT: M 272 ASN cc_start: 0.8197 (p0) cc_final: 0.7978 (m-40) REVERT: N 674 MET cc_start: 0.6649 (mmt) cc_final: 0.5351 (mtp) REVERT: N 698 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: N 904 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7501 (mtm-85) REVERT: N 913 MET cc_start: 0.8152 (tmm) cc_final: 0.7312 (tmm) REVERT: N 914 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8229 (t0) REVERT: O 619 ASP cc_start: 0.8371 (t0) cc_final: 0.7982 (t0) REVERT: O 913 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8426 (tpp) REVERT: O 921 GLU cc_start: 0.8318 (tp30) cc_final: 0.8114 (tp30) REVERT: O 930 ASP cc_start: 0.7784 (m-30) cc_final: 0.7355 (t0) REVERT: O 944 MET cc_start: 0.6973 (mmm) cc_final: 0.6649 (tpt) REVERT: P 154 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7658 (tm-30) REVERT: P 158 ASP cc_start: 0.8754 (p0) cc_final: 0.8350 (p0) REVERT: P 162 MET cc_start: 0.8640 (tpp) cc_final: 0.8371 (tpp) REVERT: P 359 GLN cc_start: 0.7210 (pt0) cc_final: 0.6695 (tp40) REVERT: P 366 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6576 (mpt) REVERT: Q 249 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: Q 250 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8111 (tm-30) REVERT: Q 267 ASN cc_start: 0.7816 (m-40) cc_final: 0.7345 (t0) REVERT: R 44 SER cc_start: 0.7479 (m) cc_final: 0.7249 (m) outliers start: 54 outliers final: 28 residues processed: 286 average time/residue: 0.6195 time to fit residues: 194.4535 Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1833 ARG Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2127 ILE Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 914 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain N residue 944 MET Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain O residue 913 MET Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 231 VAL Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 155 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 81 optimal weight: 0.0970 chunk 140 optimal weight: 0.4980 chunk 26 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN L1843 HIS L2176 GLN M 79 HIS M 179 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN O 925 GLN P 500 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094087 restraints weight = 29296.144| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.01 r_work: 0.3191 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15253 Z= 0.130 Angle : 0.585 9.512 20584 Z= 0.295 Chirality : 0.040 0.175 2300 Planarity : 0.004 0.050 2650 Dihedral : 4.121 24.629 2003 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.35 % Allowed : 20.52 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1795 helix: 1.73 (0.15), residues: 1184 sheet: -0.63 (0.92), residues: 34 loop : -1.23 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 229 TYR 0.020 0.001 TYR O 941 PHE 0.024 0.001 PHE M 17 TRP 0.011 0.001 TRP N 507 HIS 0.004 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00298 (15249) covalent geometry : angle 0.58500 (20581) hydrogen bonds : bond 0.03613 ( 918) hydrogen bonds : angle 3.93351 ( 2691) metal coordination : bond 0.00367 ( 4) metal coordination : angle 1.22985 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 399 LYS cc_start: 0.8871 (mttt) cc_final: 0.8075 (tmmt) REVERT: I 424 MET cc_start: 0.9348 (tpt) cc_final: 0.9143 (tpt) REVERT: I 457 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8289 (mt-10) REVERT: I 472 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7262 (m170) REVERT: L 1745 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7602 (tm) REVERT: L 1956 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8517 (mm-30) REVERT: L 1962 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8191 (ptmt) REVERT: M 38 MET cc_start: 0.9002 (mtp) cc_final: 0.8690 (mtm) REVERT: M 190 ARG cc_start: 0.8915 (ttm170) cc_final: 0.8351 (ttt-90) REVERT: M 272 ASN cc_start: 0.8281 (p0) cc_final: 0.8054 (t0) REVERT: N 674 MET cc_start: 0.6615 (mmt) cc_final: 0.5244 (mtm) REVERT: N 698 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: N 913 MET