Starting phenix.real_space_refine on Sun Aug 24 19:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy4_42792/08_2025/8uy4_42792_trim.cif" } resolution = 3.08 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= 0.016 sd= 0.103 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 S 24 5.16 5 C 7241 2.51 5 N 1989 2.21 5 O 2210 1.98 5 H 10495 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21959 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 21428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1346, 21428 Classifications: {'peptide': 1346} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1303} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 143 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 27} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 215 Classifications: {'peptide': 44} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 39} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 44} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 118 Classifications: {'peptide': 24} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.28, per 1000 atoms: 0.15 Number of scatterers: 21959 At special positions: 0 Unit cell: (97.76, 109.04, 116.56, 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) S 24 16.00 O 2210 8.00 N 1989 7.00 C 7241 6.00 H 10495 1.00 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: 1.62 Conformation dependent library (CDL) restraints added in 527.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 17 sheets defined 18.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 30 through 48 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.126A pdb=" N SER A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 83 Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.924A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 130 Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.205A pdb=" N LEU A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 removed outlier: 4.309A pdb=" N SER A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 299 through 307 removed outlier: 3.554A pdb=" N GLY A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.570A pdb=" N ASP A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.954A pdb=" N ILE A 411 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 4.219A pdb=" N VAL A1272 " --> pdb=" O TYR A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1360 through 1363 Processing helix chain 'A' and resid 1371 through 1375 removed outlier: 3.558A pdb=" N GLY A1375 " --> pdb=" O GLY A1372 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.582A pdb=" N UNK D 17 " --> pdb=" O UNK D 13 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK D 18 " --> pdb=" O UNK D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'C' and resid 4 through 12 removed outlier: 3.954A pdb=" N UNK C 8 " --> pdb=" O UNK C 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 23 Processing helix chain 'E' and resid 38 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 351 removed outlier: 6.355A pdb=" N PHE A 359 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406 removed outlier: 3.844A pdb=" N MET A 386 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A 455 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN A 445 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 467 through 474 removed outlier: 6.328A pdb=" N LEU A 468 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 483 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 470 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 12.790A pdb=" N TYR A 479 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N PHE A 498 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 481 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS A 495 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 507 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 497 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE A 505 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 517 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 540 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AA8, first strand: chain 'A' and resid 594 through 596 Processing sheet with id=AA9, first strand: chain 'A' and resid 629 through 630 removed outlier: 4.046A pdb=" N ARG A 638 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 669 through 672 removed outlier: 5.276A pdb=" N VAL A 679 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 6.075A pdb=" N ASN A 715 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 720 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N GLN A 719 " --> pdb=" O TYR A 735 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N TYR A 735 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL A 721 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 743 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 754 through 756 removed outlier: 4.875A pdb=" N THR A 763 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 810 through 812 Processing sheet with id=AB5, first strand: chain 'A' and resid 841 through 844 removed outlier: 5.542A pdb=" N GLN A 851 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 862 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 874 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 864 " --> pdb=" O ILE A 872 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 884 " --> pdb=" O