Starting phenix.real_space_refine on Fri Sep 11 19:15:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gtf_0064/09_2026/6gtf_0064.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 66 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1908 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9496 Classifications: {'peptide': 1280} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1251} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1576 Unresolved non-hydrogen dihedrals: 714 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 25, 'GLN:plan1': 16, 'PHE:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 17, 'HIS:plan': 5, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 545 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNAv2': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10871 At special positions: 0 Unit cell: (100.672, 133.12, 103.168, 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 17 16.00 P 66 15.00 O 2278 8.00 N 1908 7.00 C 6602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 540.4 milliseconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 35.9% alpha, 4.1% beta 4 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.069A pdb=" N ARG A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.540A pdb=" N ILE A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.848A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.617A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.895A pdb=" N ASN A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.604A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.738A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 187 " --> pdb=" O HIS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.564A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.744A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 4.147A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.903A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.827A pdb=" N GLU A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.851A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.173A pdb=" N ALA A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.503A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.967A pdb=" N GLN A 507 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.629A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 4.346A pdb=" N ILE A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 544' Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.519A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.577A pdb=" N ASN A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.814A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.600A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.543A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 5.370A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.677A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.588A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.257A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.964A pdb=" N LEU A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.646A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 999 removed outlier: 3.847A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.593A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1110 removed outlier: 3.710A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.655A pdb=" N GLU A1175 " --> pdb=" O THR A1171 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1197 removed outlier: 4.269A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.791A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1275 removed outlier: 4.113A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A1263 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 4.525A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1295 " --> pdb=" O TYR A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 4.029A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.582A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 927 through 928 Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2010 1.32 - 1.44: 3170 1.44 - 1.57: 5874 1.57 - 1.69: 129 1.69 - 1.81: 27 Bond restraints: 11210 Sorted by residual: bond pdb=" C3' DG D 0 " pdb=" O3' DG D 0 " ideal model delta sigma weight residual 1.435 1.367 0.068 1.30e-02 5.92e+03 2.77e+01 bond pdb=" C3' DT D -2 " pdb=" O3' DT D -2 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.03e+01 bond pdb=" C3' DA C -6 " pdb=" O3' DA C -6 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" N1 DC C 4 " pdb=" C6 DC C 4 " ideal model delta sigma weight residual 1.367 1.342 0.025 6.00e-03 2.78e+04 1.80e+01 bond pdb=" N1 DT D -2 " pdb=" C2 DT D -2 " ideal model delta sigma weight residual 1.376 1.344 0.032 8.00e-03 1.56e+04 1.56e+01 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 14729 2.89 - 5.77: 480 5.77 - 8.66: 53 8.66 - 11.55: 8 11.55 - 14.44: 2 Bond angle restraints: 15272 Sorted by residual: angle pdb=" C GLN A1245 " pdb=" N ALA A1246 " pdb=" CA ALA A1246 " ideal model delta sigma weight residual 120.94 134.44 -13.50 1.90e+00 2.77e-01 5.05e+01 angle pdb=" C GLY A 892 " pdb=" N ALA A 893 " pdb=" CA ALA A 893 " ideal model delta sigma weight residual 122.35 130.65 -8.30 1.46e+00 4.69e-01 