Starting phenix.real_space_refine on Sat Aug 8 04:02:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.map" model { file = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eof_28374/08_2026/8eof_28374.cif" } resolution = 3.3 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= 0.003 sd= 0.037 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 102 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15723 2.51 5 N 4552 2.21 5 O 5139 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25608 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: 8549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8549 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1043} 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: 9930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9930 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1209} 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: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 713 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "R" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 625 Classifications: {'RNAv2': 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19089 SG CYS D 891 75.837 25.268 88.543 1.00 40.13 S ATOM 19656 SG CYS D 968 74.555 28.618 89.921 1.00 14.70 S ATOM 19698 SG CYS D 975 76.016 28.337 86.351 1.00 31.54 S ATOM 19716 SG CYS D 978 72.682 26.991 87.125 1.00 38.76 S ATOM 12527 SG CYS D 60 109.712 80.455 114.313 1.00 84.53 S ATOM 12545 SG CYS D 62 111.958 82.928 115.910 1.00 98.06 S ATOM 12654 SG CYS D 75 112.415 79.183 116.650 1.00 99.63 S ATOM 12680 SG CYS D 78 109.515 81.224 118.112 1.00 91.80 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: 4.51, per 1000 atoms: 0.18 Number of scatterers: 25608 At special positions: 0 Unit cell: (132.24, 133.98, 200.1, 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 102 15.00 Mg 1 11.99 O 5139 8.00 N 4552 7.00 C 15723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " 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 78 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " Number of angles added : 12 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5566 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 43 sheets defined 35.2% alpha, 13.4% beta 42 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.655A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.682A 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: 3.935A pdb=" N ILE B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.637A pdb=" N ALA B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.283A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.814A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.778A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.503A 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 226 through 229 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.283A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.556A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.571A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.591A pdb=" N LYS C 318 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.980A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.812A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.556A pdb=" N LEU C 417 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 431 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.616A 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: 3.898A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.813A 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: 4.534A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.598A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.599A 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: 3.590A 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: 3.502A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.547A 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 Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.623A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.642A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.561A 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: 3.517A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.827A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.218A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.140A 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: 3.587A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.515A 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 147 through 184 Processing helix chain 'D' and resid 191 through 228 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.571A pdb=" N LYS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.623A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.708A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.737A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.888A 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: 3.742A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.616A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.719A 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: 3.726A 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: 3.562A 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: 3.936A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 719 " --> pdb=" O LYS D 715 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 763 removed outlier: 4.095A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 779 Processing helix chain 'D' and resid 780 through 793 removed outlier: 3.800A pdb=" N GLU D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 793 " --> pdb=" O LEU D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 4.055A 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 866 removed outlier: 3.667A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 881 removed outlier: 