ILE A 872 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A 883 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 895 " --> pdb=" O HIS A 883 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 885 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE A 893 " --> pdb=" O PHE A 904 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 901 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A 917 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN A 903 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 915 " --> pdb=" O GLN A 903 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP A 905 " --> pdb=" O ALA A 913 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA A 913 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 927 " --> pdb=" O ASN A 943 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN A 943 " --> pdb=" O THR A 927 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A 929 " --> pdb=" O ALA A 941 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 941 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 931 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A 939 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 946 " --> pdb=" O ASN A 943 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 980 through 981 removed outlier: 4.474A pdb=" N ILE A 988 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN A 999 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A1011 " --> pdb=" O ASN A 999 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A1001 " --> pdb=" O TYR A1009 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N HIS A1007 " --> pdb=" O ARG A1023 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ARG A1023 " --> pdb=" O HIS A1007 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR A1009 " --> pdb=" O PHE A1021 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1019 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR A1030 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER A1051 " --> pdb=" O TYR A1073 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A1072 " --> pdb=" O GLU A1085 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER A1082 " --> pdb=" O TYR A1094 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A1104 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 4.939A pdb=" N THR A1156 " --> pdb=" O LEU A1167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A1176 " --> pdb=" O TYR A1187 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A1180 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A1184 " --> pdb=" O THR A1200 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR A1200 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU A1186 " --> pdb=" O LYS A1198 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A1198 " --> pdb=" O GLU A1186 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A1188 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A1196 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE A1215 " --> pdb=" O TYR A1230 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A1227 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A1244 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS A1229 " --> pdb=" O GLN A1242 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN A1242 " --> pdb=" O HIS A1229 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A1231 " --> pdb=" O LEU A1240 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A1240 " --> pdb=" O TYR A1290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1300 " --> pdb=" O HIS A1291 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLN A1299 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU A1311 " --> pdb=" O GLN A1299 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET A1301 " --> pdb=" O VAL A1309 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN A1322 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1351 through 1352 removed outlier: 3.643A pdb=" N ARG A1364 " --> pdb=" O GLU A1359 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1059 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: 5.22 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: 0.82 - 1.02: 10489 1.02 - 1.22: 5 1.22 - 1.42: 5031 1.42 - 1.61: 6629 1.61 - 1.81: 42 Bond restraints: 22196 Sorted by residual: bond pdb=" CA GLN A 245 " pdb=" C GLN A 245 " ideal model delta sigma weight residual 1.524 1.430 0.093 1.29e-02 6.01e+03 5.24e+01 bond pdb=" SG CYS A 47 " pdb=" HG CYS A 47 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" ND2 ASN A 460 " pdb="HD22 ASN A 460 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN A 460 " pdb="HD21 ASN A 460 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N GLN A 245 " pdb=" CA GLN A 245 " ideal model delta sigma weight residual 1.459 1.397 0.062 1.23e-02 6.61e+03 2.52e+01 ... (remaining 22191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 39503 2.59 - 5.17: 143 5.17 - 7.76: 8 7.76 - 10.35: 4 10.35 - 12.94: 1 Bond angle restraints: 39659 Sorted by residual: angle pdb=" N GLN A 245 " pdb=" CA GLN A 245 " pdb=" C GLN A 245 " ideal model delta sigma weight residual 111.36 103.63 7.73 1.09e+00 8.42e-01 5.04e+01 angle pdb=" CA PRO A 238 " pdb=" C PRO A 238 " pdb=" O PRO A 238 " ideal model delta sigma weight residual 120.60 129.36 -8.76 1.82e+00 3.02e-01 2.32e+01 angle pdb=" N ASN A 239 " pdb=" CA ASN A 239 " pdb=" C ASN A 239 " ideal model