3.23e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 124.31 -10.21 2.00e+00 2.50e-01 2.61e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 110.05 104.77 5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 15267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5479 17.48 - 34.95: 507 34.95 - 52.43: 184 52.43 - 69.90: 89 69.90 - 87.38: 21 Dihedral angle restraints: 6280 sinusoidal: 2965 harmonic: 3315 Sorted by residual: dihedral pdb=" C4' A B -18 " pdb=" C3' A B -18 " pdb=" C2' A B -18 " pdb=" C1' A B -18 " ideal model delta sinusoidal sigma weight residual 36.34 -37.99 74.33 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' U B -10 " pdb=" C3' U B -10 " pdb=" C2' U B -10 " pdb=" C1' U B -10 " ideal model delta sinusoidal sigma weight residual 36.35 -37.41 73.75 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' U B -17 " pdb=" C3' U B -17 " pdb=" C2' U B -17 " pdb=" C1' U B -17 " ideal model delta sinusoidal sigma weight residual 36.35 -36.11 72.45 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 6277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1085 0.070 - 0.140: 330 0.140 - 0.210: 71 0.210 - 0.280: 25 0.280 - 0.351: 14 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C2' A B -18 " pdb=" C3' A B -18 " pdb=" O2' A B -18 " pdb=" C1' A B -18 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C2' U B -17 " pdb=" C3' U B -17 " pdb=" O2' U B -17 " pdb=" C1' U B -17 " both_signs ideal model delta sigma weight residual False -2.79 -2.44 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1' U B -16 " pdb=" O4' U B -16 " pdb=" C2' U B -16 " pdb=" N1 U B -16 " both_signs ideal model delta sigma weight residual False 2.46 2.12 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 1522 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 670 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1231 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A1232 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1232 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1232 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B -11 " -0.036 2.00e-02 2.50e+03 1.92e-02 8.27e+00 pdb=" N1 C B -11 " 0.042 2.00e-02 2.50e+03 pdb=" C2 C B -11 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B -11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -11 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C B -11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -11 " 0.006 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 211 2.60 - 3.18: 9059 3.18 - 3.75: 16871 3.75 - 4.33: 23040 4.33 - 4.90: 35787 Nonbonded interactions: 84968 Sorted by model distance: nonbonded pdb=" OE2 GLU A 920 " pdb=" OH TYR A1024 " model vdw 2.030 3.040 nonbonded pdb=" OE2 GLU A 594 " pdb=" N LYS A 834 " model vdw 2.101 3.120 nonbonded pdb=" N ALA A 665 " pdb=" OE2 GLU A 758 " model vdw 2.111 3.120 nonbonded pdb=" OP2 A B -18 " pdb=" N4 C B -11 " model vdw 2.121 3.120 nonbonded pdb=" NZ LYS A1221 " pdb=" OD2 ASP A1227 " model vdw 2.186 3.120 ... (remaining 84963 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.220 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 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 : 0.010 0.106 11210 Z= 0.543 Angle : 1.218 14.437 15272 Z= 0.702 Chirality : 0.079 0.351 1525 Planarity : 0.007 0.092 1810 Dihedral : 17.319 87.379 4300 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.84 (0.17), residues: 1274 helix: -4.50 (0.11), residues: 458 sheet: -3.90 (0.40), residues: 106 loop : -3.52 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 833 TYR 0.046 0.004 TYR A 178 PHE 0.036 0.004 PHE A 596 TRP 0.027 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.54 (11210) covalent geometry : angle 1.21794 / 0.70 (15272) hydrogen bonds : bond 0.32261 / 21.16 ( 206) hydrogen bonds : angle 11.53947 / 7.73 ( 543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.398 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7950 (t80) cc_final: 0.7607 (t80) REVERT: A 118 LYS cc_start: 0.8187 (mttp) cc_final: 0.7930 (mttp) REVERT: A 246 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (pt) REVERT: A 248 TYR cc_start: 0.7795 (m-10) cc_final: 0.7426 (m-10) REVERT: A 642 ASP cc_start: 0.7618 (p0) cc_final: 0.7061 (p0) REVERT: A 667 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7394 (ttmm) REVERT: A 846 LYS cc_start: 0.9096 (mtmp) cc_final: 0.8800 (pttm) REVERT: A 859 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8601 (mmtm) REVERT: A 994 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8562 (ttmt) REVERT: A 1218 ARG cc_start: 0.7951 (ttt180) cc_final: 0.6891 (ttp80) REVERT: A 1240 PHE cc_start: 0.7605 (m-10) cc_final: 0.7187 (m-80) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.1392 time to fit residues: 39.6997 Evaluate side-chains 134 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 40.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 268 ASN A 271 ASN A 301 ASN A 309 GLN A 694 HIS A 697 HIS A 759 ASN A 804 HIS ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A 938 GLN A 952 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.154170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.120764 restraints weight = 24971.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.125042 restraints weight = 11644.