Starting phenix.real_space_refine on Thu Mar 5 23:19:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exy_28665/03_2026/8exy_28665.map" } resolution = 3.2 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= 0.004 sd= 0.064 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15772 2.51 5 N 4560 2.21 5 O 5179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25711 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8540 Classifications: {'peptide': 1104} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1042} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 9953 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1212} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "T" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 772 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 770 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 625 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 24} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'G2P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19080 SG CYS D 891 76.523 25.266 87.538 1.00 66.30 S ATOM 19647 SG CYS D 968 75.181 28.520 88.983 1.00 63.87 S ATOM 19689 SG CYS D 975 76.752 28.399 85.434 1.00 49.53 S ATOM 19707 SG CYS D 978 73.419 26.929 86.039 1.00 60.43 S ATOM 12518 SG CYS D 60 109.068 80.631 114.636 1.00134.10 S ATOM 12536 SG CYS D 62 111.288 83.066 116.309 1.00146.33 S ATOM 12645 SG CYS D 75 111.700 79.345 116.977 1.00146.23 S ATOM 12671 SG CYS D 78 108.735 81.314 118.454 1.00135.45 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 6.38, per 1000 atoms: 0.25 Number of scatterers: 25711 At special positions: 0 Unit cell: (133.11, 133.98, 201.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 108 15.00 Mg 1 11.99 O 5179 8.00 N 4560 7.00 C 15772 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 968 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 78 " Number of angles added : 12 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 43 sheets defined 36.0% alpha, 13.6% beta 38 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 removed outlier: 3.507A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.694A pdb=" N LEU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.888A pdb=" N ILE B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.617A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.556A pdb=" N THR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.800A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.696A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.068A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 263 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.538A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.534A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.734A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.636A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.005A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.880A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 539' Processing helix chain 'C' and resid 582 through 587 removed outlier: 4.616A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.565A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.557A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.558A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 637' Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.514A pdb=" N GLU C 744 " --> pdb=" O ARG C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.644A pdb=" N LEU C 781 " --> pdb=" O ASP C 778 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 778 through 782' Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.677A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.648A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.591A pdb=" N LEU C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.547A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.837A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.313A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.105A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.529A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 142 through 183 removed outlier: 5.092A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 4.240A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.580A pdb=" N LYS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.771A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 removed outlier: 3.758A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.809A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 342 through 359 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.823A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 406 " --> pdb=" O SER D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 402 through 406' Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.572A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.902A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.647A pdb=" N THR D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.596A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.939A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 719 " --> pdb=" O LYS D 715 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 4.153A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 788 removed outlier: 3.939A pdb=" N THR D 782 " --> pdb=" O TRP D 778 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 804 removed outlier: 3.933A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 819 Processing helix chain 'D' and resid 845 through 