delta sigma weight residual 112.72 117.93 -5.21 1.14e+00 7.69e-01 2.09e+01 angle pdb=" CA GLN A 245 " pdb=" N GLN A 245 " pdb=" H GLN A 245 " ideal model delta sigma weight residual 114.70 101.77 12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" O PRO A 238 " pdb=" C PRO A 238 " pdb=" N ASN A 239 " ideal model delta sigma weight residual 122.64 117.60 5.04 1.35e+00 5.49e-01 1.39e+01 ... (remaining 39654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 9463 17.73 - 35.47: 781 35.47 - 53.20: 219 53.20 - 70.94: 49 70.94 - 88.67: 27 Dihedral angle restraints: 10539 sinusoidal: 5498 harmonic: 5041 Sorted by residual: dihedral pdb=" CA GLU A1280 " pdb=" C GLU A1280 " pdb=" N ARG A1281 " pdb=" CA ARG A1281 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA UNK E 15 " pdb=" C UNK E 15 " pdb=" N UNK E 16 " pdb=" CA UNK E 16 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLN A 875 " pdb=" C GLN A 875 " pdb=" N ALA A 876 " pdb=" CA ALA A 876 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 10536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1507 0.057 - 0.113: 154 0.113 - 0.170: 38 0.170 - 0.226: 1 0.226 - 0.283: 1 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CA ASN A 239 " pdb=" N ASN A 239 " pdb=" C ASN A 239 " pdb=" CB ASN A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLN A 245 " pdb=" N GLN A 245 " pdb=" C GLN A 245 " pdb=" CB GLN A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 1698 not shown) Planarity restraints: 3382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 654 " -0.241 2.00e-02 2.50e+03 2.93e-01 1.29e+03 pdb=" CD GLN A 654 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN A 654 " 0.232 2.00e-02 2.50e+03 pdb=" NE2 GLN A 654 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 654 " 0.445 2.00e-02 2.50e+03 pdb="HE22 GLN A 654 " -0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 648 " -0.237 2.00e-02 2.50e+03 2.82e-01 1.19e+03 pdb=" CD GLN A 648 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN A 648 " 0.223 2.00e-02 2.50e+03 pdb=" NE2 GLN A 648 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 648 " -0.436 2.00e-02 2.50e+03 pdb="HE22 GLN A 648 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 460 " 0.218 2.00e-02 2.50e+03 2.22e-01 7.37e+02 pdb=" CG ASN A 460 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 460 " -0.207 2.00e-02 2.50e+03 pdb=" ND2 ASN A 460 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 460 " 0.323 2.00e-02 2.50e+03 pdb="HD22 ASN A 460 " -0.315 2.00e-02 2.50e+03 ... (remaining 3379 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.00: 323 2.00 - 2.65: 30880 2.65 - 3.30: 65607 3.30 - 3.95: 87943 3.95 - 4.60: 138157 Nonbonded interactions: 322910 Sorted by model distance: nonbonded pdb=" HB2 GLN A 445 " pdb="HG13 VAL A 456 " model vdw 1.355 2.440 nonbonded pdb=" HB3 GLU A 439 " pdb="HG23 THR A 462 " model vdw 1.367 2.440 nonbonded pdb=" OD1 ASP A1117 " pdb=" H ASN A1121 " model vdw 1.544 2.450 nonbonded pdb=" HG2 GLU A 439 " pdb="HG23 THR A 462 " model vdw 1.546 2.440 nonbonded pdb=" O ILE A 561 " pdb="HH11 ARG A 562 " model vdw 1.555 2.450 ... (remaining 322905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11701 Z= 0.207 Angle : 0.587 8.761 15851 Z= 0.335 Chirality : 0.042 0.283 1701 Planarity : 0.004 0.113 2089 Dihedral : 16.413 88.671 4253 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.39 % Favored : 94.31 % Rotamer: Outliers : 1.55 % Allowed : 15.13 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.62 (0.24), residues: 1336 helix: 1.97 (0.40), residues: 181 sheet: -0.94 (0.30), residues: 312 loop : -0.72 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1305 TYR 0.011 0.001 TYR A 454 PHE 0.010 0.001 PHE A 105 TRP 0.007 0.001 TRP A 689 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00360 (11701) covalent geometry : angle 0.58661 (15851) hydrogen bonds : bond 0.23201 ( 389) hydrogen bonds : angle 10.42065 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.569 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 158 ASN cc_start: 0.9098 (m-40) cc_final: 0.8873 (t0) REVERT: A 339 SER cc_start: 0.9050 (m) cc_final: 0.8724 (t) REVERT: A 647 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 716 ASN cc_start: 0.9185 (m-40) cc_final: 0.8948 (m-40) REVERT: A 1212 ASP cc_start: 0.7558 (m-30) cc_final: 0.7124 (m-30) REVERT: A 1238 VAL cc_start: 0.9452 (t) cc_final: 0.9244 (p) outliers start: 18 outliers final: 7 residues processed: 89 average time/residue: 0.2112 time to fit residues: 27.2996 Evaluate side-chains 59 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PRO Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 GLN A 649 GLN A 926 GLN A1074 HIS A1095 GLN A1172 GLN A1225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062052 restraints weight = 92331.074| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.54 r_work: 0.3137 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 11701 Z= 0.330 Angle : 0.622 4.965 15851 Z= 0.336 Chirality : 0.043 0.191 1701 Planarity : 0.004 0.060 2089 Dihedral : 5.554 60.313 1609 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.11 % Favored : 92.74 % Rotamer: Outliers : 1.98 % Allowed : 15.22 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.89 (0.23), residues: 1336 helix: 1.93 (0.39), residues: 183 sheet: -1.39 (0.28), residues: 328 loop : -0.81 