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.127614 restraints weight = 7176.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129287 restraints weight = 5330.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130226 restraints weight = 4430.268| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11210 Z= 0.195 Angle : 1.015 17.974 15272 Z= 0.483 Chirality : 0.086 1.029 1525 Planarity : 0.005 0.075 1810 Dihedral : 19.295 128.467 2116 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 2.59 % Allowed : 11.53 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.19), residues: 1274 helix: -3.82 (0.15), residues: 491 sheet: -3.54 (0.41), residues: 107 loop : -3.26 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 918 TYR 0.037 0.002 TYR A1099 PHE 0.021 0.002 PHE A1240 TRP 0.009 0.002 TRP A 609 HIS 0.007 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (11210) covalent geometry : angle 1.01488 / 0.48 (15272) hydrogen bonds : bond 0.07862 / 5.15 ( 206) hydrogen bonds : angle 7.67508 / 5.23 ( 543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.398 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 TYR cc_start: 0.7625 (m-10) cc_final: 0.7160 (m-10) REVERT: A 614 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 846 LYS cc_start: 0.8845 (mtmp) cc_final: 0.8549 (pttm) REVERT: A 859 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8657 (mmtm) REVERT: A 1066 LYS cc_start: 0.6511 (ptpt) cc_final: 0.6048 (pttt) REVERT: A 1071 THR cc_start: 0.8119 (t) cc_final: 0.7686 (m) REVERT: A 1218 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7064 (ttp80) REVERT: A 1221 LYS cc_start: 0.6699 (mmtt) cc_final: 0.6289 (tptt) outliers start: 24 outliers final: 13 residues processed: 172 average time/residue: 0.1167 time to fit residues: 27.6049 Evaluate side-chains 133 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1176 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 790 ASN A 843 HIS A 887 ASN A 938 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.150056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116087 restraints weight = 25471.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120096 restraints weight = 12342.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.122557 restraints weight = 7732.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124222 restraints weight = 5789.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.125136 restraints weight = 4819.086| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11210 Z= 0.247 Angle : 0.891 13.549 15272 Z= 0.442 Chirality : 0.073 0.879 1525 Planarity : 0.005 0.069 1810 Dihedral : 19.225 156.823 2114 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 3.88 % Allowed : 13.04 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.20), residues: 1274 helix: -3.29 (0.17), residues: 509 sheet: -3.72 (0.40), residues: 104 loop : -3.12 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 918 TYR 0.036 0.003 TYR A1099 PHE 0.029 0.002 PHE A 888 TRP 0.008 0.002 TRP A1142 HIS 0.009 0.002 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (11210) covalent geometry : angle 0.89058 / 0.44 (15272) hydrogen bonds : bond 0.07235 / 4.80 ( 206) hydrogen bonds : angle 7.10515 / 4.88 ( 543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.392 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 719 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8036 (mmtm) REVERT: A 846 LYS cc_start: 0.8716 (mtmp) cc_final: 0.8487 (pttm) REVERT: A 859 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8609 (mmtm) REVERT: A 1071 THR cc_start: 0.8370 (t) cc_final: 0.7997 (m) REVERT: A 1130 TYR cc_start: 0.4003 (OUTLIER) cc_final: 0.2558 (m-80) REVERT: A 1218 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7216 (ttp80) REVERT: A 1221 LYS cc_start: 0.6658 (mmtt) cc_final: 0.6265 (tptt) REVERT: A 1228 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.6382 (p90) REVERT: A 1270 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8207 (mm) outliers start: 36 outliers final: 21 residues processed: 156 average time/residue: 0.1189 time to fit residues: 25.6435 Evaluate side-chains 143 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1228 TYR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.0570 chunk 55 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 114 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 588 GLN ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.152641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118874 restraints weight = 25414.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.123104 restraints weight = 12006.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.125662 restraints weight = 7401.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.127323 restraints weight = 5481.