cc_start: 0.8112 (tmm) cc_final: 0.7319 (tmm) REVERT: N 914 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8212 (t0) REVERT: O 904 ARG cc_start: 0.7968 (ptt180) cc_final: 0.7679 (ptt180) REVERT: O 921 GLU cc_start: 0.8342 (tp30) cc_final: 0.8114 (tp30) REVERT: O 930 ASP cc_start: 0.7853 (m-30) cc_final: 0.7421 (t0) REVERT: O 944 MET cc_start: 0.6850 (mmm) cc_final: 0.6494 (tpt) REVERT: P 154 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7687 (tm-30) REVERT: P 158 ASP cc_start: 0.8756 (p0) cc_final: 0.8351 (p0) REVERT: P 162 MET cc_start: 0.8634 (tpp) cc_final: 0.8408 (tpp) REVERT: P 167 ASP cc_start: 0.8465 (t0) cc_final: 0.8182 (t0) REVERT: P 330 ASP cc_start: 0.7439 (t70) cc_final: 0.7223 (t70) REVERT: P 359 GLN cc_start: 0.7180 (pt0) cc_final: 0.6706 (tp40) REVERT: P 366 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6615 (mpt) REVERT: Q 249 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: Q 267 ASN cc_start: 0.7812 (m-40) cc_final: 0.7320 (t0) REVERT: R 44 SER cc_start: 0.7331 (m) cc_final: 0.7126 (m) outliers start: 55 outliers final: 29 residues processed: 287 average time/residue: 0.6273 time to fit residues: 197.5651 Evaluate side-chains 277 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 51 TRP Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 914 ASP Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 621 ASN Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 129 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1843 HIS L1858 HIS L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 GLN M 348 GLN N 451 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 621 ASN O 925 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091903 restraints weight = 29127.162| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.00 r_work: 0.3151 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15253 Z= 0.198 Angle : 0.639 9.435 20584 Z= 0.323 Chirality : 0.042 0.181 2300 Planarity : 0.005 0.052 2650 Dihedral : 4.262 27.694 2003 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.17 % Allowed : 21.19 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1795 helix: 1.64 (0.15), residues: 1186 sheet: -0.64 (0.91), residues: 34 loop : -1.21 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 251 TYR 0.022 0.002 TYR N 462 PHE 0.023 0.002 PHE M 17 TRP 0.012 0.001 TRP O 620 HIS 0.005 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00468 (15249) covalent geometry : angle 0.63885 (20581) hydrogen bonds : bond 0.03876 ( 918) hydrogen bonds : angle 4.04236 ( 2691) metal coordination : bond 0.01092 ( 4) metal coordination : angle 1.63258 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 356 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6596 (pp30) REVERT: I 457 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8281 (mt-10) REVERT: I 472 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7374 (m170) REVERT: L 1956 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8461 (mm-30) REVERT: N 674 MET cc_start: 0.6696 (mmt) cc_final: 0.5309 (mtm) REVERT: N 698 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: N 913 MET cc_start: 0.8190 (tmm) cc_final: 0.7387 (tmm) REVERT: O 619 ASP cc_start: 0.8405 (t0) cc_final: 0.8030 (t0) REVERT: O 921 GLU cc_start: 0.8333 (tp30) cc_final: 0.8060 (tp30) REVERT: O 930 ASP cc_start: 0.7902 (m-30) cc_final: 0.7463 (t0) REVERT: P 145 GLN cc_start: 0.7722 (pm20) cc_final: 0.7520 (tt0) REVERT: P 154 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7702 (tm-30) REVERT: P 158 ASP cc_start: 0.8759 (p0) cc_final: 0.8355 (p0) REVERT: P 162 MET cc_start: 0.8687 (tpp) cc_final: 0.8421 (tpp) REVERT: P 330 ASP cc_start: 0.7545 (t70) cc_final: 0.7324 (t70) REVERT: P 359 GLN cc_start: 0.7291 (pt0) cc_final: 0.6760 (tp40) REVERT: P 366 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6689 (mpt) REVERT: Q 249 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: Q 267 ASN cc_start: 0.7809 (m-40) cc_final: 0.7306 (t0) REVERT: R 44 SER cc_start: 0.7430 (m) cc_final: 0.7216 (m) outliers start: 52 outliers final: 30 residues processed: 277 