3.574A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 880 " --> pdb=" O ARG D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.552A 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 1001 removed outlier: 3.725A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.528A pdb=" N THR D1008 " --> pdb=" O GLU D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1119 through 1126 removed outlier: 3.818A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.751A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN D1139 " --> pdb=" O VAL D1135 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1160 removed outlier: 3.824A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.607A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.620A 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: 3.650A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.701A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.357A 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 28 removed outlier: 4.312A pdb=" N GLU G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 Processing helix chain 'G' and resid 102 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.702A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.006A 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: 6.851A 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: 3.838A 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 removed outlier: 7.037A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.591A 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: 3.584A pdb=" N GLU B 24 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 191 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.606A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (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 173 removed outlier: 6.873A 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: 6.498A 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: 5.807A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.799A 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: 6.358A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 185 Processing sheet with id=AB7, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AB8, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.122A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 removed outlier: 3.552A pdb=" N GLU C 569 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.641A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.868A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.536A 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: 6.026A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.685A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 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 1042 through 1044 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.909A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.820A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.623A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.727A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 443 through 444 removed outlier: 6.143A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.598A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1063 Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE6, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.863A pdb=" N ARG G 37 " --> pdb=" O GLU G 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 48 through 49 788 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 226 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6755 1.33 - 1.45: 4739 1.45 - 1.57: 14411 1.57 - 1.69: 200 1.69 - 1.81: 157 Bond restraints: 26262 Sorted by residual: bond pdb=" C3' DG T 31 " pdb=" O3' DG T 31 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DG T 26 " pdb=" C2' DG T 26 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DA T 27 " pdb=" C2' DA T 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C1' DC N 15 " pdb=" N1 DC N 15 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.14e+00 ... (remaining 26257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 34584 1.69 - 3.38: 1253 3.38 - 5.07: 162 5.07 - 6.75: 19 6.75 - 8.44: 8 Bond angle restraints: 36026 Sorted by residual: angle pdb=" C3' DG T 31 " pdb=" O3' DG T 31 " pdb=" P DC T 32 " ideal model delta sigma weight residual 119.70 127.77 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" O5' DC N 10 " pdb=" C5' DC N 10 " pdb=" C4' DC N 10 " ideal model delta sigma weight residual 109.40 114.01 -4.61 8.00e-01 1.56e+00 3.32e+01 angle pdb=" O5' DC N 15 " pdb=" C5' DC N 15 " pdb=" C4' DC N 15 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" C3' DC T 32 " pdb=" O3' DC T 32 " pdb=" P DA T 33 " ideal model delta sigma weight residual 119.70 126.27 -6.57 1.20e+00 6.94e-01 3.00e+01 angle pdb=" O4' DA T 30 " pdb=" C1' DA T 30 " pdb=" N9 DA T 30 " ideal model delta sigma weight residual 108.00 104.27 3.73 7.00e-01 2.04e+00 2.84e+01 ... (remaining 36021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 14371 35.48 - 70.97: 1342 70.97 - 106.45: 49 106.45 - 141.93: 2 141.93 - 177.41: 2 Dihedral angle restraints: 15766 sinusoidal: 7099 harmonic: 8667 Sorted by residual: dihedral pdb=" C4' A R 21 " pdb=" C3' A R 21 " pdb=" C2' A R 21 " pdb=" C1' A R 21 " ideal model delta sinusoidal sigma weight residual 36.34 -37.19 73.54 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' C R 20 " pdb=" C3' C R 20 " pdb=" C2' C R 20 " pdb=" C1' C R 20 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' C R 11 " pdb=" C3' C R 11 " pdb=" C2' C R 11 " pdb=" C1' C R 11 " ideal model delta sinusoidal sigma weight residual 36.34 -35.27 71.62 1 3.10e+00 1.04e-01 6.84e+02 ... (remaining 15763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3132 0.056 - 0.111: 831 0.111 - 0.167: 114 0.167 - 0.223: 16 0.223 - 0.278: 29 Chirality restraints: 4122 Sorted by residual: chirality