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.128281 restraints weight = 4559.060| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11210 Z= 0.167 Angle : 0.799 11.424 15272 Z= 0.399 Chirality : 0.065 0.683 1525 Planarity : 0.004 0.052 1810 Dihedral : 19.016 160.360 2114 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 3.34 % Allowed : 15.19 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.20), residues: 1274 helix: -2.95 (0.18), residues: 506 sheet: -3.57 (0.41), residues: 104 loop : -2.99 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 921 TYR 0.031 0.002 TYR A1099 PHE 0.018 0.002 PHE A 888 TRP 0.010 0.001 TRP A 175 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (11210) covalent geometry : angle 0.79936 / 0.40 (15272) hydrogen bonds : bond 0.05619 / 3.72 ( 206) hydrogen bonds : angle 6.67405 / 4.55 ( 543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.395 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: symmetry clash revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8735 (tp) cc_final: 0.8324 (mm) REVERT: A 585 TYR cc_start: 0.6611 (t80) cc_final: 0.6384 (t80) REVERT: A 596 PHE cc_start: 0.7083 (p90) cc_final: 0.6761 (p90) REVERT: A 846 LYS cc_start: 0.8711 (mtmp) cc_final: 0.8459 (pttm) REVERT: A 935 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.6133 (pt) REVERT: A 1071 THR cc_start: 0.8222 (t) cc_final: 0.7865 (m) REVERT: A 1130 TYR cc_start: 0.3962 (OUTLIER) cc_final: 0.2492 (m-80) REVERT: A 1270 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8197 (mm) outliers start: 31 outliers final: 18 residues processed: 155 average time/residue: 0.1147 time to fit residues: 25.1599 Evaluate side-chains 136 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 46 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 63 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1036 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.148186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114375 restraints weight = 25790.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118243 restraints weight = 12613.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.120715 restraints weight = 7954.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.122312 restraints weight = 5948.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.123124 restraints weight = 4968.705| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11210 Z= 0.280 Angle : 0.880 12.668 15272 Z= 0.440 Chirality : 0.070 0.841 1525 Planarity : 0.005 0.066 1810 Dihedral : 18.976 166.177 2114 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 4.74 % Allowed : 15.41 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.21), residues: 1274 helix: -2.76 (0.19), residues: 507 sheet: -3.80 (0.40), residues: 104 loop : -3.00 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1244 TYR 0.028 0.003 TYR A 773 PHE 0.024 0.003 PHE A1204 TRP 0.008 0.002 TRP A1142 HIS 0.010 0.002 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.28 (11210) covalent geometry : angle 0.88022 / 0.44 (15272) hydrogen bonds : bond 0.06330 / 4.22 ( 206) hydrogen bonds : angle 6.72948 / 4.61 ( 543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 123 time to evaluate : 0.398 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 178 TYR cc_start: 0.6973 (t80) cc_final: 0.6247 (t80) REVERT: A 719 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8080 (mmtm) REVERT: A 846 LYS cc_start: 0.8714 (mtmp) cc_final: 0.8480 (pttm) REVERT: A 1071 THR cc_start: 0.8374 (t) cc_final: 0.8026 (m) REVERT: A 1099 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.3945 (t80) REVERT: A 1130 TYR cc_start: 0.3918 (OUTLIER) cc_final: 0.2508 (m-80) REVERT: A 1198 GLU cc_start: 0.8196 (tp30) cc_final: 0.7695 (tm-30) REVERT: A 1217 MET cc_start: 0.4595 (mmt) cc_final: 0.3871 (mmt) REVERT: A 1270 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8190 (mm) outliers start: 44 outliers final: 31 residues processed: 154 average time/residue: 0.1125 time to fit residues: 24.3644 Evaluate side-chains 147 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1056 GLN Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.152303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.118857 restraints weight = 25396.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.123040 restraints weight = 11906.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.125590 restraints weight = 7312.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.127270 restraints weight = 5402.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.128169 restraints weight = 4506.484| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11210 Z= 0.156 Angle : 0.761 10.862 15272 Z= 0.385 Chirality : 0.061 0.632 1525 Planarity : 0.004 0.054 1810 Dihedral : 18.878 165.534 2114 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 3.77 % Allowed : 18.10 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.21), residues: 1274 helix: -2.49 (0.20), residues: 506 sheet: -3.60 (0.40), residues: 104 loop : -2.88 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 964 TYR 0.035 0.002 TYR A 773 PHE 0.032 0.002 PHE A 258 TRP 0.011 0.001 TRP A 175 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (11210) covalent geometry : angle 0.76140 / 0.38 (15272) hydrogen bonds : bond 0.04855 / 3.23 ( 206) hydrogen bonds : angle 6.31749 / 4.29 ( 543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.447 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: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.6717 (t80) cc_final: 0.5971 (t80) REVERT: A 642 ASP cc_start: 0.7421 (p0) cc_final: 0.6855 (p0) REVERT: A 646 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.4970 (mp) REVERT: A 846 LYS cc_start: 0.8625 (mtmp) cc_final: 0.8393 (pttm) REVERT: A 1071 THR cc_start: 0.8243 (t) cc_final: 0.7935 (m) REVERT: A 1099 TYR cc_start: 0.4827 (OUTLIER) cc_final: 0.3430 (t80) REVERT: A 1130 TYR cc_start: 0.3926 (OUTLIER) cc_final: 0.2582 (m-80) REVERT: A 1217 MET cc_start: 0.4913 (mmt) cc_final: 0.4365 (mmt) REVERT: A 1270 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8194 (mm) outliers start: 35 outliers final: 25 residues processed: 142 average time/residue: 0.1227 time to fit residues: 24.2615 Evaluate side-chains 137 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 790 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.113346 restraints weight = 25483.