Starting phenix.real_space_refine on Mon Aug 25 07:07:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehq_28149/08_2025/8ehq_28149.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.065 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 105 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 15855 2.51 5 N 4580 2.21 5 O 5196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25828 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: 8689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8689 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1059} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 9953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 9953 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1212} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 110, 869 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} bond proxies already assigned to first conformer: 877 Chain: "T" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 772 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "N" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 770 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "R" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 625 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 24} Chain: "D" Number of atoms: 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 19229 SG CYS D 891 76.624 25.051 88.601 1.00 53.75 S ATOM 19796 SG CYS D 968 75.437 28.412 90.021 1.00 28.25 S ATOM 19838 SG CYS D 975 76.906 28.116 86.457 1.00 45.52 S ATOM 19856 SG CYS D 978 73.470 26.852 87.264 1.00 38.30 S ATOM 12667 SG CYS D 60 109.506 80.880 114.793 1.00 81.63 S ATOM 12685 SG CYS D 62 111.746 83.357 116.339 1.00 92.60 S ATOM 12794 SG CYS D 75 112.160 79.504 117.050 1.00 96.18 S ATOM 12820 SG CYS D 78 109.368 81.713 118.578 1.00 88.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU G 15 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU G 15 " occ=0.50 Time building chain proxies: 6.04, per 1000 atoms: 0.23 Number of scatterers: 25828 At special positions: 0 Unit cell: (133.11, 133.11, 201.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 105 15.00 Mg 1 11.99 O 5196 8.00 N 4580 7.00 C 15855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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 891 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 968 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 75 " Number of angles added : 12 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 46 sheets defined 37.0% alpha, 16.0% beta 38 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.521A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.896A pdb=" N ARG A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.736A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.631A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.559A pdb=" N VAL B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 217' Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.572A pdb=" N LEU B 225 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.564A pdb=" N THR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.826A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 removed outlier: 3.790A pdb=" N GLU C 88 " --> pdb=" O GLY C 84 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.506A 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 234 through 241 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.562A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.774A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 removed outlier: 3.593A pdb=" N LEU C 417 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.638A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 4.002A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 removed outlier: 3.909A pdb=" N ARG C 538 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.751A 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: 4.584A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.542A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.537A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.510A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.524A pdb=" N ILE C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.578A 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 815 through 825 removed outlier: 3.805A pdb=" N LEU C 820 " --> pdb=" O PRO C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.612A 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 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.817A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.790A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C1086 " --> pdb=" O ALA C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.135A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 4.189A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C1130 " --> pdb=" O LYS C1126 " (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: 3.610A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.551A 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 141 through 185 removed outlier: 5.780A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.540A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.791A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.607A pdb=" N LYS D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.683A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 305 removed outlier: 3.822A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.855A 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 removed outlier: 3.534A pdb=" N VAL D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.773A pdb=" N LEU D 405 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.639A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.907A 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: 3.541A pdb=" N LEU D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.599A 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: 3.867A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 718 " --> pdb=" O ASP D 714 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 719 " --> pdb=" O LYS D 715 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.517A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 753 " --> pdb=" O TYR D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 791 removed outlier: 3.958A pdb=" N GLU D 780 " --> pdb=" O GLU D 776 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA D 781 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 782 " --> pdb=" O TRP D 778 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 804 removed outlier: 4.138A 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 881 removed outlier: 3.622A pdb=" N THR D 853 " --> pdb=" O TYR D 849 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D 856 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP D 879 " --> pdb=" O ARG D 875 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 880 " --> pdb=" O ARG D 876 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 954 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.576A 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 1005 removed outlier: 3.922A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D1000 " --> pdb=" O GLY D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.902A pdb=" N ARG D1123 " --> pdb=" O HIS D1119 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 4.194A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.196A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D1156 " --> pdb=" O LYS D1152 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D1161 " --> pdb=" O ILE D1157 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D1162 " --> pdb=" O VAL D1158 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 removed outlier: 3.534A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.600A 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: 3.554A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.799A 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: 3.833A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 63 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'G' and resid 14 through 30 removed outlier: 3.927A pdb=" N GLY