pdb=" C2' C R 20 " pdb=" C3' C R 20 " pdb=" O2' C R 20 " pdb=" C1' C R 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' A R 21 " pdb=" C4' A R 21 " pdb=" O3' A R 21 " pdb=" C2' A R 21 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C R 11 " pdb=" C3' C R 11 " pdb=" O2' C R 11 " pdb=" C1' C R 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4119 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 870 " 0.029 2.00e-02 2.50e+03 5.86e-02 3.44e+01 pdb=" C SER D 870 " -0.101 2.00e-02 2.50e+03 pdb=" O SER D 870 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY D 871 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 32 " 0.034 2.00e-02 2.50e+03 3.20e-02 2.31e+01 pdb=" N1 DC T 32 " -0.078 2.00e-02 2.50e+03 pdb=" C2 DC T 32 " 0.042 2.00e-02 2.50e+03 pdb=" O2 DC T 32 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC T 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC T 32 " 0.002 2.00e-02 2.50e+03 pdb=" N4 DC T 32 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC T 32 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DC T 32 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.069 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO C 82 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 101 2.55 - 3.14: 17793 3.14 - 3.72: 37018 3.72 - 4.31: 51356 4.31 - 4.90: 88342 Nonbonded interactions: 194610 Sorted by model distance: nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 1.961 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 2.049 2.170 nonbonded pdb=" O ILE D1210 " pdb=" OG SER D1214 " model vdw 2.136 3.040 nonbonded pdb=" O LYS C 518 " pdb=" OG SER C 525 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP D 383 " pdb=" OG SER D 403 " model vdw 2.205 3.040 ... (remaining 194605 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.620 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.006 0.074 26270 Z= 0.289 Angle : 0.734 8.443 36038 Z= 0.445 Chirality : 0.054 0.278 4122 Planarity : 0.006 0.106 4374 Dihedral : 22.379 177.414 10200 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.59 % Favored : 89.65 % Rotamer: Outliers : 17.49 % Allowed : 25.37 % Favored : 57.13 % 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: -3.14 (0.14), residues: 3018 helix: -1.69 (0.16), residues: 985 sheet: -1.50 (0.27), residues: 371 loop : -2.54 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 55 TYR 0.020 0.002 TYR A 168 PHE 0.019 0.002 PHE C 431 TRP 0.013 0.002 TRP C 944 HIS 0.014 0.002 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.29 (26262) covalent geometry : angle 0.73198 / 0.44 (36026) hydrogen bonds : bond 0.17847 / 12.08 ( 895) hydrogen bonds : angle 6.16548 / 4.13 ( 2404) metal coordination : bond 0.00612 / 0.30 ( 8) metal coordination : angle 2.89834 / 1.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 444 poor density : 154 time to evaluate : 0.927 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: A 125 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 71 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: C 221 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6911 (p) REVERT: C 275 LEU cc_start: 0.8416 (mt) cc_final: 0.7999 (mp) REVERT: D 663 MET cc_start: 0.8145 (mmt) cc_final: 0.7862 (mmt) REVERT: D 1081 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8070 (t) REVERT: D 1084 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7195 (pm20) outliers start: 444 outliers final: 104 residues processed: 559 average time/residue: 0.1890 time to fit residues: 159.6716 Evaluate side-chains 214 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 105 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 203 SER 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 201 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 696 VAL 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 D residue 60 CYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1011 THR 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 1081 SER Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 98 PRO Chi-restraints excluded: chain G residue 101 LEU 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: 0.4980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 79 ASN A 152 ASN B 119 HIS C 323 HIS C 415 GLN C 435 GLN C 543 GLN C 585 GLN C 610 ASN C 612 GLN C 662 HIS C 685 ASN C 751 HIS C 841 HIS C 935 HIS C1066 GLN C1077 GLN C1111 ASN C1129 GLN D 5 ASN D 22 GLN D 145 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 352 ASN D 368 ASN D 396 ASN D 410 GLN D 525 HIS D 564 ASN D 606 HIS D 759 GLN D 852 ASN D 882 GLN D1032 GLN D1084 GLN D1110 GLN D1125 GLN 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.068983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043442 restraints weight = 90975.766| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.59 r_work: 0.2655 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26270 Z= 0.155 Angle : 0.719 17.404 36038 Z= 0.365 Chirality : 0.057 1.129 4122 Planarity : 0.006 0.077 4374 Dihedral : 17.083 162.722 4611 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 6.15 % Allowed : 27.07 % Favored : 66.78 % 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: -2.23 (0.14), residues: 3018 helix: -0.58 (0.16), residues: 1005 sheet: -1.09 (0.27), residues: 391 loop : -2.23 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 69 TYR 0.022 0.001 TYR D1062 PHE 0.021 0.001 PHE D 70 TRP 0.010 0.001 TRP D 23 HIS 0.005 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (26262) covalent geometry : angle 0.71598 / 0.36 (36026) hydrogen bonds : bond 0.04823 / 3.22 ( 895) hydrogen bonds : angle 4.60753 / 3.11 ( 2404) metal coordination : bond 0.00478 / 0.22 ( 8) metal coordination : angle 3.61677 / 2.