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1305 TYR 0.013 0.002 TYR A 608 PHE 0.016 0.002 PHE A 412 TRP 0.011 0.001 TRP A 588 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00708 (11701) covalent geometry : angle 0.62239 (15851) hydrogen bonds : bond 0.04580 ( 389) hydrogen bonds : angle 7.24073 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.379 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 158 ASN cc_start: 0.9262 (m-40) cc_final: 0.9000 (t0) REVERT: A 216 TRP cc_start: 0.9377 (p-90) cc_final: 0.9058 (p-90) REVERT: A 260 GLN cc_start: 0.9038 (mm110) cc_final: 0.8524 (pp30) REVERT: A 339 SER cc_start: 0.9143 (m) cc_final: 0.8713 (t) REVERT: A 412 PHE cc_start: 0.9354 (m-10) cc_final: 0.9124 (m-10) REVERT: A 1058 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: A 1095 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: A 1212 ASP cc_start: 0.8178 (m-30) cc_final: 0.7658 (m-30) outliers start: 23 outliers final: 11 residues processed: 73 average time/residue: 0.1852 time to fit residues: 21.0125 Evaluate side-chains 56 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 821 TYR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 GLN A1172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.084035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.063407 restraints weight = 91263.253| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.62 r_work: 0.3159 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11701 Z= 0.168 Angle : 0.509 4.710 15851 Z= 0.271 Chirality : 0.040 0.147 1701 Planarity : 0.003 0.049 2089 Dihedral : 4.789 43.924 1598 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 0.95 % Allowed : 15.82 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.88 (0.23), residues: 1336 helix: 1.99 (0.38), residues: 183 sheet: -1.60 (0.27), residues: 350 loop : -0.67 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.011 0.001 TYR A 608 PHE 0.011 0.001 PHE A 444 TRP 0.010 0.001 TRP A 422 HIS 0.003 0.001 HIS A1229 Details of bonding type rmsd covalent geometry : bond 0.00366 (11701) covalent geometry : angle 0.50947 (15851) hydrogen bonds : bond 0.03936 ( 389) hydrogen bonds : angle 6.79753 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.506 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 158 ASN cc_start: 0.9247 (m-40) cc_final: 0.9015 (t0) REVERT: A 216 TRP cc_start: 0.9357 (p-90) cc_final: 0.9119 (p-90) REVERT: A 260 GLN cc_start: 0.9065 (mm110) cc_final: 0.8519 (pp30) REVERT: A 339 SER cc_start: 0.9164 (m) cc_final: 0.8764 (t) REVERT: A 412 PHE cc_start: 0.9364 (m-10) cc_final: 0.9121 (m-10) REVERT: A 1058 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: A 1106 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: A 1212 ASP cc_start: 0.8090 (m-30) cc_final: 0.7552 (m-30) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.1842 time to fit residues: 16.5146 Evaluate side-chains 51 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1275 ARG Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.083201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063061 restraints weight = 91480.706| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.49 r_work: 0.3173 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11701 Z= 0.134 Angle : 0.472 4.395 15851 Z= 0.250 Chirality : 0.039 0.157 1701 Planarity : 0.003 0.043 2089 Dihedral : 4.536 45.965 1598 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 1.38 % Allowed : 15.05 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.70 (0.24), residues: 1336 helix: 2.18 (0.39), residues: 184 sheet: -1.46 (0.27), residues: 347 loop : -0.58 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.010 0.001 TYR A 608 PHE 0.013 0.001 PHE A 105 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00292 (11701) covalent geometry : angle 0.47159 (15851) hydrogen bonds : bond 0.03196 ( 389) hydrogen bonds : angle 6.25873 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.576 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 158 ASN cc_start: 0.9240 (m-40) cc_final: 0.9035 (t0) REVERT: A 260 GLN cc_start: 0.9072 (mm110) cc_final: 0.8509 (pp30) REVERT: A 339 SER cc_start: 0.9174 (m) cc_final: 0.8804 (t) REVERT: A 412 PHE cc_start: 0.9319 (m-10) cc_final: 0.8986 (m-10) REVERT: A 1058 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: A 1212 ASP cc_start: 0.8047 (m-30) cc_final: 0.7601 (m-30) outliers start: 16 outliers final: 6 residues processed: 61 average time/residue: 0.1983 time to fit residues: 18.9260 Evaluate side-chains 49 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 7.9990 chunk 142 optimal weight: 50.0000 chunk 115 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.082557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.062450 restraints weight = 90671.937| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.46 r_work: 0.3158 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11701 Z= 0.148 Angle : 0.463 4.436 15851 Z= 0.246 Chirality : 0.039 0.178 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.205 21.261 1593 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.86 % Allowed : 15.39 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.64 (0.24), residues: 1336 helix: 2.23 (0.38), residues: 184 sheet: -1.41 (0.27), residues: 357 loop : -0.52 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.010 0.001 TYR A1352 PHE 0.007 0.001 PHE A 863 TRP 0.009 