Starting phenix.real_space_refine on Thu Mar 5 08:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936.map" model { file = "/net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rmg_4936/03_2026/6rmg_4936_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 784 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6442 2.51 5 N 1556 2.21 5 O 1761 1.98 5 H 9327 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A ARG 1114": not complete - not flipped Time to flip 26 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: 19137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 16284 Classifications: {'peptide': 1026} Link IDs: {'CIS': 2, 'PTRANS': 45, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2369 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 455 Unusual residues: {'NAG': 5, 'Y01': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.30, per 1000 atoms: 0.17 Number of scatterers: 19137 At special positions: 0 Unit cell: (91.9933, 126.186, 140.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1761 8.00 N 1556 7.00 C 6442 6.00 H 9327 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG C 1 " - " ASN A1000 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 534.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 140 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 182 " 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 58.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.730A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.895A pdb=" N ALA A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.803A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.812A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.529A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.780A pdb=" N ASP A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 294' Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 4.018A pdb=" N ALA A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 458 Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.636A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.827A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.612A pdb=" N GLU A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.581A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.583A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.644A pdb=" N LEU A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 745' Processing helix chain 'A' and resid 746 through 770 removed outlier: 4.369A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 811 through 814 Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.742A pdb=" N GLU A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.735A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.501A pdb=" N GLY A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1005 removed outlier: 3.648A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A1005 " --> pdb=" O TYR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.502A pdb=" N LEU A1016 " --> pdb=" O GLY A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.645A pdb=" N SER A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1075 removed outlier: 3.545A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1103 removed outlier: 3.639A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A1101 " --> pdb=" O THR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1121 removed outlier: 3.602A pdb=" N HIS A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1152 through 1168 Processing helix chain 'A' and resid 1169 through 1178 removed outlier: 3.925A pdb=" N VAL A1173 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.135A pdb=" N GLU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 157 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.199A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.661A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 803 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 86 removed outlier: 6.844A pdb=" N ASP B 147 " --> pdb=" O THR B 125 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1332 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: 4.74 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9311 1.03 - 1.22: 29 1.22 - 