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.117127 restraints weight = 12696.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.119548 restraints weight = 8090.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121023 restraints weight = 6095.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.121924 restraints weight = 5134.565| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 11210 Z= 0.351 Angle : 0.920 12.685 15272 Z= 0.462 Chirality : 0.070 0.858 1525 Planarity : 0.005 0.069 1810 Dihedral : 18.950 170.539 2114 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 4.85 % Allowed : 17.03 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.21), residues: 1274 helix: -2.53 (0.20), residues: 506 sheet: -3.86 (0.39), residues: 104 loop : -2.97 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1244 TYR 0.025 0.003 TYR A 47 PHE 0.026 0.003 PHE A 258 TRP 0.013 0.002 TRP A 175 HIS 0.006 0.002 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.35 (11210) covalent geometry : angle 0.91959 / 0.46 (15272) hydrogen bonds : bond 0.06381 / 4.25 ( 206) hydrogen bonds : angle 6.53155 / 4.47 ( 543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.412 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 719 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8089 (mmtm) REVERT: A 846 LYS cc_start: 0.8856 (mtmp) cc_final: 0.8574 (pttm) REVERT: A 962 LYS cc_start: 0.9103 (ptpt) cc_final: 0.8854 (mmtm) REVERT: A 1099 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.3273 (t80) REVERT: A 1130 TYR cc_start: 0.3979 (OUTLIER) cc_final: 0.2841 (m-80) REVERT: A 1270 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8128 (mm) outliers start: 45 outliers final: 33 residues processed: 139 average time/residue: 0.1162 time to fit residues: 22.8953 Evaluate side-chains 139 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.0020 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.116381 restraints weight = 25175.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.120499 restraints weight = 12070.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.122989 restraints weight = 7488.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.124669 restraints weight = 5582.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.125482 restraints weight = 4653.417| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11210 Z= 0.199 Angle : 0.803 12.142 15272 Z= 0.405 Chirality : 0.063 0.718 1525 Planarity : 0.004 0.062 1810 Dihedral : 18.890 169.396 2114 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.88 % Allowed : 18.75 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.21), residues: 1274 helix: -2.39 (0.20), residues: 508 sheet: -3.62 (0.40), residues: 106 loop : -2.83 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 918 TYR 0.034 0.002 TYR A 773 PHE 0.023 0.002 PHE A1240 TRP 0.012 0.002 TRP A 175 HIS 0.004 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (11210) covalent geometry : angle 0.80320 / 0.41 (15272) hydrogen bonds : bond 0.05353 / 3.57 ( 206) hydrogen bonds : angle 6.26869 / 4.27 ( 543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.490 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 178 TYR cc_start: 0.6908 (t80) cc_final: 0.6151 (t80) REVERT: A 719 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8058 (mmtm) REVERT: A 846 LYS cc_start: 0.8701 (mtmp) cc_final: 0.8421 (pttm) REVERT: A 1099 TYR cc_start: 0.4267 (OUTLIER) cc_final: 0.2822 (t80) REVERT: A 1130 TYR cc_start: 0.4242 (OUTLIER) cc_final: 0.2936 (m-80) REVERT: A 1270 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8189 (mm) outliers start: 36 outliers final: 28 residues processed: 135 average time/residue: 0.1176 time to fit residues: 22.3041 Evaluate side-chains 136 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 71 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.152227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.118883 restraints weight = 25169.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.123032 restraints weight = 11951.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.125703 restraints weight = 7378.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.127338 restraints weight = 5429.