852 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 857 through 864 removed outlier: 3.618A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 881 removed outlier: 3.943A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 880 " --> pdb=" O ARG D 876 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.512A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1014 Proline residue: D1006 - end of helix Processing helix chain 'D' and resid 1024 through 1036 Proline residue: D1029 - end of helix Processing helix chain 'D' and resid 1119 through 1126 removed outlier: 3.908A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.825A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D1139 " --> pdb=" O VAL D1135 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1162 removed outlier: 3.760A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.539A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.747A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.609A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 72 removed outlier: 3.756A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 63 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 14 through 30 removed outlier: 3.666A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 81 Processing helix chain 'G' and resid 90 through 94 removed outlier: 4.449A pdb=" N GLY G 93 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.728A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.790A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.852A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.618A pdb=" N SER A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 10 removed outlier: 3.635A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 177 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 100 removed outlier: 3.510A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 54 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.878A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.599A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.957A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.310A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.905A pdb=" N SER C 201 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.132A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.640A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.772A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 671 removed outlier: 7.022A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.519A pdb=" N GLY C 893 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 757 removed outlier: 3.582A pdb=" N VAL C 869 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 796 " --> pdb=" O GLY C 845 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.764A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY C 804 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N THR C 835 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD2, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.883A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.810A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.832A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 135 through 139 removed outlier: 5.418A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 443 through 444 removed outlier: 6.255A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.790A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE2, first strand: chain 'D' and resid 1051 through 1052 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1062 Processing sheet with id=AE4, first strand: chain 'D' and resid 1089 through 1090 Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'G' and resid 35 through 39 removed outlier: 4.260A pdb=" N ARG G 37 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 39 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU G 66 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL G 7 " --> pdb=" O PHE G 88 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE G 88 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS G 9 " --> pdb=" O THR G 86 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5409 1.33 - 1.46: 7789 1.46 - 1.59: 12804 1.59 - 1.72: 211 1.72 - 1.85: 159 Bond restraints: 26372 Sorted by residual: bond pdb=" C1' G2P D2004 " pdb=" O4' G2P D2004 " ideal model delta sigma weight residual 1.389 1.602 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C1' G2P D2004 " pdb=" C2' G2P D2004 " ideal model delta sigma weight residual 1.537 1.343 0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C2 G2P D2004 " pdb=" N3 G2P D2004 " ideal model delta sigma weight residual 1.305 1.462 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" C4 G2P D2004 " pdb=" N3 G2P D2004 " ideal model delta sigma weight residual 1.345 1.493 -0.148 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C5 G2P D2004 " pdb=" C6 G2P D2004 " ideal model delta sigma weight residual 1.420 1.548 -0.128 2.00e-02 2.50e+03 4.11e+01 ... (remaining 26367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 35630 2.10 - 4.19: 514 4.19 - 6.29: 37 6.29 - 8.39: 11 8.39 - 10.48: 6 Bond angle restraints: 36198 Sorted by residual: angle pdb=" CA PRO D1006 " pdb=" N PRO D1006 " pdb=" CD PRO D1006 " ideal model delta sigma weight residual 112.00 103.95 8.05 1.40e+00 5.10e-01 3.31e+01 angle pdb=" C3A G2P D2004 " pdb=" PA G2P D2004 " pdb=" O5' G2P D2004 " ideal model delta sigma weight residual 99.14 109.62 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C GLU D1036 " pdb=" N