average time/residue: 0.5977 time to fit residues: 181.7263 Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 472 HIS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 301 LEU Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 205 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 91 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 119 optimal weight: 0.0770 chunk 113 optimal weight: 0.3980 chunk 172 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 147 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1843 HIS L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093852 restraints weight = 29473.726| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.01 r_work: 0.3192 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15253 Z= 0.138 Angle : 0.626 11.049 20584 Z= 0.314 Chirality : 0.040 0.181 2300 Planarity : 0.005 0.052 2650 Dihedral : 4.165 28.299 2003 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.92 % Allowed : 22.17 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1795 helix: 1.73 (0.15), residues: 1187 sheet: -0.58 (0.91), residues: 34 loop : -1.13 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Q 251 TYR 0.022 0.001 TYR N 462 PHE 0.024 0.001 PHE M 17 TRP 0.012 0.001 TRP N 507 HIS 0.004 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00321 (15249) covalent geometry : angle 0.62605 (20581) hydrogen bonds : bond 0.03672 ( 918) hydrogen bonds : angle 3.96181 ( 2691) metal coordination : bond 0.00435 ( 4) metal coordination : angle 1.38397 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 457 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8284 (mt-10) REVERT: I 466 ARG cc_start: 0.8593 (tmm160) cc_final: 0.8321 (tmm-80) REVERT: L 1745 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7609 (tm) REVERT: L 1956 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8426 (mm-30) REVERT: L 1962 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8159 (ptmt) REVERT: N 674 MET cc_start: 0.6604 (mmt) cc_final: 0.5420 (mtp) REVERT: N 698 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: N 913 MET cc_start: 0.8153 (tmm) cc_final: 0.7353 (tmm) REVERT: N 914 ASP cc_start: 0.8428 (t0) cc_final: 0.8206 (t0) REVERT: O 917 ARG cc_start: 0.8996 (ttm-80) cc_final: 0.8764 (ptp-110) REVERT: O 921 GLU cc_start: 0.8319 (tp30) cc_final: 0.8069 (tp30) REVERT: O 930 ASP cc_start: 0.7824 (m-30) cc_final: 0.7407 (t0) REVERT: O 944 MET cc_start: 0.6494 (mmm) cc_final: 0.6261 (tpt) REVERT: P 145 GLN cc_start: 0.7675 (pm20) cc_final: 0.7430 (tt0) REVERT: P 154 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7676 (tm-30) REVERT: P 158 ASP cc_start: 0.8757 (p0) cc_final: 0.8336 (p0) REVERT: P 162 MET cc_start: 0.8685 (tpp) cc_final: 0.8466 (tpp) REVERT: P 330 ASP cc_start: 0.7560 (t70) cc_final: 0.7316 (t70) REVERT: P 359 GLN cc_start: 0.7178 (pt0) cc_final: 0.6673 (tp40) REVERT: P 366 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6736 (mpt) REVERT: Q 249 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: Q 253 GLN cc_start: 0.8617 (tp40) cc_final: 0.8113 (mm110) REVERT: Q 267 ASN cc_start: 0.7798 (m-40) cc_final: 0.7261 (t0) outliers start: 48 outliers final: 32 residues processed: 276 average time/residue: 0.6023 time to fit residues: 182.6127 Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2104 SER Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 918 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 77 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2176 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 451 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091999 restraints weight = 29347.471| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.00 r_work: 0.3157 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15253 Z= 0.214 Angle : 0.667 10.077 20584 Z= 0.338 Chirality : 0.043 0.179 2300 Planarity : 0.005 0.067 2650 Dihedral : 4.310 29.805 2003 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.80 % Allowed : 22.72 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1795 helix: 1.59 (0.14), residues: 1188 sheet: -0.68 (0.91), residues: 34 loop : -1.11 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 251 TYR 0.023 0.002 TYR N 462 PHE 0.024 0.002 PHE M 17 TRP 0.011 0.001 TRP O 507 HIS 0.005 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00505 (15249) covalent geometry : angle 0.66716 (20581) hydrogen bonds : bond 0.03956 ( 918) hydrogen bonds : angle 4.08212 ( 2691) metal coordination : bond 0.01195 ( 4) metal coordination : angle 1.68271 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 457 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8383 (mt-10) REVERT: L 1705 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8650 (t0) REVERT: L 1745 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7657 (tm) REVERT: L 1956 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8513 (mm-30) REVERT: L 1962 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8142 (ptmt) REVERT: M 46 ARG cc_start: 0.8500 (ptm160) cc_final: 0.8300 (ptm160) REVERT: N 674 MET cc_start: 0.6721 (mmt) cc_final: 0.5325 (mtm) REVERT: N 698 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: N 913 MET cc_start: 0.8183 (tmm) cc_final: 0.7366 (tmm) REVERT: O 619 ASP cc_start: 0.8392 (t0) cc_final: 0.7994 (t0) REVERT: O 917 ARG cc_start: 0.9060 (ttm-80) cc_final: 0.8783 (ptp-110) REVERT: O 921 GLU cc_start: 0.8301 (tp30) cc_final: 0.8040 (tp30) REVERT: O 930 ASP cc_start: 0.7868 (m-30) cc_final: 0.7417 (t0) REVERT: O 944 MET cc_start: 0.6360 (mmm) cc_final: 0.6129 (tpt) REVERT: P 154 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7736 (tm-30) REVERT: P 158 ASP cc_start: 0.8771 (p0) cc_final: 0.8359 (p0) REVERT: P 162 MET cc_start: 0.8697 (tpp) cc_final: 0.8424 (tpp) REVERT: P 359 GLN cc_start: 0.7593 (pt0) cc_final: 0.6737 (tp40) REVERT: P 366 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6744 (mpt) REVERT: Q 249 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: Q 267 ASN cc_start: 0.7806 (m-40) cc_final: 0.7261 (t0) outliers start: 46 outliers final: 31 residues processed: 268 average time/residue: 0.6126 time to fit residues: 180.0047 Evaluate side-chains 266 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1705 ASN Chi-restraints excluded: chain L residue 1745 LEU Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2104 SER Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain L residue 2263 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 438 VAL Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain P residue 457 GLN Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 176 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094533 restraints weight = 28862.694| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.96 r_work: 0.3235 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 15253 Z= 0.210 Angle : 0.677 11.488 20584 Z= 0.342 Chirality : 0.043 0.184 2300 Planarity : 0.005 0.066 2650 Dihedral : 4.393 30.622 2003 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.74 % Allowed : 22.90 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1795 helix: 1.56 (0.14), residues: 1187 sheet: -0.72 (0.91), residues: 34 loop : -1.12 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG Q 251 TYR 0.023 0.002 TYR N 462 PHE 0.023 0.002 PHE M 17 TRP 0.011 0.001 TRP O 507 HIS 0.004 0.001 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00496 (15249) covalent geometry : angle 0.67717 (20581) hydrogen bonds : bond 0.04020 ( 918) hydrogen bonds : angle 4.12307 ( 2691) metal coordination : bond 0.01146 ( 4) metal coordination : angle 1.74008 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 457 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8274 (mt-10) REVERT: L 1956 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8542 (mm-30) REVERT: L 1962 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8202 (ptmt) REVERT: N 674 MET cc_start: 0.6772 (mmt) cc_final: 0.5374 (mtm) REVERT: N 698 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: N 913 MET cc_start: 0.8202 (tmm) cc_final: 0.7428 (tmm) REVERT: O 619 ASP cc_start: 0.8307 (t0) cc_final: 0.8002 (t0) REVERT: O 917 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8827 (ptp-110) REVERT: O 921 GLU cc_start: 0.8238 (tp30) cc_final: 0.7987 (tp30) REVERT: O 930 ASP cc_start: 0.7817 (m-30) cc_final: 0.7449 (t0) REVERT: O 944 MET cc_start: 0.6526 (mmm) cc_final: 0.6238 (tpt) REVERT: P 154 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7779 (tm-30) REVERT: P 158 ASP cc_start: 0.8696 (p0) cc_final: 0.8336 (p0) REVERT: P 162 MET cc_start: 0.8649 (tpp) cc_final: 0.8422 (tpp) REVERT: P 359 GLN cc_start: 0.7685 (pt0) cc_final: 0.6895 (tp40) REVERT: P 366 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6875 (mpt) REVERT: P 441 MET cc_start: 0.9224 (mpp) cc_final: 0.8938 (mmt) REVERT: Q 229 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7371 (mtm180) REVERT: Q 249 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: Q 253 GLN cc_start: 0.8671 (tp40) cc_final: 0.8229 (mm110) REVERT: Q 267 ASN cc_start: 0.7917 (m-40) cc_final: 0.7341 (t0) outliers start: 45 outliers final: 30 residues processed: 261 average time/residue: 0.6035 time to fit residues: 172.8250 Evaluate side-chains 255 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 356 GLN Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain L residue 1639 ILE Chi-restraints excluded: chain L residue 1664 ILE Chi-restraints excluded: chain L residue 1850 ASP Chi-restraints excluded: chain L residue 1853 GLU Chi-restraints excluded: chain L residue 1962 LYS Chi-restraints excluded: chain L residue 2104 SER Chi-restraints excluded: chain L residue 2187 VAL Chi-restraints excluded: chain L residue 2239 LEU Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain N residue 673 VAL Chi-restraints excluded: chain N residue 685 ASP Chi-restraints excluded: chain N residue 698 GLU Chi-restraints excluded: chain N residue 939 LEU Chi-restraints excluded: chain O residue 438 VAL Chi-restraints excluded: chain O residue 603 GLU Chi-restraints excluded: chain O residue 659 LEU Chi-restraints excluded: chain O residue 709 THR Chi-restraints excluded: chain O residue 712 VAL Chi-restraints excluded: chain O residue 884 ILE Chi-restraints excluded: chain O residue 892 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 339 CYS Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 439 GLU Chi-restraints excluded: chain Q residue 215 VAL Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 220 THR Chi-restraints excluded: chain Q residue 241 LEU Chi-restraints excluded: chain Q residue 249 GLU Chi-restraints excluded: chain R residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 123 optimal weight: 0.3980 chunk 9 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 0.0670 chunk 30 optimal weight: 0.0050 overall best weight: 0.0828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 356 GLN I 464 GLN ** L1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1741 GLN L1843 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 267 ASN ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 925 GLN P 362 HIS ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098966 restraints weight = 28375.717| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.91 r_work: 0.3310 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15253 Z= 0.125 Angle : 0.650 11.659 20584 Z= 0.325 Chirality : 0.040 0.207 2300 Planarity : 0.005 0.055 2650 Dihedral : 4.142 31.898 2003 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.83 % Allowed : 24.30 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1795 helix: 1.82 (0.15), residues: 1185 sheet: -0.69 (0.93), residues: 34 loop : -0.90 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 251 TYR 0.015 0.001 TYR M 313 PHE 0.028 0.001 PHE M 17 TRP 0.012 0.001 TRP O 620 HIS 0.004 0.000 HIS Q 252 Details of bonding type rmsd covalent geometry : bond 0.00278 (15249) covalent geometry : angle 0.64985 (20581) hydrogen bonds : bond 0.03570 ( 918) hydrogen bonds : angle 3.93225 ( 2691) metal coordination : bond 0.00752 ( 4) metal coordination : angle 1.03402 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.87 seconds wall clock time: 110 minutes 50.97 seconds (6650.97 seconds total)