1.42: 4095 1.42 - 1.61: 5854 1.61 - 1.81: 109 Bond restraints: 19398 Sorted by residual: bond pdb=" CAE Y01 A1814 " pdb=" CBI Y01 A1814 " ideal model delta sigma weight residual 1.532 1.673 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" CAE Y01 A1813 " pdb=" CBI Y01 A1813 " ideal model delta sigma weight residual 1.532 1.666 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" CAE Y01 A1817 " pdb=" CBI Y01 A1817 " ideal model delta sigma weight residual 1.532 1.664 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" CAE Y01 A1811 " pdb=" CBI Y01 A1811 " ideal model delta sigma weight residual 1.532 1.663 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CAV Y01 A1817 " pdb=" CBC Y01 A1817 " ideal model delta sigma weight residual 1.523 1.645 -0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 19393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 34397 3.26 - 6.52: 358 6.52 - 9.78: 119 9.78 - 13.04: 24 13.04 - 16.30: 14 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CAM Y01 A1813 " pdb=" CAY Y01 A1813 " pdb=" OAW Y01 A1813 " ideal model delta sigma weight residual 111.19 127.49 -16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1818 " pdb=" CAY Y01 A1818 " pdb=" OAW Y01 A1818 " ideal model delta sigma weight residual 111.19 127.48 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1808 " pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 111.19 127.43 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CAM Y01 A1809 " pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 111.19 127.35 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CAM Y01 A1810 " pdb=" CAY Y01 A1810 " pdb=" OAW Y01 A1810 " ideal model delta sigma weight residual 111.19 127.33 -16.14 3.00e+00 1.11e-01 2.90e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9578 35.97 - 71.94: 227 71.94 - 107.92: 15 107.92 - 143.89: 0 143.89 - 179.86: 1 Dihedral angle restraints: 9821 sinusoidal: 5674 harmonic: 4147 Sorted by residual: dihedral pdb=" CD ARG A1114 " pdb=" NE ARG A1114 " pdb=" CZ ARG A1114 " pdb=" NH1 ARG A1114 " ideal model delta sinusoidal sigma weight residual 0.00 179.86 -179.86 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ALA A 75 " pdb=" C ALA A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta harmonic sigma weight residual 180.00 136.27 43.73 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 9818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1472 0.103 - 0.206: 76 0.206 - 0.308: 10 0.308 - 0.411: 13 0.411 - 0.514: 11 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CBG Y01 A1816 " pdb=" CAQ Y01 A1816 " pdb=" CBD Y01 A1816 " pdb=" CBI Y01 A1816 " both_signs ideal model delta sigma weight residual False -2.33 -2.85 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CBG Y01 A1813 " pdb=" CAQ Y01 A1813 " pdb=" CBD Y01 A1813 " pdb=" CBI Y01 A1813 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CBG Y01 A1810 " pdb=" CAQ Y01 A1810 " pdb=" CBD Y01 A1810 " pdb=" CBI Y01 A1810 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 1579 not shown) Planarity restraints: 2799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 310 " 0.237 2.00e-02 2.50e+03 3.16e-01 1.50e+03 pdb=" CG ASN A 310 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 310 " -0.231 2.00e-02 2.50e+03 pdb=" ND2 ASN A 310 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 310 " -0.486 2.00e-02 2.50e+03 pdb="HD22 ASN A 310 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " 0.216 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN A 915 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " -0.215 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 915 " -0.408 2.00e-02 2.50e+03 pdb="HD22 ASN A 915 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 417 " -0.186 2.00e-02 2.50e+03 2.08e-01 6.46e+02 pdb=" CD GLN A 417 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 417 " 0.171 2.00e-02 2.50e+03 pdb=" NE2 GLN A 417 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 417 " 0.307 2.00e-02 2.50e+03 pdb="HE22 GLN A 417 " -0.317 2.00e-02 2.50e+03 ... (remaining 2796 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1913 2.25 - 2.84: 42325 2.84 - 3.42: 48394 3.42 - 4.01: 65874 4.01 - 