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 108 time to evaluate : 0.975 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 221 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8273 (pp) REVERT: C 373 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8325 (t80) REVERT: C 454 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7145 (mpt90) REVERT: C 926 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8131 (mpp) REVERT: C 1051 MET cc_start: 0.8990 (mmm) cc_final: 0.8429 (mtm) REVERT: D 92 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8591 (mtm) REVERT: D 375 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8241 (tp40) REVERT: D 443 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8913 (mp) REVERT: D 1081 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7741 (t) REVERT: D 1084 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: D 1093 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8282 (p0) REVERT: D 1112 MET cc_start: 0.7846 (mmm) cc_final: 0.7123 (mmt) REVERT: E 41 ASP cc_start: 0.8594 (p0) cc_final: 0.8361 (p0) REVERT: E 42 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8184 (mp0) REVERT: E 70 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7322 (pt0) REVERT: G 71 MET cc_start: 0.8204 (tpt) cc_final: 0.7851 (mmm) REVERT: G 73 ASP cc_start: 0.8516 (m-30) cc_final: 0.7999 (t0) outliers start: 156 outliers final: 83 residues processed: 254 average time/residue: 0.1597 time to fit residues: 66.4914 Evaluate side-chains 192 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 99 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER 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 94 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 867 GLU 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 974 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 606 HIS Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1081 SER Chi-restraints excluded: chain D residue 1084 GLN Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 110 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 173 optimal weight: 50.0000 chunk 63 optimal weight: 7.9990 chunk 157 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 ASN C 372 HIS C 585 GLN D 145 HIS D 533 ASN D 606 HIS D 657 GLN D 693 GLN D1032 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.067305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.041765 restraints weight = 91371.514| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.59 r_work: 0.2601 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 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 = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26270 Z= 0.213 Angle : 0.659 15.696 36038 Z= 0.336 Chirality : 0.051 0.807 4122 Planarity : 0.005 0.055 4374 Dihedral : 16.570 154.956 4538 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 5.48 % Allowed : 25.61 % Favored : 68.91 % 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: -1.86 (0.15), residues: 3018 helix: -0.07 (0.17), residues: 1010 sheet: -1.00 (0.26), residues: 402 loop : -2.13 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 478 TYR 0.029 0.001 TYR D 251 PHE 0.011 0.001 PHE C 906 TRP 0.011 0.001 TRP D 23 HIS 0.017 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (26262) covalent geometry : angle 0.65677 / 0.34 (36026) hydrogen bonds : bond 0.05054 / 3.37 ( 895) hydrogen bonds : angle 4.26650 / 2.90 ( 2404) metal coordination : bond 0.00802 / 0.38 ( 8) metal coordination : angle 3.11588 / 1.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 103 time to evaluate : 0.901 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: B 133 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8550 (mptt) REVERT: B 152 ASN cc_start: 0.8212 (t0) cc_final: 0.7965 (t0) REVERT: C 275 LEU cc_start: 0.9558 (mt) cc_final: 0.9216 (mt) REVERT: C 454 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7230 (mpt90) REVERT: C 661 MET cc_start: 0.8737 (tpp) cc_final: 0.8435 (tmm) REVERT: C 926 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8197 (mpp) REVERT: C 1051 MET cc_start: 0.8928 (mmm) cc_final: 0.8463 (mtm) REVERT: D 56 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8195 (ttm-80) REVERT: D 92 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8818 (mtm) REVERT: D 375 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: D 443 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8946 (mp) REVERT: D 663 MET cc_start: 0.8862 (mmt) cc_final: 0.8644 (mmt) REVERT: D 865 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D 1093 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.7906 (p0) REVERT: D 1266 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7753 (mtp85) outliers start: 139 outliers final: 82 residues processed: 227 average time/residue: 0.1638 time to fit residues: 60.5382 Evaluate side-chains 191 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 99 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 109 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 687 CYS 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 973 SER Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 120 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS C 266 ASN D 145 HIS D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.067025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041549 restraints weight = 91293.128| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.58 r_work: 0.2605 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 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 = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26270 Z= 0.181 Angle : 0.611 11.783 36038 Z= 0.313 Chirality : 0.049 0.514 4122 Planarity : 0.005 0.056 4374 Dihedral : 16.294 154.294 4507 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 4.89 % Allowed : 25.81 % Favored : 69.31 % 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: -1.61 (0.15), residues: 3018 helix: 0.22 (0.17), residues: 1010 sheet: -0.90 (0.26), residues: 409 loop : -2.03 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 37 TYR 0.016 0.001 TYR D 251 PHE 0.011 0.001 PHE D 107 TRP 0.008 0.001 TRP D 23 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (26262) covalent geometry : angle 0.60848 / 0.31 (36026) hydrogen bonds : bond 0.04567 / 3.04 ( 895) hydrogen bonds : angle 4.10769 / 2.79 ( 2404) metal coordination : bond 0.00678 / 0.32 ( 8) metal coordination : angle 2.86932 / 1.