Starting phenix.real_space_refine on Fri Jan 24 22:06:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy4_42792/01_2025/8uy4_42792_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy4_42792/01_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_42792/01_2025/8uy4_42792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy4_42792/01_2025/8uy4_42792.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy4_42792/01_2025/8uy4_42792_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy4_42792/01_2025/8uy4_42792_trim.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG: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: 9.99, per 1000 atoms: 0.45 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: 5.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.49 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: 10.93 Time building geometry restraints manager: 7.02 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: 0.920 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: 0.400 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 48.980 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- 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= 0.237 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (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 TRP 0.007 0.001 TRP A 689 HIS 0.002 0.001 HIS A 347 PHE 0.010 0.001 PHE A 105 TYR 0.011 0.001 TYR A 454 ARG 0.006 0.000 ARG A1305 *********************** 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 : 1.432 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 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: 0.8946 (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: 0.5335 time to fit residues: 68.6335 Evaluate side-chains 61 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 120 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN A 649 GLN A 943 ASN ** A 962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 HIS A1083 GLN A1095 GLN A1172 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.084595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063908 restraints weight = 90549.635| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.61 r_work: 0.3173 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11701 Z= 0.344 Angle : 0.575 5.198 15851 Z= 0.310 Chirality : 0.042 0.181 1701 Planarity : 0.004 0.062 2089 Dihedral : 5.420 64.811 1609 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.66 % Favored : 93.19 % Rotamer: Outliers : 1.46 % Allowed : 15.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1336 helix: 2.01 (0.39), residues: 183 sheet: -1.40 (0.28), residues: 344 loop : -0.62 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.006 0.001 HIS A 347 PHE 0.017 0.001 PHE A 412 TYR 0.012 0.001 TYR A1226 ARG 0.005 0.001 ARG A 143 *********************** 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 70 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.744 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: 0.9220 (m-40) cc_final: 0.8982 (t0) REVERT: A 216 TRP cc_start: 0.9354 (p-90) cc_final: 0.9015 (p-90) REVERT: A 260 GLN cc_start: 0.9010 (mm110) cc_final: 0.8496 (pp30) REVERT: A 339 SER cc_start: 0.9152 (m) cc_final: 0.8718 (t) REVERT: A 412 PHE cc_start: 0.9360 (m-10) cc_final: 0.9141 (m-10) REVERT: A 716 ASN cc_start: 0.9318 (m-40) cc_final: 0.9116 (m-40) REVERT: A 1058 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: A 1095 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: A 1212 ASP cc_start: 0.8041 (m-30) cc_final: 0.7490 (m-30) outliers start: 17 outliers final: 7 residues processed: 69 average time/residue: 0.4619 time to fit residues: 49.5761 Evaluate side-chains 55 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 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 1276 ASN 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 116 optimal weight: 4.9990 chunk 136 optimal weight: 50.0000 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.083791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063711 restraints weight = 90248.351| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.48 r_work: 0.3181 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11701 Z= 0.236 Angle : 0.505 4.994 15851 Z= 0.270 Chirality : 0.040 0.164 1701 Planarity : 0.003 0.053 2089 Dihedral : 4.404 26.726 1594 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.39 % Rotamer: Outliers : 1.20 % Allowed : 15.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1336 helix: 2.12 (0.39), residues: 183 sheet: -1.53 (0.27), residues: 350 loop : -0.59 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.003 0.001 HIS A1229 PHE 0.011 0.001 PHE A 444 TYR 0.010 0.001 TYR A 608 ARG 0.004 0.000 ARG A 143 *********************** 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 64 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.751 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: 0.9249 (m-40) cc_final: 0.9007 (t0) REVERT: A 216 TRP cc_start: 0.9376 (p-90) cc_final: 0.9130 (p-90) REVERT: A 260 GLN cc_start: 0.9034 (mm110) cc_final: 0.8483 (pp30) REVERT: A 339 SER cc_start: 0.9174 (m) cc_final: 0.8777 (t) REVERT: A 412 PHE cc_start: 0.9331 (m-10) cc_final: 0.9018 (m-10) REVERT: A 1058 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 1106 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: A 1212 ASP cc_start: 0.8063 (m-30) cc_final: 0.7608 (m-30) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.4798 time to fit residues: 47.1189 Evaluate side-chains 53 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 946 SER Chi-restraints excluded: chain A residue 1003 TYR 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 1379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 GLN A1225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.082202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062146 restraints weight = 