ALA D1037 " pdb=" CA ALA D1037 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C ILE B 3 " pdb=" N SER B 4 " pdb=" CA SER B 4 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" PA G2P D2004 " pdb=" C3A G2P D2004 " pdb=" PB G2P D2004 " ideal model delta sigma weight residual 120.83 110.71 10.12 3.00e+00 1.11e-01 1.14e+01 ... (remaining 36193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 13642 26.75 - 53.50: 1862 53.50 - 80.24: 410 80.24 - 106.99: 30 106.99 - 133.74: 1 Dihedral angle restraints: 15945 sinusoidal: 7272 harmonic: 8673 Sorted by residual: dihedral pdb=" O4' A R 21 " pdb=" C1' A R 21 " pdb=" N9 A R 21 " pdb=" C4 A R 21 " ideal model delta sinusoidal sigma weight residual -106.00 -177.24 71.24 1 1.70e+01 3.46e-03 2.25e+01 dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C4' DC T 23 " pdb=" C3' DC T 23 " pdb=" O3' DC T 23 " pdb=" P DA T 24 " ideal model delta sinusoidal sigma weight residual 220.00 86.26 133.74 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 15942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2595 0.033 - 0.067: 1045 0.067 - 0.100: 342 0.100 - 0.133: 147 0.133 - 0.166: 13 Chirality restraints: 4142 Sorted by residual: chirality pdb=" CA GLU D1005 " pdb=" N GLU D1005 " pdb=" C GLU D1005 " pdb=" CB GLU D1005 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ASP D 946 " pdb=" N ASP D 946 " pdb=" C ASP D 946 " pdb=" CB ASP D 946 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ASP A 57 " pdb=" N ASP A 57 " pdb=" C ASP A 57 " pdb=" CB ASP A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 4139 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 82 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D1121 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C VAL D1121 " -0.060 2.00e-02 2.50e+03 pdb=" O VAL D1121 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D1122 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D1031 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C VAL D1031 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL D1031 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN D1032 " -0.019 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 169 2.60 - 3.17: 19385 3.17 - 3.75: 37914 3.75 - 4.32: 51864 4.32 - 4.90: 87532 Nonbonded interactions: 196864 Sorted by model distance: nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 2.020 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2001 " model vdw 2.046 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2001 " model vdw 2.204 2.170 nonbonded pdb=" O LYS C 518 " pdb=" OG SER C 525 " model vdw 2.242 3.040 ... (remaining 196859 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.213 26380 Z= 0.207 Angle : 0.624 10.482 36210 Z= 0.338 Chirality : 0.043 0.166 4142 Planarity : 0.006 0.103 4380 Dihedral : 22.951 133.741 10375 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.41 % Favored : 89.82 % Rotamer: Outliers : 20.94 % Allowed : 23.58 % Favored : 55.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.15 (0.13), residues: 3020 helix: -1.62 (0.15), residues: 990 sheet: -1.87 (0.27), residues: 328 loop : -2.50 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.017 0.001 TYR D1062 PHE 0.014 0.001 PHE C1011 TRP 0.013 0.001 TRP D 23 HIS 0.013 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00452 (26372) covalent geometry : angle 0.62286 (36198) hydrogen bonds : bond 0.18240 ( 911) hydrogen bonds : angle 6.27550 ( 2467) metal coordination : bond 0.00636 ( 8) metal coordination : angle 2.54685 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 532 poor density : 147 time to evaluate : 0.986 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 3 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 120 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8341 (m110) REVERT: A 187 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7409 (p) REVERT: B 159 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7528 (tp) REVERT: B 187 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 205 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9142 (mp) REVERT: C 213 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: C 783 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8474 (p0) REVERT: C 807 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7273 (t) REVERT: D 196 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5606 (ptmt) REVERT: D 198 ARG cc_start: 0.0106 (OUTLIER) cc_final: -0.0231 (mtm-85) REVERT: D 207 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: D 209 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6045 (mmp80) REVERT: D 235 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8832 (mt) REVERT: D 581 MET cc_start: 0.8709 (mtt) cc_final: 0.8392 (mtt) REVERT: D 1006 PRO cc_start: 0.9441 (OUTLIER) cc_final: 0.9226 (Cg_exo) REVERT: D 1014 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.6826 (m) REVERT: D 1056 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5424 (mt-10) REVERT: D 1088 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8712 (p) REVERT: D 1115 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (m) REVERT: G 10 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8878 (p) REVERT: G 52 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6237 (mmtt) outliers start: 532 outliers final: 121 residues processed: 639 average time/residue: 0.2064 time to fit residues: 194.6520 Evaluate side-chains 234 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 92 