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.128142 restraints weight = 4501.135| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11210 Z= 0.151 Angle : 0.751 12.212 15272 Z= 0.381 Chirality : 0.058 0.629 1525 Planarity : 0.004 0.061 1810 Dihedral : 18.808 168.525 2114 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 3.66 % Allowed : 19.40 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.22), residues: 1274 helix: -2.11 (0.21), residues: 500 sheet: -3.45 (0.40), residues: 106 loop : -2.73 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 918 TYR 0.030 0.002 TYR A 773 PHE 0.022 0.002 PHE A1240 TRP 0.012 0.002 TRP A 175 HIS 0.003 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (11210) covalent geometry : angle 0.75146 / 0.38 (15272) hydrogen bonds : bond 0.04609 / 3.10 ( 206) hydrogen bonds : angle 6.10552 / 4.16 ( 543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.402 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 178 TYR cc_start: 0.6738 (t80) cc_final: 0.6014 (t80) REVERT: A 719 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8108 (mmtm) REVERT: A 846 LYS cc_start: 0.8681 (mtmp) cc_final: 0.8388 (pttm) REVERT: A 859 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8155 (tptp) REVERT: A 918 ARG cc_start: 0.5286 (mmt90) cc_final: 0.3633 (ttp-170) REVERT: A 925 TYR cc_start: 0.7751 (t80) cc_final: 0.7250 (m-80) REVERT: A 1099 TYR cc_start: 0.4257 (OUTLIER) cc_final: 0.2700 (t80) REVERT: A 1130 TYR cc_start: 0.4047 (OUTLIER) cc_final: 0.2910 (m-80) REVERT: A 1217 MET cc_start: 0.5366 (mmt) cc_final: 0.4416 (mmt) REVERT: A 1270 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8170 (mm) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 0.1172 time to fit residues: 22.3317 Evaluate side-chains 131 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 53 optimal weight: 50.0000 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 0.0000 chunk 30 optimal weight: 20.0000 chunk 85 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.153842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120496 restraints weight = 25224.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124748 restraints weight = 11792.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.127471 restraints weight = 7216.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.129072 restraints weight = 5284.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.130110 restraints weight = 4383.774| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11210 Z= 0.135 Angle : 0.721 12.032 15272 Z= 0.366 Chirality : 0.056 0.608 1525 Planarity : 0.004 0.049 1810 Dihedral : 18.715 167.596 2114 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.12 % Allowed : 19.72 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.22), residues: 1274 helix: -1.89 (0.22), residues: 499 sheet: -3.30 (0.41), residues: 104 loop : -2.69 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 921 TYR 0.028 0.002 TYR A 773 PHE 0.020 0.002 PHE A 281 TRP 0.012 0.002 TRP A 175 HIS 0.002 0.001 HIS A1261 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (11210) covalent geometry : angle 0.72073 / 0.37 (15272) hydrogen bonds : bond 0.04264 / 2.88 ( 206) hydrogen bonds : angle 5.85188 / 3.93 ( 543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.397 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 178 TYR cc_start: 0.6663 (t80) cc_final: 0.5940 (t80) REVERT: A 719 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8114 (mmtm) REVERT: A 846 LYS cc_start: 0.8798 (mtmp) cc_final: 0.8409 (pttm) REVERT: A 859 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8116 (tptp) REVERT: A 925 TYR cc_start: 0.7626 (t80) cc_final: 0.6966 (m-80) REVERT: A 1099 TYR cc_start: 0.3954 (OUTLIER) cc_final: 0.2675 (t80) REVERT: A 1130 TYR cc_start: 0.3562 (OUTLIER) cc_final: 0.2723 (m-80) REVERT: A 1270 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8041 (mm) outliers start: 29 outliers final: 21 residues processed: 133 average time/residue: 0.1166 time to fit residues: 21.8331 Evaluate side-chains 129 residues out of total 1166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 980 MET Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 67 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.152558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.118948 restraints weight = 25445.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123057 restraints weight = 12050.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.125733 restraints weight = 7469.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.127316 restraints weight = 5500.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.128380 restraints weight = 4575.005| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11210 Z= 0.168 Angle : 0.748 14.256 15272 Z= 0.378 Chirality : 0.057 0.693 1525 Planarity : 0.004 0.045 1810 Dihedral : 18.703 169.132 2114 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.12 % Allowed : 20.58 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.22), residues: 1274 helix: -1.79 (0.22), residues: 501 sheet: -3.31 (0.41), residues: 104 loop : -2.68 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 964 TYR 0.026 0.002 TYR A 773 PHE 0.021 0.002 PHE A1240 TRP 0.018 0.002 TRP A 175 HIS 0.003 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (11210) covalent geometry : angle 0.74828 / 0.38 (15272) hydrogen bonds : bond 0.04438 / 3.01 ( 206) hydrogen bonds : angle 5.84355 / 3.92 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.32 seconds wall clock time: 42 minutes 46.05 seconds (2566.05 seconds total)