92161.503| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.43 r_work: 0.3144 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11701 Z= 0.291 Angle : 0.507 5.463 15851 Z= 0.270 Chirality : 0.040 0.174 1701 Planarity : 0.003 0.044 2089 Dihedral : 4.422 24.495 1594 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % Rotamer: Outliers : 1.38 % Allowed : 14.62 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1336 helix: 2.14 (0.39), residues: 184 sheet: -1.60 (0.27), residues: 359 loop : -0.59 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A 802 PHE 0.010 0.001 PHE A 863 TYR 0.012 0.001 TYR A 608 ARG 0.004 0.000 ARG A 143 *********************** 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 : 1.633 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: 0.9253 (m-40) cc_final: 0.9043 (t0) REVERT: A 260 GLN cc_start: 0.9069 (mm110) cc_final: 0.8512 (pp30) REVERT: A 339 SER cc_start: 0.9183 (m) cc_final: 0.8830 (t) REVERT: A 412 PHE cc_start: 0.9302 (m-10) cc_final: 0.8969 (m-10) REVERT: A 1058 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: A 1212 ASP cc_start: 0.8125 (m-30) cc_final: 0.7594 (m-30) outliers start: 16 outliers final: 8 residues processed: 61 average time/residue: 0.4136 time to fit residues: 40.8512 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 : 1.784 ------------------------------------------------------------------------------- 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 555 THR 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 1379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.081841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062026 restraints weight = 92011.005| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.40 r_work: 0.3155 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11701 Z= 0.251 Angle : 0.486 5.053 15851 Z= 0.257 Chirality : 0.040 0.170 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.329 22.263 1594 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 1.03 % Allowed : 15.05 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1336 helix: 2.36 (0.39), residues: 184 sheet: -1.53 (0.27), residues: 349 loop : -0.59 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.004 0.001 HIS A1000 PHE 0.008 0.001 PHE A 105 TYR 0.011 0.001 TYR A 608 ARG 0.004 0.000 ARG A1305 *********************** 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: 12 poor density : 42 time to evaluate : 1.657 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: 0.9096 (mm110) cc_final: 0.8516 (pp30) REVERT: A 339 SER cc_start: 0.9156 (m) cc_final: 0.8841 (t) REVERT: A 412 PHE cc_start: 0.9248 (m-10) cc_final: 0.8912 (m-10) REVERT: A 1058 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: A 1212 ASP cc_start: 0.8152 (m-30) cc_final: 0.7669 (m-30) outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.4375 time to fit residues: 36.7402 Evaluate side-chains 47 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 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 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 111 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.082139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062218 restraints weight = 91672.275| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.45 r_work: 0.3162 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11701 Z= 0.183 Angle : 0.458 4.550 15851 Z= 0.243 Chirality : 0.039 0.166 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.150 21.486 1593 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1336 helix: 2.43 (0.39), residues: 184 sheet: -1.50 (0.27), residues: 339 loop : -0.51 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.002 0.001 HIS A1229 PHE 0.007 0.001 PHE A 877 TYR 0.009 0.001 TYR A 608 ARG 0.003 0.000 ARG A1305 *********************** 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 52 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9116 (mm110) cc_final: 0.8527 (pp30) REVERT: A 339 SER cc_start: 0.9146 (m) cc_final: 0.8829 (t) REVERT: A 412 PHE cc_start: 0.9276 (m-10) cc_final: 0.8938 (m-10) REVERT: A 1058 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: A 1212 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7680 (m-30) outliers start: 11 outliers final: 6 residues processed: 49 average time/residue: 0.4868 time to fit residues: 36.9485 Evaluate side-chains 45 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1212 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 141 optimal weight: 60.0000 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.080923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061207 restraints weight = 92763.409| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.40 r_work: 0.3134 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11701 Z= 0.294 Angle : 0.487 5.578 15851 Z= 0.257 Chirality : 0.039 0.178 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.233 21.729 1593 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 0.77 % Allowed : 15.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1336 helix: 2.52 (0.39), residues: 184 sheet: -1.47 (0.27), residues: 341 loop : -0.59 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 PHE 0.008 0.001 PHE A 863 TYR 0.011 0.001 TYR A1352 ARG 0.003 0.000 ARG A1305 *********************** 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 46 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9105 (mm110) cc_final: 0.8487 (pp30) REVERT: A 339 SER cc_start: 0.9182 (m) cc_final: 0.8903 (t) REVERT: A 412 PHE cc_start: 0.9244 (m-10) cc_final: 0.8900 (m-10) REVERT: A 1058 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8313 (tm-30) REVERT: A 1212 ASP cc_start: 0.8140 (m-30) cc_final: 0.7633 (m-30) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.4589 time to fit residues: 32.5933 Evaluate side-chains 45 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 1058 GLU Chi-restraints excluded: chain A residue 1111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 140 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 0.0670 overall best weight: 1.9122 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.081714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.061766 restraints weight = 92489.223| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.47 r_work: 0.3149 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3182 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= 0.189 Angle : 0.457 4.679 15851 Z= 0.242 Chirality : 0.039 0.183 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.117 21.946 1593 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 0.95 % Allowed : 15.39 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.24), residues: 1336 helix: 2.62 (0.39), residues: 184 sheet: -1.38 (0.28), residues: 331 loop : -0.54 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.002 0.001 HIS A1000 PHE 0.006 0.001 PHE A1287 TYR 0.009 0.001 TYR A 608 ARG 0.003 0.000 ARG A1305 *********************** 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 48 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9124 (mm110) cc_final: 0.8494 (pp30) REVERT: A 339 SER cc_start: 0.9138 (m) cc_final: 0.8834 (t) REVERT: A 412 PHE cc_start: 0.9266 (m-10) cc_final: 0.8922 (m-10) REVERT: A 767 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 1058 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: A 1212 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7644 (m-30) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.4198 time to fit residues: 31.3677 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 : 1.876 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1212 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.080959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061033 restraints weight = 92562.661| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.45 r_work: 0.3131 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11701 Z= 0.254 Angle : 0.474 4.744 15851 Z= 0.251 Chirality : 0.039 0.172 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.176 22.175 1593 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 1.12 % Allowed : 15.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1336 helix: 2.62 (0.39), residues: 184 sheet: -1.45 (0.28), residues: 335 loop : -0.60 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 PHE 0.007 0.001 PHE A 863 TYR 0.011 0.001 TYR A1352 ARG 0.003 0.000 ARG A1275 *********************** 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: 13 poor density : 37 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9138 (mm110) cc_final: 0.8506 (pp30) REVERT: A 339 SER cc_start: 0.9159 (m) cc_final: 0.8892 (t) REVERT: A 374 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (ptp) REVERT: A 412 PHE cc_start: 0.9252 (m-10) cc_final: 0.8907 (m-10) REVERT: A 767 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9104 (p) REVERT: A 1058 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8307 (tm-30) REVERT: A 1212 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7660 (m-30) outliers start: 13 outliers final: 8 residues processed: 46 average time/residue: 0.4099 time to fit residues: 31.1559 Evaluate side-chains 47 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 476 HIS Chi-restraints excluded: chain A residue 555 THR 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 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 112 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.081418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061616 restraints weight = 92956.648| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.43 r_work: 0.3144 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11701 Z= 0.195 Angle : 0.456 5.081 15851 Z= 0.241 Chirality : 0.039 0.188 1701 Planarity : 0.003 0.038 2089 Dihedral : 4.105 22.234 1593 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.95 % Allowed : 15.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1336 helix: 2.73 (0.39), residues: 184 sheet: -1.44 (0.28), residues: 335 loop : -0.56 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A1000 PHE 0.006 0.001 PHE A 863 TYR 0.009 0.001 TYR A 608 ARG 0.003 0.000 ARG A1305 ********************** 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 49 residues out of total 1172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9146 (mm110) cc_final: 0.8508 (pp30) REVERT: A 339 SER cc_start: 0.9154 (m) cc_final: 0.8883 (t) REVERT: A 412 PHE cc_start: 0.9261 (m-10) cc_final: 0.8920 (m-10) REVERT: A 767 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9104 (p) REVERT: A 1058 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: A 1212 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 1377 MET cc_start: 0.8624 (tpp) cc_final: 0.8380 (mpp) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 0.4186 time to fit residues: 31.6335 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 : 1.738 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.082084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062350 restraints weight = 92187.014| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.43 r_work: 0.3167 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11701 Z= 0.141 Angle : 0.442 5.096 15851 Z= 0.232 Chirality : 0.039 0.186 1701 Planarity : 0.003 0.039 2089 Dihedral : 3.973 22.334 1593 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.77 % Allowed : 15.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1336 helix: 2.82 (0.39), residues: 184 sheet: -1.45 (0.27), residues: 350 loop : -0.42 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.003 0.001 HIS A 811 PHE 0.007 0.001 PHE A 877 TYR 0.009 0.001 TYR A 608 ARG 0.003 0.000 ARG A1305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9717.96 seconds wall clock time: 172 minutes 48.72 seconds (10368.72 seconds total)