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 749 SER Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 732 SER Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 LYS Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1005 GLU Chi-restraints excluded: chain D residue 1006 PRO Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1032 GLN Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1063 LYS Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1079 LYS Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1085 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 112 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 61 HIS A 79 ASN A 120 ASN A 152 ASN B 119 HIS ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 349 HIS C 435 GLN ** C 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN C 585 GLN C 610 ASN C 662 HIS C 685 ASN C 700 GLN C 875 GLN C1066 GLN C1077 GLN C1111 ASN C1129 GLN D 5 ASN D 207 GLN D 262 GLN D 352 ASN D 368 ASN D 375 GLN D 396 ASN D 410 GLN D 525 HIS D 564 ASN D 606 HIS D 787 GLN D 797 ASN D 852 ASN D 882 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1273 GLN E 63 GLN G 21 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.064353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.042817 restraints weight = 115607.577| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.66 r_work: 0.2859 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26380 Z= 0.141 Angle : 0.607 12.247 36210 Z= 0.319 Chirality : 0.043 0.184 4142 Planarity : 0.005 0.076 4380 Dihedral : 17.621 131.772 4875 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 6.73 % Allowed : 26.97 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3020 helix: -0.32 (0.16), residues: 1017 sheet: -1.25 (0.26), residues: 374 loop : -2.19 (0.13), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 667 TYR 0.017 0.001 TYR D1062 PHE 0.011 0.001 PHE D 107 TRP 0.013 0.001 TRP D 23 HIS 0.005 0.001 HIS C 662 Details of bonding type rmsd covalent geometry : bond 0.00323 (26372) covalent geometry : angle 0.60462 (36198) hydrogen bonds : bond 0.04415 ( 911) hydrogen bonds : angle 4.54450 ( 2467) metal coordination : bond 0.00493 ( 8) metal coordination : angle 2.76591 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 100 time to evaluate : 0.872 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 3 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 120 ASN cc_start: 0.9094 (m-40) cc_final: 0.8529 (m110) REVERT: A 185 GLN cc_start: 0.8676 (mp10) cc_final: 0.8403 (pm20) REVERT: A 200 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: A 221 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8920 (pt) REVERT: B 60 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8455 (pt) REVERT: B 159 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (tp) REVERT: C 138 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: C 305 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8666 (mmm-85) REVERT: C 783 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8556 (p0) REVERT: D 73 ILE cc_start: 0.8817 (mp) cc_final: 0.8476 (tp) REVERT: D 196 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.6036 (pttt) REVERT: D 1056 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5699 (mt-10) REVERT: D 1112 MET cc_start: 0.7354 (tpp) cc_final: 0.6977 (tpp) REVERT: G 31 MET cc_start: 0.8210 (tpp) cc_final: 0.7564 (tpp) REVERT: G 71 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7320 (tpp) REVERT: G 80 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7397 (tmt-80) outliers start: 171 outliers final: 86 residues processed: 262 average time/residue: 0.1706 time to fit residues: 70.8288 Evaluate side-chains 187 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 89 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 741 ARG Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1032 GLN Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 71 MET Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 94 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 169 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN C 935 HIS D 505 HIS D 533 ASN D 606 HIS D 657 GLN D 854 HIS ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.063099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.041494 restraints weight = 117082.378| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.64 r_work: 0.2817 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26380 Z= 0.182 Angle : 0.583 10.110 36210 Z= 0.305 Chirality : 0.043 0.157 4142 Planarity : 0.005 0.074 4380 Dihedral : 17.055 130.161 4734 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 5.55 % Allowed : 26.50 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 3020 helix: 0.26 (0.17), residues: 1013 sheet: -1.10 (0.27), residues: 370 loop : -1.96 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 830 TYR 0.019 0.001 TYR D1062 PHE 0.012 0.001 PHE D 107 TRP 0.010 0.001 TRP C 70 HIS 0.004 0.001 HIS D 103 Details of bonding type rmsd covalent geometry : bond 0.00428 (26372) covalent geometry : angle 0.57972 (36198) hydrogen bonds : bond 0.04482 ( 911) hydrogen bonds : angle 4.30890 ( 2467) metal coordination : bond 0.00764 ( 8) metal coordination : angle 3.18186 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 87 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7752 (tp) REVERT: A 120 ASN cc_start: 0.9106 (m-40) cc_final: 0.8601 (t0) REVERT: A 200 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8461 (m-40) REVERT: B 1 MET cc_start: 0.8582 (mmm) cc_final: 0.8173 (mtm) REVERT: C 138 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: C 783 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8770 (p0) REVERT: C 926 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8434 (mpp) REVERT: D 196 LYS cc_start: 0.6262 (OUTLIER) cc_final: 0.5818 (tptp) REVERT: D 209 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7046 (mmp80) REVERT: D 260 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8828 (p) REVERT: D 310 MET cc_start: 0.9248 (mmm) cc_final: 0.8911 (tpt) REVERT: D 1032 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: G 31 MET cc_start: 0.8295 (tpp) cc_final: 0.7844 (tpp) REVERT: G 80 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7453 (tmt-80) outliers start: 141 outliers final: 83 residues processed: 220 average time/residue: 0.1765 time to fit residues: 62.0178 Evaluate side-chains 178 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 85 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 783 ASP Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1032 GLN Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 195 optimal weight: 0.0670 chunk 123 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 301 optimal weight: 10.0000 chunk 269 optimal weight: 0.8980 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 124 HIS D 505 HIS ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.062576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040790 restraints weight = 116517.746| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.67 r_work: 0.2803 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26380 Z= 0.183 Angle : 0.563 8.641 36210 Z= 0.295 Chirality : 0.042 0.179 4142 Planarity : 0.005 0.064 4380 Dihedral : 16.879 130.192 4711 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 4.88 % Allowed : 26.26 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.15), residues: 3020 helix: 0.54 (0.17), residues: 1012 sheet: -0.93 (0.28), residues: 354 loop : -1.84 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1085 TYR 0.015 0.001 TYR D1062 PHE 0.011 0.001 PHE D 107 TRP 0.011 0.001 TRP C 70 HIS 0.013 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00436 (26372) covalent geometry : angle 0.56060 (36198) hydrogen bonds : bond 0.04376 ( 911) hydrogen bonds : angle 4.23668 ( 2467) metal coordination : bond 0.00749 ( 8) metal coordination : angle 3.01324 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 87 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.9117 (m-40) cc_final: 0.8611 (t0) REVERT: A 185 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: A 200 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8444 (m-40) REVERT: B 1 MET cc_start: 0.8612 (mmm) cc_final: 0.8140 (mtm) REVERT: C 138 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: C 305 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8611 (mmm-85) REVERT: C 926 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8404 (mpp) REVERT: D 73 ILE cc_start: 0.8731 (mp) cc_final: 0.8494 (tp) REVERT: D 196 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5842 (tptp) REVERT: D 260 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8899 (p) REVERT: D 310 MET cc_start: 0.9265 (mmm) cc_final: 0.8893 (tpt) REVERT: D 1032 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (mt0) REVERT: D 1112 MET cc_start: 0.7437 (tpp) cc_final: 0.7170 (tpp) REVERT: G 31 MET cc_start: 0.8349 (tpp) cc_final: 0.7849 (tpp) REVERT: G 71 MET cc_start: 0.7914 (tpt) cc_final: 0.7507 (tpp) REVERT: G 80 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7396 (tmt-80) outliers start: 124 outliers final: 77 residues processed: 203 average time/residue: 0.1564 time to fit residues: 52.7267 Evaluate side-chains 169 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 83 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 1032 GLN Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN D 505 HIS D1084 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.062653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041161 restraints weight = 115669.805| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.58 r_work: 0.2810 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26380 Z= 0.145 Angle : 0.532 8.168 36210 Z= 0.279 Chirality : 0.041 0.172 4142 Planarity : 0.004 0.067 4380 Dihedral : 16.722 130.049 4691 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.37 % Favored : 94.50 % Rotamer: Outliers : 4.88 % Allowed : 26.22 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3020 helix: 0.76 (0.17), residues: 1007 sheet: -0.83 (0.28), residues: 358 loop : -1.71 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 334 TYR 0.014 0.001 TYR D1062 PHE 0.010 0.001 PHE D 107 TRP 0.010 0.001 TRP C 70 HIS 0.010 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00342 (26372) covalent geometry : angle 0.52937 (36198) hydrogen bonds : bond 0.04012 ( 911) hydrogen bonds : angle 4.12134 ( 2467) metal coordination : bond 0.00602 ( 8) metal coordination : angle 3.02785 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 85 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.9100 (m-40) cc_final: 0.8624 (t0) REVERT: A 200 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: B 1 MET cc_start: 0.8610 (mmm) cc_final: 0.8169 (mtm) REVERT: B 128 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8708 (tp) REVERT: C 138 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8576 (tm-30) REVERT: C 305 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8586 (mmm-85) REVERT: C 673 