0.001 TRP A 422 HIS 0.004 0.001 HIS A1000 Details of bonding type rmsd covalent geometry : bond 0.00321 (11701) covalent geometry : angle 0.46307 (15851) hydrogen bonds : bond 0.03101 ( 389) hydrogen bonds : angle 6.03867 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.653 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 260 GLN cc_start: 0.9088 (mm110) cc_final: 0.8505 (pp30) REVERT: A 339 SER cc_start: 0.9179 (m) cc_final: 0.8821 (t) REVERT: A 412 PHE cc_start: 0.9318 (m-10) cc_final: 0.8979 (m-10) REVERT: A 1058 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: A 1212 ASP cc_start: 0.8098 (m-30) cc_final: 0.7631 (m-30) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.2023 time to fit residues: 16.9603 Evaluate side-chains 45 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 102 optimal weight: 7.9990 chunk 26 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 141 optimal weight: 60.0000 chunk 132 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059397 restraints weight = 93369.509| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.43 r_work: 0.3076 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 11701 Z= 0.355 Angle : 0.582 4.989 15851 Z= 0.311 Chirality : 0.041 0.174 1701 Planarity : 0.004 0.039 2089 Dihedral : 4.698 21.671 1593 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.92 % Rotamer: Outliers : 1.03 % Allowed : 15.74 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -1.05 (0.23), residues: 1336 helix: 2.10 (0.39), residues: 184 sheet: -1.79 (0.27), residues: 351 loop : -0.81 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1101 TYR 0.015 0.002 TYR A 979 PHE 0.014 0.002 PHE A 863 TRP 0.010 0.002 TRP A 576 HIS 0.005 0.001 HIS A1291 Details of bonding type rmsd covalent geometry : bond 0.00758 (11701) covalent geometry : angle 0.58205 (15851) hydrogen bonds : bond 0.03491 ( 389) hydrogen bonds : angle 6.24735 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.575 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 260 GLN cc_start: 0.9149 (mm110) cc_final: 0.8549 (pp30) REVERT: A 339 SER cc_start: 0.9159 (m) cc_final: 0.8819 (t) REVERT: A 412 PHE cc_start: 0.9286 (m-10) cc_final: 0.8930 (m-10) REVERT: A 1058 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: A 1212 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7963 (m-30) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.2090 time to fit residues: 16.0343 Evaluate side-chains 48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 8 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 ASN ** A1015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.079730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059867 restraints weight = 93521.348| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.40 r_work: 0.3102 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11701 Z= 0.264 Angle : 0.518 4.420 15851 Z= 0.277 Chirality : 0.040 0.176 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.572 21.891 1593 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 1.29 % Allowed : 15.74 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.98 (0.24), residues: 1336 helix: 2.22 (0.38), residues: 184 sheet: -1.77 (0.27), residues: 349 loop : -0.77 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.012 0.001 TYR A 979 PHE 0.009 0.001 PHE A 863 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 Details of bonding type rmsd covalent geometry : bond 0.00571 (11701) covalent geometry : angle 0.51829 (15851) hydrogen bonds : bond 0.03191 ( 389) hydrogen bonds : angle 6.11432 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.626 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 76 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 260 GLN cc_start: 0.9134 (mm110) cc_final: 0.8495 (pp30) REVERT: A 339 SER cc_start: 0.9145 (m) cc_final: 0.8872 (t) REVERT: A 412 PHE cc_start: 0.9234 (m-10) cc_final: 0.8896 (m-10) REVERT: A 1058 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: A 1212 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7949 (m-30) outliers start: 15 outliers final: 9 residues processed: 50 average time/residue: 0.1978 time to fit residues: 16.3608 Evaluate side-chains 48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1212 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 ASN A1172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.080979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061217 restraints weight = 92206.064| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.40 r_work: 0.3138 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11701 Z= 0.130 Angle : 0.476 9.018 15851 Z= 0.251 Chirality : 0.040 0.185 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.345 22.119 1593 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 1.12 % Allowed : 15.99 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.81 (0.24), residues: 1336 helix: 2.23 (0.38), residues: 184 sheet: -1.67 (0.27), residues: 339 loop : -0.63 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.009 0.001 TYR A 861 PHE 0.011 0.001 PHE A 105 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A1229 Details of bonding type rmsd covalent geometry : bond 0.00281 (11701) covalent geometry : angle 0.47647 (15851) hydrogen bonds : bond 0.02899 ( 389) hydrogen bonds : angle 5.94855 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.557 