4.60: 102270 Nonbonded interactions: 260776 Sorted by model distance: nonbonded pdb=" HE2 HIS A 178 " pdb=" OG1 THR A 362 " model vdw 1.661 2.450 nonbonded pdb=" O ALA A 412 " pdb=" H SER A 415 " model vdw 1.686 2.450 nonbonded pdb=" O THR B 55 " pdb=" H GLY B 60 " model vdw 1.697 2.450 nonbonded pdb="HH21 ARG A 135 " pdb=" OE2 GLU A1019 " model vdw 1.699 2.450 nonbonded pdb=" O THR B 40 " pdb=" HE ARG B 163 " model vdw 1.713 2.450 ... (remaining 260771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.330 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.011 0.141 10083 Z= 0.531 Angle : 1.451 16.299 13767 Z= 0.613 Chirality : 0.075 0.514 1582 Planarity : 0.006 0.081 1670 Dihedral : 13.224 179.859 4376 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % Twisted General : 0.09 % 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: -3.98 (0.21), residues: 1170 helix: -2.64 (0.16), residues: 609 sheet: -2.58 (0.55), residues: 70 loop : -2.46 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 602 TYR 0.026 0.003 TYR B 44 PHE 0.032 0.003 PHE A 848 TRP 0.023 0.002 TRP A 399 HIS 0.014 0.002 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.01112 (10071) covalent geometry : angle 1.45019 (13740) SS BOND : bond 0.00170 ( 3) SS BOND : angle 2.04412 ( 6) hydrogen bonds : bond 0.16069 ( 463) hydrogen bonds : angle 9.12714 ( 1332) metal coordination : bond 0.07411 ( 2) link_BETA1-4 : bond 0.00110 ( 1) link_BETA1-4 : angle 2.21673 ( 3) link_NAG-ASN : bond 0.00336 ( 6) link_NAG-ASN : angle 1.95125 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7071 (tmmt) cc_final: 0.6706 (mmmt) REVERT: A 156 GLN cc_start: 0.7054 (mp10) cc_final: 0.6356 (mp10) REVERT: A 293 ASP cc_start: 0.8244 (m-30) cc_final: 0.8015 (t0) REVERT: A 380 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 460 TRP cc_start: 0.6848 (t-100) cc_final: 0.6592 (t60) REVERT: A 874 LYS cc_start: 0.9235 (ptmm) cc_final: 0.8860 (pttt) REVERT: A 1079 SER cc_start: 0.8939 (p) cc_final: 0.8493 (t) REVERT: B 72 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7267 (mtm-85) REVERT: B 100 GLN cc_start: 0.7546 (tp40) cc_final: 0.6715 (tp-100) REVERT: B 104 ASP cc_start: 0.7447 (m-30) cc_final: 0.6876 (m-30) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.2864 time to fit residues: 84.7903 Evaluate side-chains 123 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 386 ASN A 408 HIS A 872 ASN A 889 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099043 restraints weight = 45745.859| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.47 r_work: 0.3151 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10083 Z= 0.145 Angle : 0.663 6.350 13767 Z= 0.335 Chirality : 0.040 0.174 1582 Planarity : 0.005 0.068 1670 Dihedral : 10.799 171.902 2205 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.60 % Allowed : 9.70 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.24), residues: 1170 helix: -0.77 (0.19), residues: 618 sheet: -1.99 (0.60), residues: 67 loop : -1.90 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1150 TYR 0.012 0.001 TYR B 174 PHE 0.021 0.002 PHE A 790 TRP 0.010 0.001 TRP A 399 HIS 0.008 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00325 (10071) covalent geometry : angle 0.66164 (13740) SS BOND : bond 0.00345 ( 3) SS BOND : angle 1.09655 ( 6) hydrogen bonds : bond 0.04586 ( 463) hydrogen bonds : angle 5.58229 ( 1332) metal coordination : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00223 ( 1) link_BETA1-4 : angle 0.56565 ( 3) link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 1.39842 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7389 (tmmt) cc_final: 0.6914 (mmmt) REVERT: A 293 ASP cc_start: 0.8347 (m-30) cc_final: 0.7990 (t0) REVERT: A 740 TYR cc_start: 0.8931 (t80) cc_final: 0.8455 (t80) REVERT: A 869 MET cc_start: 0.8239 (tmm) cc_final: 0.7972 (pmm) REVERT: A 874 LYS cc_start: 0.9193 (ptmm) cc_final: 0.8948 (pttt) REVERT: A 901 GLN cc_start: 0.8001 (tt0) cc_final: 0.7763 (tt0) REVERT: A 1079 SER cc_start: 0.8974 (p) cc_final: 0.8543 (t) REVERT: B 72 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7543 (mtm-85) REVERT: B 100 GLN cc_start: 0.7515 (tp40) cc_final: 0.7274 (tp-100) outliers