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (mtp-110) REVERT: C 926 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8388 (mpp) REVERT: D 56 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8426 (mtp180) REVERT: D 73 ILE cc_start: 0.8783 (mp) cc_final: 0.8517 (pt) REVERT: D 196 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5825 (tptp) REVERT: D 260 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 310 MET cc_start: 0.9267 (mmm) cc_final: 0.8899 (tpt) REVERT: D 766 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.9060 (p0) REVERT: D 1056 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5950 (mt-10) REVERT: D 1112 MET cc_start: 0.7441 (tpp) cc_final: 0.7162 (tpp) REVERT: E 76 LEU cc_start: 0.6000 (pp) cc_final: 0.5633 (pp) REVERT: G 31 MET cc_start: 0.8383 (tpp) cc_final: 0.7847 (tpp) REVERT: G 71 MET cc_start: 0.7888 (tpt) cc_final: 0.7510 (tpp) REVERT: G 80 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7409 (tmt-80) outliers start: 124 outliers final: 80 residues processed: 204 average time/residue: 0.1598 time to fit residues: 53.5752 Evaluate side-chains 176 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 84 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 766 ASN Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 119 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 285 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 259 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN ** G 32 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 = 0.3595 r_free = 0.3595 target = 0.062218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040636 restraints weight = 117031.898| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.65 r_work: 0.2796 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26380 Z= 0.171 Angle : 0.545 8.223 36210 Z= 0.285 Chirality : 0.042 0.206 4142 Planarity : 0.004 0.070 4380 Dihedral : 16.630 129.790 4680 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.37 % Rotamer: Outliers : 4.45 % Allowed : 26.46 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3020 helix: 0.84 (0.17), residues: 1014 sheet: -0.71 (0.29), residues: 352 loop : -1.65 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 144 TYR 0.013 0.001 TYR D1062 PHE 0.010 0.001 PHE C 906 TRP 0.010 0.001 TRP C 70 HIS 0.009 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00407 (26372) covalent geometry : angle 0.54247 (36198) hydrogen bonds : bond 0.04170 ( 911) hydrogen bonds : angle 4.12081 ( 2467) metal coordination : bond 0.00715 ( 8) metal coordination : angle 3.00384 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 86 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.9112 (m-40) cc_final: 0.8636 (t0) REVERT: A 200 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: B 1 MET cc_start: 0.8680 (mmm) cc_final: 0.8215 (mtm) REVERT: C 138 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8590 (tm-30) REVERT: C 305 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8592 (mmm-85) REVERT: C 673 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8329 (mtp-110) REVERT: C 926 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: D 196 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5851 (tptp) REVERT: D 260 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.8965 (p) REVERT: D 310 MET cc_start: 0.9287 (mmm) cc_final: 0.8917 (tpt) REVERT: D 1056 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5942 (mt-10) REVERT: D 1112 MET cc_start: 0.7490 (tpp) cc_final: 0.7177 (tpp) REVERT: G 31 MET cc_start: 0.8388 (tpp) cc_final: 0.7839 (tpp) REVERT: G 80 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7453 (tmt-80) outliers start: 113 outliers final: 85 residues processed: 194 average time/residue: 0.1712 time to fit residues: 54.7442 Evaluate side-chains 177 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 83 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 266 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 271 optimal weight: 0.0570 chunk 182 optimal weight: 2.9990 chunk 308 optimal weight: 50.0000 chunk 265 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 198 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.3616 r_free = 0.3616 target = 0.062975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.041495 restraints weight = 116084.419| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.65 r_work: 0.2829 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 26380 Z= 0.107 Angle : 0.499 8.078 36210 Z= 0.261 Chirality : 0.041 0.202 4142 Planarity : 0.004 0.069 4380 Dihedral : 16.521 128.889 4679 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 3.50 % Allowed : 27.44 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3020 helix: 1.09 (0.17), residues: 1008 sheet: -0.54 (0.29), residues: 353 loop : -1.46 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 981 TYR 0.014 0.001 TYR D1062 PHE 0.008 0.001 PHE D 107 TRP 0.008 0.001 TRP D 23 HIS 0.007 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00246 (26372) covalent geometry : angle 0.49655 (36198) hydrogen bonds : bond 0.03407 ( 911) hydrogen bonds : angle 3.90379 ( 2467) metal coordination : bond 0.00359 ( 8) metal coordination : angle 2.93668 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 89 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 120 ASN cc_start: 0.9090 (m-40) cc_final: 0.8639 (t0) REVERT: A 200 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: B 1 MET cc_start: 0.8696 (mmm) cc_final: 0.8282 (mtm) REVERT: C 