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 99 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 152 ASN cc_start: 0.8172 (t0) cc_final: 0.7824 (t0) REVERT: C 275 LEU cc_start: 0.9561 (mt) cc_final: 0.9230 (mt) REVERT: C 373 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.8144 (t80) REVERT: C 379 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7803 (mtp180) REVERT: C 454 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7125 (mpt90) REVERT: C 661 MET cc_start: 0.8637 (tpp) cc_final: 0.8291 (tmm) REVERT: C 767 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: C 926 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8228 (mpp) REVERT: C 1051 MET cc_start: 0.8917 (mmm) cc_final: 0.8404 (mtm) REVERT: D 56 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8182 (ttm-80) REVERT: D 92 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8721 (mtm) REVERT: D 310 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9122 (tpp) REVERT: D 375 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: D 443 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8904 (mp) REVERT: D 460 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8505 (mp) REVERT: D 865 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8963 (mm) REVERT: D 1055 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8388 (mp) REVERT: D 1077 TYR cc_start: 0.7776 (m-80) cc_final: 0.7551 (m-80) REVERT: D 1093 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 1112 MET cc_start: 0.7964 (mmm) cc_final: 0.7508 (mmm) outliers start: 124 outliers final: 77 residues processed: 212 average time/residue: 0.1563 time to fit residues: 54.1601 Evaluate side-chains 191 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 99 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 202 ILE 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 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 767 GLU 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 973 SER Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 211 optimal weight: 0.4980 chunk 238 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 chunk 300 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 145 HIS D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.042050 restraints weight = 92780.921| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.60 r_work: 0.2650 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 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 = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26270 Z= 0.117 Angle : 0.560 9.417 36038 Z= 0.288 Chirality : 0.046 0.434 4122 Planarity : 0.004 0.058 4374 Dihedral : 16.101 153.088 4496 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 4.18 % Allowed : 26.00 % Favored : 69.82 % 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: -1.35 (0.15), residues: 3018 helix: 0.47 (0.17), residues: 1010 sheet: -0.73 (0.26), residues: 408 loop : -1.90 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 401 TYR 0.014 0.001 TYR D1062 PHE 0.010 0.001 PHE C 153 TRP 0.007 0.001 TRP D 23 HIS 0.004 0.001 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (26262) covalent geometry : angle 0.55854 / 0.29 (36026) hydrogen bonds : bond 0.03965 / 2.65 ( 895) hydrogen bonds : angle 3.90734 / 2.65 ( 2404) metal coordination : bond 0.00398 / 0.18 ( 8) metal coordination : angle 2.52064 / 1.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 99 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 152 ASN cc_start: 0.8169 (t0) cc_final: 0.7790 (t0) REVERT: C 373 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8205 (t80) REVERT: C 379 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7786 (mtp180) REVERT: C 454 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7095 (mpt90) REVERT: C 661 MET cc_start: 0.8619 (tpp) cc_final: 0.8327 (tmm) REVERT: C 767 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: C 807 THR cc_start: 0.4107 (OUTLIER) cc_final: 0.3638 (m) REVERT: C 926 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8078 (mpp) REVERT: C 1051 MET cc_start: 0.8932 (mmm) cc_final: 0.8418 (mtm) REVERT: D 56 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8259 (ttp-110) REVERT: D 92 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8670 (mtm) REVERT: D 375 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8301 (tp40) REVERT: D 443 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8929 (mp) REVERT: D 460 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 865 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9005 (mm) REVERT: D 1093 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7539 (p0) REVERT: D 1112 MET cc_start: 0.8090 (mmm) cc_final: 0.7588 (mmm) REVERT: D 1266 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7799 (mtp85) REVERT: G 29 MET cc_start: 0.8616 (mtt) cc_final: 0.8161 (mtm) REVERT: G 73 ASP cc_start: 0.8536 (m-30) cc_final: 0.7963 (t0) outliers start: 106 outliers final: 68 residues processed: 193 average time/residue: 0.1614 time to fit residues: 51.1907 Evaluate side-chains 179 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 96 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR 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 150 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 767 GLU 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 973 SER Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 1083 ARG Chi-restraints excluded: chain D residue 1092 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 210 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 301 optimal weight: 40.0000 chunk 208 optimal weight: 6.9990 chunk 307 optimal weight: 50.