start: 6 outliers final: 4 residues processed: 147 average time/residue: 0.2086 time to fit residues: 43.8694 Evaluate side-chains 119 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 0.0980 chunk 112 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093734 restraints weight = 46500.031| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.45 r_work: 0.3070 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10083 Z= 0.166 Angle : 0.622 6.016 13767 Z= 0.320 Chirality : 0.040 0.169 1582 Planarity : 0.005 0.068 1670 Dihedral : 9.916 175.049 2205 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.80 % Allowed : 10.80 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -1.31 (0.25), residues: 1170 helix: -0.08 (0.21), residues: 620 sheet: -1.65 (0.63), residues: 67 loop : -1.73 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.019 0.001 TYR A 193 PHE 0.019 0.001 PHE A 848 TRP 0.008 0.001 TRP A 844 HIS 0.006 0.001 HIS A1121 Details of bonding type rmsd covalent geometry : bond 0.00381 (10071) covalent geometry : angle 0.61812 (13740) SS BOND : bond 0.00342 ( 3) SS BOND : angle 1.17122 ( 6) hydrogen bonds : bond 0.04314 ( 463) hydrogen bonds : angle 5.09727 ( 1332) metal coordination : bond 0.00133 ( 2) link_BETA1-4 : bond 0.00287 ( 1) link_BETA1-4 : angle 1.00402 ( 3) link_NAG-ASN : bond 0.00977 ( 6) link_NAG-ASN : angle 1.89572 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7365 (tmmt) cc_final: 0.6941 (mmmt) REVERT: A 449 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7567 (ttp) REVERT: A 1079 SER cc_start: 0.9046 (p) cc_final: 0.8614 (t) REVERT: B 72 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7545 (mtm-85) REVERT: B 100 GLN cc_start: 0.7587 (tp40) cc_final: 0.6843 (tp-100) REVERT: B 104 ASP cc_start: 0.7807 (m-30) cc_final: 0.7377 (m-30) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.2159 time to fit residues: 40.7140 Evaluate side-chains 124 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 151 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095091 restraints weight = 46839.382| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.52 r_work: 0.3073 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10083 Z= 0.124 Angle : 0.576 5.819 13767 Z= 0.296 Chirality : 0.039 0.164 1582 Planarity : 0.005 0.065 1670 Dihedral : 9.525 174.922 2205 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.80 % Allowed : 11.60 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.85 (0.25), residues: 1170 helix: 0.33 (0.21), residues: 623 sheet: -1.49 (0.63), residues: 67 loop : -1.58 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.013 0.001 TYR A 193 PHE 0.015 0.001 PHE A 790 TRP 0.008 0.001 TRP A 844 HIS 0.003 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00279 (10071) covalent geometry : angle 0.57295 (13740) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.98081 ( 6) hydrogen bonds : bond 0.03910 ( 463) hydrogen bonds : angle 4.73185 ( 1332) metal coordination : bond 0.00074 ( 2) link_BETA1-4 : bond 0.00038 ( 1) link_BETA1-4 : angle 0.88208 ( 3) link_NAG-ASN : bond 0.00209 ( 6) link_NAG-ASN : angle 1.57757 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7372 (tmmt) cc_final: 0.6945 (mmmt) REVERT: A 449 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7561 (ttp) REVERT: A 740 TYR cc_start: 0.8953 (t80) cc_final: 0.8414 (t80) REVERT: A 1079 SER cc_start: 0.9084 (p) cc_final: 0.8666 (t) REVERT: B 72 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7578 (mtm-85) REVERT: B 100 GLN cc_start: 0.7596 (tp40) cc_final: 0.7183 (tm-30) REVERT: B 104 ASP cc_start: 0.7826 (m-30) cc_final: 0.7256 (m-30) outliers start: 18 outliers final: 13 residues processed: 130 average time/residue: 0.2128 time to fit residues: 39.3476 Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 730 TRP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 62 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 111 optimal weight: 0.0070 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094449 restraints weight = 46875.257| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.48 r_work: 0.3078 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10083 Z= 0.108 Angle : 0.555 5.719 13767 Z= 0.283 Chirality : 0.038 0.158 1582 Planarity : 0.004 0.060 1670 Dihedral : 9.019 176.737 2205 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.70 % Allowed : 12.30 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.52 (0.26), residues: 1170 helix: 0.67 (0.22), residues: 622 sheet: -1.56 (0.60), residues: 77 loop : -1.48 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.011 0.001 TYR A 193 PHE 0.014 0.001 PHE A 848 TRP 0.010 0.001 TRP A 337 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00243 (10071) covalent geometry : angle 0.55216 (13740) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.91437 ( 6) hydrogen bonds : bond 0.03572 ( 463) hydrogen bonds : angle 4.45051 ( 1332) metal coordination : bond 0.00054 ( 2) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 1.03316 ( 3) link_NAG-ASN : bond 0.00159 ( 6) link_NAG-ASN : angle 1.41635 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7388 (tmtt) REVERT: A 1079 SER cc_start: 0.9034 (p) cc_final: 0.8658 (t) REVERT: B 72 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7586 (mtm-85) REVERT: B 100 GLN cc_start: 0.7614 (tp40) cc_final: 0.7210 (tm-30) REVERT: B 104 ASP cc_start: 0.7866 (m-30) cc_final: 0.7325 (m-30) outliers start: 17 outliers final: 12 residues processed: 134 average time/residue: 0.1991 time to fit residues: 38.5292 Evaluate side-chains 122 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 104 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091580 restraints weight = 47311.901| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.50 r_work: 0.3008 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10083 Z= 0.186 Angle : 0.594 5.790 13767 Z= 0.307 Chirality : 0.040 0.167 1582 Planarity : 0.004 0.065 1670 Dihedral : 9.020 176.709 2205 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.00 % Allowed : 12.60 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.36 (0.26), residues: 1170 helix: 0.79 (0.22), residues: 623 sheet: -1.19 (0.67), residues: 67 loop : -1.46 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.010 0.001 TYR A 403 PHE 0.016 0.001 PHE A 848 TRP 0.008 0.001 TRP A 844 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00435 (10071) covalent geometry : angle 0.59074 (13740) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.16357 ( 6) hydrogen bonds : bond 0.03882 ( 463) hydrogen bonds : angle 4.48274 ( 1332) metal coordination : bond 0.00181 ( 2) link_BETA1-4 : bond 0.00017 ( 1) link_BETA1-4 : angle 1.12606 ( 3) link_NAG-ASN : bond 0.00111 ( 6) link_NAG-ASN : angle 1.60319 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 89 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7432 (tmtt) REVERT: A 216 MET cc_start: 0.8427 (tpp) cc_final: 0.8226 (tpp) REVERT: A 740 TYR cc_start: 0.9009 (t80) cc_final: 0.8458 (t80) REVERT: A 1026 HIS cc_start: 0.7718 (m-70) cc_final: 0.7160 (t70) REVERT: A 1079 SER cc_start: 0.9202 (p) cc_final: 0.8739 (t) REVERT: B 72 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7533 (mtm-85) REVERT: B 100 GLN cc_start: 0.7768 (tp40) cc_final: 0.7391 (tm-30) REVERT: B 104 ASP cc_start: 0.8254 (m-30) cc_final: 0.7733 (m-30) REVERT: B 114 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8452 (mtm) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.2071 time to fit residues: 37.0794 Evaluate side-chains 120 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 114 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 37 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090403 restraints weight = 47472.749| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.45 r_work: 0.3006 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10083 Z= 0.147 Angle : 0.569 5.698 13767 Z= 0.293 Chirality : 0.039 0.162 1582 Planarity : 0.004 0.065 1670 Dihedral : 8.812 177.196 2205 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.20 (0.26), residues: 1170 helix: 0.95 (0.22), residues: 621 sheet: -1.19 (0.67), residues: 67 loop : -1.42 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.009 0.001 TYR B 175 PHE 0.015 0.001 PHE A 790 TRP 0.009 0.001 TRP A 844 HIS 0.005 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00345 (10071) covalent