138 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: C 305 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8560 (mmm-85) REVERT: D 196 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5900 (tptp) REVERT: D 260 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8974 (p) REVERT: D 275 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: D 310 MET cc_start: 0.9285 (mmm) cc_final: 0.8888 (tpt) REVERT: D 581 MET cc_start: 0.9157 (mtt) cc_final: 0.8940 (mtt) REVERT: D 1056 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.5886 (mt-10) REVERT: D 1112 MET cc_start: 0.7520 (tpp) cc_final: 0.7221 (tpp) REVERT: E 76 LEU cc_start: 0.5786 (pp) cc_final: 0.5509 (pp) REVERT: G 31 MET cc_start: 0.8443 (tpp) cc_final: 0.7902 (tpp) REVERT: G 71 MET cc_start: 0.7888 (tpt) cc_final: 0.7251 (tpp) outliers start: 89 outliers final: 66 residues processed: 175 average time/residue: 0.1499 time to fit residues: 44.4655 Evaluate side-chains 159 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 85 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 254 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 228 optimal weight: 0.0020 chunk 181 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 47 optimal weight: 0.0000 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 372 HIS ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.062392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040877 restraints weight = 116817.129| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.64 r_work: 0.2807 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26380 Z= 0.134 Angle : 0.515 8.097 36210 Z= 0.269 Chirality : 0.041 0.203 4142 Planarity : 0.004 0.072 4380 Dihedral : 16.499 129.049 4674 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 3.58 % Allowed : 27.24 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3020 helix: 1.18 (0.17), residues: 1015 sheet: -0.53 (0.29), residues: 349 loop : -1.40 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 981 TYR 0.012 0.001 TYR D1062 PHE 0.009 0.001 PHE C 906 TRP 0.008 0.001 TRP C 70 HIS 0.006 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00316 (26372) covalent geometry : angle 0.51200 (36198) hydrogen bonds : bond 0.03804 ( 911) hydrogen bonds : angle 3.92415 ( 2467) metal coordination : bond 0.00548 ( 8) metal coordination : angle 2.95514 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 85 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8065 (tp) REVERT: A 120 ASN cc_start: 0.9087 (m-40) cc_final: 0.8663 (t0) REVERT: A 200 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: B 1 MET cc_start: 0.8696 (mmm) cc_final: 0.8273 (mtm) REVERT: C 138 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8611 (tm-30) REVERT: C 305 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8562 (mmm-85) REVERT: C 673 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8339 (mtp-110) REVERT: D 196 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.6034 (tptp) REVERT: D 260 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 310 MET cc_start: 0.9275 (mmm) cc_final: 0.8906 (tpt) REVERT: D 1056 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5860 (mt-10) REVERT: D 1112 MET cc_start: 0.7583 (tpp) cc_final: 0.7276 (tpp) REVERT: E 76 LEU cc_start: 0.6058 (pp) cc_final: 0.5336 (pp) REVERT: G 31 MET cc_start: 0.8463 (tpp) cc_final: 0.7936 (tpp) REVERT: G 71 MET cc_start: 0.7787 (tpt) cc_final: 0.7208 (tpp) REVERT: G 80 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7443 (tmt-80) outliers start: 91 outliers final: 72 residues processed: 172 average time/residue: 0.1691 time to fit residues: 47.8852 Evaluate side-chains 165 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 84 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 187 optimal weight: 0.0980 chunk 214 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 476 HIS D 146 ASN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.062316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.040721 restraints weight = 118173.042| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.68 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26380 Z= 0.139 Angle : 0.513 8.661 36210 Z= 0.268 Chirality : 0.041 0.202 4142 Planarity : 0.004 0.070 4380 Dihedral : 16.472 129.322 4670 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 3.50 % Allowed : 27.17 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3020 helix: 1.19 (0.17), residues: 1015 sheet: -0.51 (0.29), residues: 349 loop : -1.35 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 334 TYR 0.011 0.001 TYR D1062 PHE 0.009 0.001 PHE C 906 TRP 0.008 0.001 TRP C 70 HIS 0.006 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00330 (26372) covalent geometry : angle 0.50986 (36198) hydrogen bonds : bond 0.03759 ( 911) hydrogen bonds : angle 3.91856 ( 2467) metal coordination : bond 0.00557 ( 8) metal coordination : angle 2.93393 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 88 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8175 (tp) REVERT: A 120 ASN cc_start: 0.8985 (m-40) cc_final: 0.8588 (t0) REVERT: A 200 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8233 (m-40) REVERT: B 1 MET cc_start: 0.8441 (mmm) cc_final: 0.8072 (mtm) REVERT: C 138 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: C 305 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8264 (mmm-85) REVERT: C 673 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7959 (mtp-110) REVERT: D 196 LYS cc_start: 0.6377 (OUTLIER) cc_final: 0.6045 (tptp) REVERT: D 260 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8870 (p) REVERT: D 310 MET cc_start: 0.9158 (mmm) cc_final: 0.8777 (tpt) REVERT: D 1056 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5904 (mt-10) REVERT: D 1112 MET cc_start: 0.7370 (tpp) cc_final: 0.7088 (tpp) REVERT: E 76 LEU cc_start: 0.6361 (pp) cc_final: 0.5720 (pp) REVERT: G 31 MET cc_start: 0.8499 (tpp) cc_final: 0.7983 (tpp) REVERT: G 71 MET cc_start: 0.7736 (tpt) cc_final: 0.7197 (tpp) REVERT: G 80 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7298 (tmt-80) outliers start: 89 outliers final: 71 residues processed: 173 average time/residue: 0.1754 time to fit residues: 49.4787 Evaluate side-chains 166 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 86 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 200 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 293 optimal weight: 8.9990 chunk 214 optimal weight: 0.0270 chunk 267 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 overall best weight: 1.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.3605 r_free = 0.3605 target = 0.062511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041021 restraints weight = 116638.407| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.66 r_work: 0.2814 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26380 Z= 0.117 Angle : 0.505 9.805 36210 Z= 0.263 Chirality : 0.041 0.201 4142 Planarity : 0.004 0.070 4380 Dihedral : 16.393 129.497 4667 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.15 % Allowed : 27.56 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3020 helix: 1.29 (0.17), residues: 1022 sheet: -0.46 (0.29), residues: 350 loop : -1.27 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.011 0.001 TYR D1062 PHE 0.009 0.001 PHE C 153 TRP 0.008 0.001 TRP C 70 HIS 0.006 0.001 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00274 (26372) covalent geometry : angle 0.50221 (36198) hydrogen bonds : bond 0.03504 ( 911) hydrogen bonds : angle 3.85212 ( 2467) metal coordination : bond 0.00463 ( 8) metal coordination : angle 3.10807 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6040 Ramachandran restraints generated. 3020 Oldfield, 0 Emsley, 3020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 87 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8188 (tp) REVERT: A 120 ASN cc_start: 0.9084 (m-40) cc_final: 0.8689 (t0) REVERT: A 200 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: B 1 MET cc_start: 0.8647 (mmm) cc_final: 0.8241 (mtm) REVERT: B 59 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8633 (p) REVERT: C 138 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: C 305 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8562 (mmm-85) REVERT: C 673 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8351 (mtp-110) REVERT: D 196 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.6022 (tptp) REVERT: D 260 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.8919 (p) REVERT: D 310 MET cc_start: 0.9307 (mmm) cc_final: 0.8932 (tpt) REVERT: D 1056 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5913 (mt-10) REVERT: D 1112 MET cc_start: 0.7568 (tpp) cc_final: 0.7266 (tpp) REVERT: E 76 LEU cc_start: 0.6113 (pp) cc_final: 0.4775 (pp) REVERT: E 77 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7923 (pp20) REVERT: G 31 MET cc_start: 0.8470 (tpp) cc_final: 0.7725 (tpp) REVERT: G 71 MET cc_start: 0.7676 (tpt) cc_final: 0.7133 (tpp) outliers start: 80 outliers final: 70 residues processed: 162 average time/residue: 0.1637 time to fit residues: 44.1962 Evaluate side-chains 165 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 86 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 673 ARG Chi-restraints excluded: chain C residue 754 GLU Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 826 ASN Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1052 ARG Chi-restraints excluded: chain D residue 1056 GLU Chi-restraints excluded: chain D residue 1066 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 249 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 20 optimal weight: 7.9990 chunk 223 optimal weight: 0.2980 chunk 196 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 505 HIS ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 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 = 0.3622 r_free = 0.3622 target = 0.063124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041647 restraints weight = 117360.794| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.70 r_work: 0.2836 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26380 Z= 0.097 Angle : 0.487 9.315 36210 Z= 0.253 Chirality : 0.040 0.201 4142 Planarity : 0.004 0.072 4380 Dihedral : 16.310 128.892 4666 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 3.03 % Allowed : 27.72 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3020 helix: 1.32 (0.17), residues: 1031 sheet: -0.39 (0.29), residues: 350 loop : -1.18 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 459 TYR 0.012 0.001 TYR D1062 PHE 0.009 0.001 PHE C 153 TRP 0.008 0.001 TRP C 70 HIS 0.006 0.000 HIS B 124 Details of bonding type rmsd covalent geometry : bond 0.00223 (26372) covalent geometry : angle 0.48462 (36198) hydrogen bonds : bond 0.03158 ( 911) hydrogen bonds : angle 3.74626 ( 2467) metal coordination : bond 0.00314 ( 8) metal coordination : angle 2.91958 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8020.03 seconds wall clock time: 137 minutes 7.19 seconds (8227.19 seconds total)