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 76 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7807 (t0) REVERT: A 260 GLN cc_start: 0.9126 (mm110) cc_final: 0.8477 (pp30) REVERT: A 339 SER cc_start: 0.9170 (m) cc_final: 0.8899 (t) REVERT: A 412 PHE cc_start: 0.9232 (m-10) cc_final: 0.8899 (m-10) REVERT: A 767 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9099 (p) REVERT: A 1058 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: A 1212 ASP cc_start: 0.8151 (m-30) cc_final: 0.7761 (m-30) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1915 time to fit residues: 15.7019 Evaluate side-chains 46 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 90 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.079607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059832 restraints weight = 93749.995| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.39 r_work: 0.3098 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11701 Z= 0.269 Angle : 0.522 5.806 15851 Z= 0.277 Chirality : 0.040 0.182 1701 Planarity : 0.003 0.037 2089 Dihedral : 4.485 22.378 1593 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.61 % Favored : 91.32 % Rotamer: Outliers : 1.20 % Allowed : 15.56 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.93 (0.24), residues: 1336 helix: 2.25 (0.38), residues: 184 sheet: -1.72 (0.27), residues: 349 loop : -0.74 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1101 TYR 0.012 0.001 TYR A1352 PHE 0.009 0.001 PHE A 863 TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 Details of bonding type rmsd covalent geometry : bond 0.00580 (11701) covalent geometry : angle 0.52181 (15851) hydrogen bonds : bond 0.03109 ( 389) hydrogen bonds : angle 6.00221 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.569 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 260 GLN cc_start: 0.9191 (mm110) cc_final: 0.8543 (pp30) REVERT: A 339 SER cc_start: 0.9147 (m) cc_final: 0.8856 (t) REVERT: A 412 PHE cc_start: 0.9251 (m-10) cc_final: 0.8909 (m-10) REVERT: A 767 THR cc_start: 0.9347 (OUTLIER) cc_final: 0.9090 (p) REVERT: A 1058 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: A 1212 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7924 (m-30) outliers start: 14 outliers final: 8 residues processed: 48 average time/residue: 0.1781 time to fit residues: 13.9745 Evaluate side-chains 47 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1212 ASP Chi-restraints excluded: chain A residue 1379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061179 restraints weight = 92835.288| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.38 r_work: 0.3138 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11701 Z= 0.135 Angle : 0.473 5.746 15851 Z= 0.250 Chirality : 0.040 0.181 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.285 22.532 1593 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.95 % Allowed : 15.74 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.73 (0.24), residues: 1336 helix: 2.40 (0.38), residues: 184 sheet: -1.67 (0.27), residues: 341 loop : -0.58 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.011 0.001 TYR A 608 PHE 0.008 0.001 PHE A 877 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A 802 Details of bonding type rmsd covalent geometry : bond 0.00298 (11701) covalent geometry : angle 0.47344 (15851) hydrogen bonds : bond 0.02823 ( 389) hydrogen bonds : angle 5.83016 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7766 (t0) REVERT: A 260 GLN cc_start: 0.9183 (mm110) cc_final: 0.8522 (pp30) REVERT: A 339 SER cc_start: 0.9147 (m) cc_final: 0.8879 (t) REVERT: A 412 PHE cc_start: 0.9245 (m-10) cc_final: 0.8910 (m-10) REVERT: A 767 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9120 (p) REVERT: A 1058 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: A 1212 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7772 (m-30) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.1757 time to fit residues: 13.0124 Evaluate side-chains 48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 936 SER Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 1003 TYR Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1212 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 83 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.080544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060859 restraints weight = 92962.344| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.39 r_work: 0.3128 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11701 Z= 0.166 Angle : 0.474 5.219 15851 Z= 0.251 Chirality : 0.039 0.183 1701 Planarity : 0.003 0.039 2089 Dihedral : 4.258 22.685 1593 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.95 % Allowed : 15.65 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: -0.73 (0.24), residues: 1336 helix: 2.40 (0.39), residues: 184 sheet: -1.65 (0.27), residues: 343 loop : -0.59 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1305 TYR 0.010 0.001 TYR A1352 PHE 0.007 0.001 PHE A1287 TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 Details of bonding type rmsd covalent geometry : bond 0.00359 (11701) covalent geometry : angle 0.47449 (15851) hydrogen bonds : bond 0.02843 ( 389) hydrogen bonds : angle 5.79672 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4763.17 seconds wall clock time: 81 minutes 34.12 seconds (4894.12 seconds total)