geometry : angle 0.56598 (13740) SS BOND : bond 0.00280 ( 3) SS BOND : angle 1.00316 ( 6) hydrogen bonds : bond 0.03765 ( 463) hydrogen bonds : angle 4.39115 ( 1332) metal coordination : bond 0.00134 ( 2) link_BETA1-4 : bond 0.00461 ( 1) link_BETA1-4 : angle 1.10328 ( 3) link_NAG-ASN : bond 0.00155 ( 6) link_NAG-ASN : angle 1.57988 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8610 (tt) REVERT: A 89 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7485 (tmtt) REVERT: A 374 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: A 740 TYR cc_start: 0.8998 (t80) cc_final: 0.8503 (t80) REVERT: A 1026 HIS cc_start: 0.7788 (m-70) cc_final: 0.7279 (t70) REVERT: A 1079 SER cc_start: 0.9172 (p) cc_final: 0.8742 (t) REVERT: B 72 ARG cc_start: 0.7919 (mtp-110) cc_final: 0.7526 (mtm-85) REVERT: B 100 GLN cc_start: 0.7716 (tp40) cc_final: 0.7360 (tm-30) REVERT: B 104 ASP cc_start: 0.8311 (m-30) cc_final: 0.7822 (m-30) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.1959 time to fit residues: 34.8171 Evaluate side-chains 118 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094065 restraints weight = 47109.311| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.48 r_work: 0.3048 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10083 Z= 0.099 Angle : 0.542 6.564 13767 Z= 0.275 Chirality : 0.038 0.156 1582 Planarity : 0.004 0.059 1670 Dihedral : 8.421 178.112 2205 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.80 % Allowed : 13.10 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.03 (0.26), residues: 1170 helix: 1.17 (0.22), residues: 623 sheet: -1.11 (0.69), residues: 67 loop : -1.36 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1114 TYR 0.008 0.001 TYR A 193 PHE 0.014 0.001 PHE A 790 TRP 0.010 0.001 TRP A 337 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00223 (10071) covalent geometry : angle 0.53941 (13740) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.81402 ( 6) hydrogen bonds : bond 0.03391 ( 463) hydrogen bonds : angle 4.18389 ( 1332) metal coordination : bond 0.00054 ( 2) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 0.95096 ( 3) link_NAG-ASN : bond 0.00228 ( 6) link_NAG-ASN : angle 1.41202 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8584 (tt) REVERT: A 89 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7437 (tmtt) REVERT: A 374 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: A 740 TYR cc_start: 0.8971 (t80) cc_final: 0.8524 (t80) REVERT: A 1026 HIS cc_start: 0.7775 (m-70) cc_final: 0.7331 (t70) REVERT: A 1079 SER cc_start: 0.9135 (p) cc_final: 0.8708 (t) REVERT: B 72 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7511 (mtm-85) REVERT: B 100 GLN cc_start: 0.7658 (tp40) cc_final: 0.7329 (tm-30) REVERT: B 104 ASP cc_start: 0.8269 (m-30) cc_final: 0.7827 (m-30) outliers start: 18 outliers final: 15 residues processed: 121 average time/residue: 0.1775 time to fit residues: 31.7777 Evaluate side-chains 121 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.090465 restraints weight = 47693.590| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.52 r_work: 0.3012 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10083 Z= 0.158 Angle : 0.572 5.808 13767 Z= 0.294 Chirality : 0.039 0.162 1582 Planarity : 0.004 0.061 1670 Dihedral : 8.489 178.721 2205 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.80 % Allowed : 13.30 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.09 (0.26), residues: 1170 helix: 1.23 (0.22), residues: 622 sheet: -1.04 (0.69), residues: 67 loop : -1.35 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.009 0.001 TYR B 175 PHE 0.014 0.001 PHE A 848 TRP 0.010 0.001 TRP A1051 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00371 (10071) covalent geometry : angle 0.56887 (13740) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.17630 ( 6) hydrogen bonds : bond 0.03672 ( 463) hydrogen bonds : angle 4.25683 ( 1332) metal coordination : bond 0.00134 ( 2) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.17287 ( 3) link_NAG-ASN : bond 0.00117 ( 6) link_NAG-ASN : angle 1.61295 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 89 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7461 (tmtt) REVERT: A 370 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7591 (tptt) REVERT: A 374 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: A 597 SER cc_start: 0.9165 (m) cc_final: 0.8955 (p) REVERT: A 740 TYR cc_start: 0.9005 (t80) cc_final: 0.8548 (t80) REVERT: A 1026 HIS cc_start: 0.7715 (m-70) cc_final: 0.7332 (t70) REVERT: A 1063 MET cc_start: 0.8974 (ttm) cc_final: 0.8597 (ttm) REVERT: B 72 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7523 (mtm-85) REVERT: B 100 GLN cc_start: 0.7740 (tp40) cc_final: 0.7412 (tm-30) REVERT: B 104 ASP cc_start: 0.8409 (m-30) cc_final: 0.7940 (m-30) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 0.1911 time to fit residues: 32.9586 Evaluate side-chains 118 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.114761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093015 restraints weight = 47248.032| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.49 r_work: 0.3045 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10083 Z= 0.114 Angle : 0.550 6.424 13767 Z= 0.281 Chirality : 0.038 0.187 1582 Planarity : 0.004 0.060 1670 Dihedral : 8.309 178.671 2205 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.50 % Allowed : 13.70 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.25 (0.26), residues: 1170 helix: 1.37 (0.22), residues: 617 sheet: -1.02 (0.69), residues: 67 loop : -1.25 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1114 TYR 0.008 0.001 TYR A1009 PHE 0.015 0.001 PHE A 790 TRP 0.009 0.001 TRP A1051 HIS 0.004 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00266 (10071) covalent geometry : angle 0.54790 (13740) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.92420 ( 6) hydrogen bonds : bond 0.03477 ( 463) hydrogen bonds : angle 4.14475 ( 1332) metal coordination : bond 0.00080 ( 2) link_BETA1-4 : bond 0.00241 ( 1) link_BETA1-4 : angle 0.96170 ( 3) link_NAG-ASN : bond 0.00177 ( 6) link_NAG-ASN : angle 1.47017 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 89 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7397 (tmtt) REVERT: A 374 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 491 ILE cc_start: 0.8696 (pp) cc_final: 0.8323 (pt) REVERT: A 597 SER cc_start: 0.9154 (m) cc_final: 0.8938 (p) REVERT: A 740 TYR cc_start: 0.8975 (t80) cc_final: 0.8536 (t80) REVERT: A 1026 HIS cc_start: 0.7736 (m-70) cc_final: 0.7361 (t70) REVERT: A 1063 MET cc_start: 0.8929 (ttm) cc_final: 0.8559 (ttm) REVERT: A 1079 SER cc_start: 0.9181 (p) cc_final: 0.8743 (t) REVERT: B 72 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7536 (mtm-85) REVERT: B 100 GLN cc_start: 0.7722 (tp40) cc_final: 0.7377 (tm-30) REVERT: B 104 ASP cc_start: 0.8295 (m-30) cc_final: 0.7796 (m-30) outliers start: 15 outliers final: 13 residues processed: 123 average time/residue: 0.2027 time to fit residues: 36.4226 Evaluate side-chains 122 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 62 TYR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092654 restraints weight = 47296.731| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.47 r_work: 0.3036 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10083 Z= 0.119 Angle : 0.545 6.083 13767 Z= 0.279 Chirality : 0.038 0.184 1582 Planarity : 0.004 0.059 1670 Dihedral : 8.209 179.329 2205 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.80 % Allowed : 14.20 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.35 (0.26), residues: 1170 helix: 1.47 (0.22), residues: 617 sheet: -1.04 (0.69), residues: 67 loop : -1.22 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1114 TYR 0.008 0.001 TYR A1009 PHE 0.014 0.001 PHE A 790 TRP 0.010 0.001 TRP A1051 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00278 (10071) covalent geometry : angle 0.54238 (13740) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.95362 ( 6) hydrogen bonds : bond 0.03448 ( 463) hydrogen bonds : angle 4.09453 ( 1332) metal coordination : bond 0.00090 ( 2) link_BETA1-4 : bond 0.00217 ( 1) link_BETA1-4 : angle 1.02609 ( 3) link_NAG-ASN : bond 0.00161 ( 6) link_NAG-ASN : angle 1.49154 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.54 seconds wall clock time: 73 minutes 19.41 seconds (4399.41 seconds total)