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** 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 = 0.3474 r_free = 0.3474 target = 0.065877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.039986 restraints weight = 93701.467| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.62 r_work: 0.2558 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 26270 Z= 0.253 Angle : 0.639 10.995 36038 Z= 0.327 Chirality : 0.048 0.393 4122 Planarity : 0.005 0.051 4374 Dihedral : 16.101 152.474 4491 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 4.73 % Allowed : 25.69 % Favored : 69.58 % 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: -1.41 (0.15), residues: 3018 helix: 0.42 (0.17), residues: 1020 sheet: -0.83 (0.26), residues: 418 loop : -1.95 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 866 TYR 0.013 0.001 TYR G 11 PHE 0.012 0.002 PHE D 382 TRP 0.009 0.001 TRP G 76 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (26262) covalent geometry : angle 0.63737 / 0.33 (36026) hydrogen bonds : bond 0.05107 / 3.38 ( 895) hydrogen bonds : angle 4.09485 / 2.76 ( 2404) metal coordination : bond 0.00965 / 0.47 ( 8) metal coordination : angle 2.87008 / 1.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 99 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8843 (pp) REVERT: C 62 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 373 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8133 (t80) REVERT: C 379 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: C 454 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7166 (mpt90) REVERT: C 556 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: C 661 MET cc_start: 0.8674 (tpp) cc_final: 0.8290 (tmm) REVERT: C 767 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: C 807 THR cc_start: 0.4505 (OUTLIER) cc_final: 0.3990 (m) REVERT: C 926 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: D 92 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8865 (mtm) REVERT: D 256 MET cc_start: 0.8788 (ptp) cc_final: 0.8364 (ptm) REVERT: D 375 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: D 460 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 865 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 1055 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8363 (mt) REVERT: D 1093 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7783 (p0) REVERT: D 1112 MET cc_start: 0.8168 (mmm) cc_final: 0.7637 (mmm) REVERT: D 1266 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7867 (mtp85) REVERT: E 42 GLU cc_start: 0.8628 (tp30) cc_final: 0.8357 (tp30) REVERT: G 29 MET cc_start: 0.8534 (mtt) cc_final: 0.8025 (mtm) REVERT: G 73 ASP cc_start: 0.8634 (m-30) cc_final: 0.8068 (t0) outliers start: 120 outliers final: 79 residues processed: 210 average time/residue: 0.1594 time to fit residues: 55.4961 Evaluate side-chains 192 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 97 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 216 VAL 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 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 136 VAL 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 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 767 GLU 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 973 SER Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1049 VAL Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1221 LEU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 252 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 194 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 545 ASN D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.067468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.041847 restraints weight = 92931.841| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.61 r_work: 0.2644 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 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 = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26270 Z= 0.106 Angle : 0.556 8.948 36038 Z= 0.286 Chirality : 0.045 0.368 4122 Planarity : 0.004 0.059 4374 Dihedral : 15.894 151.978 4477 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 3.23 % Allowed : 27.15 % Favored : 69.62 % 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: -1.12 (0.15), residues: 3018 helix: 0.66 (0.17), residues: 1018 sheet: -0.67 (0.26), residues: 421 loop : -1.76 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1083 TYR 0.016 0.001 TYR D1062 PHE 0.010 0.001 PHE C 153 TRP 0.009 0.001 TRP D 23 HIS 0.003 0.001 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26262) covalent geometry : angle 0.55426 / 0.29 (36026) hydrogen bonds : bond 0.03799 / 2.55 ( 895) hydrogen bonds : angle 3.80120 / 2.57 ( 2404) metal coordination : bond 0.00302 / 0.13 ( 8) metal coordination : angle 2.31463 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 100 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8880 (pp) REVERT: C 373 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8146 (t80) REVERT: C 379 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7812 (mtp180) REVERT: C 454 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7178 (mpt90) REVERT: C 556 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: C 843 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: C 926 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8146 (mpp) REVERT: C 1051 MET cc_start: 0.8963 (mmm) cc_final: 0.8538 (mtm) REVERT: D 56 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8256 (ttp-110) REVERT: D 375 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (tp40) REVERT: D 443 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 460 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8625 (mp) REVERT: D 865 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9026 (mm) REVERT: D 1093 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7630 (p0) REVERT: D 1112 MET cc_start: 0.8132 (mmm) cc_final: 0.7501 (mmm) REVERT: D 1266 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: E 42 GLU cc_start: 0.8526 (tp30) cc_final: 0.8239 (tp30) REVERT: G 29 MET cc_start: 0.8571 (mtt) cc_final: 0.8285 (mtt) REVERT: G 73 ASP cc_start: 0.8457 (m-30) cc_final: 0.7930 (t0) outliers start: 82 outliers final: 55 residues processed: 173 average time/residue: 0.1642 time to fit residues: 47.1160 Evaluate side-chains 166 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 97 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL 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 196 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 843 GLU 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 973 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.066803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.041329 restraints weight = 93523.853| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.57 r_work: 0.2631 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 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 = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26270 Z= 0.171 Angle : 0.574 9.458 36038 Z= 0.294 Chirality : 0.046 0.355 4122 Planarity : 0.004 0.054 4374 Dihedral : 15.885 151.615 4474 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 3.35 % Allowed : 27.23 % Favored : 69.42 % 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: -1.06 (0.15), residues: 3018 helix: 0.73 (0.17), residues: 1019 sheet: -0.66 (0.26), residues: 420 loop : -1.74 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1083 TYR 0.010 0.001 TYR C 731 PHE 0.011 0.001 PHE C 153 TRP 0.005 0.001 TRP D1220 HIS 0.003 0.001 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (26262) covalent geometry : angle 0.57272 / 0.29 (36026) hydrogen bonds : bond 0.04259 / 2.84 ( 895) hydrogen bonds : angle 3.86364 / 2.61 ( 2404) metal coordination : bond 0.00636 / 0.30 ( 8) metal coordination : angle 2.42443 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 97 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7721 (tpp) cc_final: 0.7367 (tmm) REVERT: A 221 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8924 (pp) REVERT: C 275 LEU cc_start: 0.9454 (mm) cc_final: 0.9135 (mm) REVERT: C 373 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8144 (t80) REVERT: C 379 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7925 (mtp180) REVERT: C 454 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7171 (mpt90) REVERT: C 556 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: C 843 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: C 926 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8215 (mpp) REVERT: C 1051 MET cc_start: 0.8926 (mmm) cc_final: 0.8466 (mtm) REVERT: D 256 MET cc_start: 0.8670 (ptp) cc_final: 0.8275 (ptm) REVERT: D 375 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: D 460 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8656 (mp) REVERT: D 865 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9013 (mm) REVERT: D 1112 MET cc_start: 0.8172 (mmm) cc_final: 0.7570 (mmm) REVERT: D 1266 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7902 (mtp85) REVERT: E 42 GLU cc_start: 0.8577 (tp30) cc_final: 0.8349 (tp30) REVERT: G 29 MET cc_start: 0.8586 (mtt) cc_final: 0.8323 (mtt) REVERT: G 73 ASP cc_start: 0.8465 (m-30) cc_final: 0.7949 (t0) outliers start: 85 outliers final: 65 residues processed: 173 average time/residue: 0.1559 time to fit residues: 45.0192 Evaluate side-chains 172 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 96 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 136 VAL 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 196 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 843 GLU 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 973 SER Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.066906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.041319 restraints weight = 94357.959| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.58 r_work: 0.2628 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 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 = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26270 Z= 0.138 Angle : 0.554 8.434 36038 Z= 0.284 Chirality : 0.045 0.339 4122 Planarity : 0.004 0.056 4374 Dihedral : 15.838 151.234 4471 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 3.11 % Allowed : 27.62 % Favored : 69.27 % 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: -0.92 (0.15), residues: 3018 helix: 0.81 (0.17), residues: 1013 sheet: -0.50 (0.26), residues: 415 loop : -1.64 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1083 TYR 0.016 0.001 TYR D 251 PHE 0.010 0.001 PHE C 153 TRP 0.006 0.001 TRP D 723 HIS 0.003 0.001 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (26262) covalent geometry : angle 0.55210 / 0.28 (36026) hydrogen bonds : bond 0.03963 / 2.64 ( 895) hydrogen bonds : angle 3.77123 / 2.55 ( 2404) metal coordination : bond 0.00463 / 0.22 ( 8) metal coordination : angle 2.25490 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 97 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 275 LEU cc_start: 0.9374 (mm) cc_final: 0.9029 (mm) REVERT: C 373 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8115 (t80) REVERT: C 379 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.7905 (mtp180) REVERT: C 454 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7194 (mpt90) REVERT: C 556 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: C 661 MET cc_start: 0.8592 (tpp) cc_final: 0.8305 (tpp) REVERT: C 843 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: C 926 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8194 (mpp) REVERT: C 1051 MET cc_start: 0.8937 (mmm) cc_final: 0.8468 (mtm) REVERT: D 256 MET cc_start: 0.8626 (ptp) cc_final: 0.8264 (ptm) REVERT: D 375 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: D 443 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8897 (mp) REVERT: D 460 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8652 (mp) REVERT: D 865 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9017 (mm) REVERT: D 1112 MET cc_start: 0.8145 (mmm) cc_final: 0.7514 (mmm) REVERT: D 1266 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7858 (mtp85) REVERT: E 42 GLU cc_start: 0.8559 (tp30) cc_final: 0.8326 (tp30) REVERT: G 29 MET cc_start: 0.8533 (mtt) cc_final: 0.8266 (mtt) REVERT: G 73 ASP cc_start: 0.8528 (m-30) cc_final: 0.8007 (t0) outliers start: 79 outliers final: 63 residues processed: 169 average time/residue: 0.1593 time to fit residues: 45.2071 Evaluate side-chains 170 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 95 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 136 VAL 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 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 843 GLU 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 973 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 179 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 196 optimal weight: 6.9990 chunk 240 optimal weight: 0.1980 chunk 33 optimal weight: 20.0000 chunk 222 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 16 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.067873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042380 restraints weight = 93785.817| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.59 r_work: 0.2664 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 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 = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26270 Z= 0.098 Angle : 0.534 9.459 36038 Z= 0.273 Chirality : 0.044 0.324 4122 Planarity : 0.004 0.064 4374 Dihedral : 15.747 150.362 4467 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.60 % Allowed : 28.05 % Favored : 69.35 % 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: -0.73 (0.15), residues: 3018 helix: 0.96 (0.17), residues: 1008 sheet: -0.30 (0.27), residues: 401 loop : -1.52 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1083 TYR 0.013 0.001 TYR D 251 PHE 0.011 0.001 PHE D 252 TRP 0.008 0.001 TRP D 23 HIS 0.003 0.000 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (26262) covalent geometry : angle 0.53344 / 0.27 (36026) hydrogen bonds : bond 0.03366 / 2.26 ( 895) hydrogen bonds : angle 3.62716 / 2.46 ( 2404) metal coordination : bond 0.00215 / 0.09 ( 8) metal coordination : angle 1.90636 / 1.07 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 96 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: C 275 LEU cc_start: 0.9339 (mm) cc_final: 0.8994 (mm) REVERT: C 373 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.7990 (t80) REVERT: C 379 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8865 (mtm180) REVERT: C 454 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7134 (mpt90) REVERT: C 661 MET cc_start: 0.8613 (tpp) cc_final: 0.8374 (tpp) REVERT: C 713 MET cc_start: 0.9197 (ttm) cc_final: 0.8968 (tpp) REVERT: C 843 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 1051 MET cc_start: 0.8943 (mmm) cc_final: 0.8468 (mtm) REVERT: D 256 MET cc_start: 0.8430 (ptp) cc_final: 0.8111 (ptm) REVERT: D 460 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8676 (mp) REVERT: D 865 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8952 (mm) REVERT: D 1112 MET cc_start: 0.8133 (mmm) cc_final: 0.7531 (mmm) REVERT: E 42 GLU cc_start: 0.8612 (tp30) cc_final: 0.8335 (tp30) REVERT: G 29 MET cc_start: 0.8620 (mtt) cc_final: 0.8348 (mtt) REVERT: G 73 ASP cc_start: 0.8479 (m-30) cc_final: 0.8016 (t0) outliers start: 66 outliers final: 51 residues processed: 157 average time/residue: 0.1645 time to fit residues: 43.4893 Evaluate side-chains 151 residues out of total 2559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 136 VAL 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 196 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 747 ASP Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 1073 GLU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 178 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 277 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 256 optimal weight: 0.5980 chunk 300 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 693 GLN ** D1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** 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 = 0.3541 r_free = 0.3541 target = 0.067912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042537 restraints weight = 93590.151| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.59 r_work: 0.2663 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26270 Z= 0.100 Angle : 0.522 8.819 36038 Z= 0.267 Chirality : 0.044 0.316 4122 Planarity : 0.004 0.062 4374 Dihedral : 15.701 149.607 4465 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 2.32 % Allowed : 28.29 % Favored : 69.39 % 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: -0.60 (0.15), residues: 3018 helix: 1.07 (0.17), residues: 1004 sheet: -0.23 (0.27), residues: 400 loop : -1.45 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1083 TYR 0.011 0.001 TYR D1062 PHE 0.010 0.001 PHE C 153 TRP 0.006 0.001 TRP C 70 HIS 0.003 0.000 HIS D 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (26262) covalent geometry : angle 0.52133 / 0.27 (36026) hydrogen bonds : bond 0.03372 / 2.26 ( 895) hydrogen bonds : angle 3.57988 / 2.42 ( 2404) metal coordination : bond 0.00243 / 0.11 ( 8) metal coordination : angle 1.83115 / 1.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.38 seconds wall clock time: 117 minutes 19.42 seconds (7039.42 seconds total)