G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 102 through 112 removed outlier: 3.769A pdb=" N ARG G 112 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.606A pdb=" N GLU A 24 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N PHE A 189 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA A 180 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.819A 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 100 removed outlier: 3.612A pdb=" N LEU A 138 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 7.120A pdb=" N GLY A 103 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR A 127 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.917A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 3.714A pdb=" N LEU B 14 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 196 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.810A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.904A 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 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.588A 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: 5.699A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (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: 6.430A 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 191 Processing sheet with id=AB7, first strand: chain 'C' and resid 214 through 216 Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.251A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.330A 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: 3.617A 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: 6.601A 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: 6.974A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.785A 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 removed outlier: 3.501A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.507A pdb=" N GLY C 893 " --> pdb=" O LEU C 885 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.704A 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: 3.579A pdb=" N GLY C1026 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 4.679A 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: 6.615A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.500A 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 801 through 803 removed outlier: 6.825A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) 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 1042 through 1044 Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.853A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.808A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.625A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.614A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 443 through 444 removed outlier: 6.222A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.612A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 903 through 904 Processing sheet with id=AE4, first strand: chain 'D' and resid 1067 through 1068 removed outlier: 3.567A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1055 through 1056 removed outlier: 4.129A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE8, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE9, first strand: chain 'G' and resid 35 through 39 removed outlier: 3.833A pdb=" N ARG G 37 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE G 69 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN G 4 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 48 through 49 847 hydrogen bonds defined for protein. 2349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 2.98 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: 7411 1.33 - 1.45: 4210 1.45 - 1.57: 14502 1.57 - 1.69: 210 1.69 - 1.81: 157 Bond restraints: 26490 Sorted by residual: bond pdb=" CB PRO C 572 " pdb=" CG PRO C 572 " ideal model delta sigma weight residual 1.492 1.673 -0.181 5.00e-02 4.00e+02 1.32e+01 bond pdb=" CB PRO D 601 " pdb=" CG PRO D 601 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.66e+00 bond pdb=" CG PRO C 572 " pdb=" CD PRO C 572 " ideal model delta sigma weight residual 1.503 1.435 0.068 3.40e-02 8.65e+02 4.02e+00 bond pdb=" N PRO C 572 " pdb=" CD PRO C 572 " ideal model delta sigma weight residual 1.473 1.499 -0.026 1.40e-02 5.10e+03 3.51e+00 bond pdb=" N PRO D 601 " pdb=" CA PRO D 601 " ideal model delta sigma weight residual 1.474 1.455 0.019 1.33e-02 5.65e+03 2.03e+00 ... (remaining 26485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 36169 2.85 - 5.70: 163 5.70 - 8.55: 14 8.55 - 11.40: 2 11.40 - 14.25: 2 Bond angle restraints: 36350 Sorted by residual: angle pdb=" CA PRO C 572 " pdb=" N PRO C 572 " pdb=" CD PRO C 572 " ideal model delta sigma weight residual 112.00 97.75 14.25 1.40e+00 5.10e-01 1.04e+02 angle pdb=" CA PRO D 601 " pdb=" N PRO D 601 " pdb=" CD PRO D 601 " ideal model delta sigma weight residual 112.00 103.02 8.98 1.40e+00 5.10e-01 4.11e+01 angle pdb=" N PRO C 572 " pdb=" CD PRO C 572 " pdb=" CG PRO C 572 " ideal model delta sigma weight residual 103.20 95.73 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" CB MET D 205 " pdb=" CG MET D 205 " pdb=" SD MET D 205 " ideal model delta sigma weight residual 112.70 124.47 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA MET D 205 " pdb=" CB MET D 205 " pdb=" CG MET D 205 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 ... (remaining 36345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.61: 14032 26.61 - 53.22: 1683 53.22 - 79.83: 272 79.83 - 106.45: 22 106.45 - 133.06: 1 Dihedral angle restraints: 16010 sinusoidal: 7284 harmonic: 8726 Sorted by residual: dihedral pdb=" CA ARG C 822 " pdb=" C ARG C 822 " pdb=" N ALA C 823 " pdb=" CA ALA C 823 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" O4' A R 21 " pdb=" C1' A R 21 " pdb=" N9 A R 21 " pdb=" C4 A R 21 " ideal model delta sinusoidal sigma weight residual -106.00 -175.98 69.98 1 1.70e+01 3.46e-03 2.18e+01 dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual 180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 16007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3099 0.045 - 0.090: 793 0.090 - 0.135: 254 0.135 - 0.180: 12 0.180 - 0.225: 3 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CA PRO C 572 " pdb=" N PRO C 572 " pdb=" C PRO C 572 " pdb=" CB PRO C 572 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR A 187 " pdb=" CA THR A 187 " pdb=" OG1 THR A 187 " pdb=" CG2 THR A 187 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CB ILE D 235 " pdb=" CA ILE D 235 " pdb=" CG1 ILE D 235 " pdb=" CG2 ILE D 235 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 4158 not shown) Planarity restraints: 4407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 82 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 571 " 0.078 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO C 572 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 572 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 572 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 600 " -0.068 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO D 601 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO D 601 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 601 " -0.052 5.00e-02 4.00e+02 ... (remaining 4404 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 121 2.57 - 3.15: 18634 3.15 - 3.74: 37703 3.74 - 4.32: 51602 4.32 - 4.90: 88986 Nonbonded interactions: 197046 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2001 " model vdw 1.990 2.170 nonbonded pdb=" O3' A R 30 " pdb="MG MG D2001 " model vdw 2.183 2.170 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D2001 " model vdw 2.185 2.170 nonbonded pdb=" O THR C 433 " pdb=" OG1 THR C 433 " model vdw 2.228 3.040 nonbonded pdb=" O2 C R 20 " pdb=" N6 A R 21 " model vdw 2.247 3.120 ... (remaining 197041 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 31.180 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 26498 Z= 0.166 Angle : 0.585 14.249 36362 Z= 0.318 Chirality : 0.044 0.225 4161 Planarity : 0.006 0.122 4407 Dihedral : 21.014 133.057 10406 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 6.46 % Allowed : 33.53 % Favored : 60.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.14), residues: 3040 helix: -0.13 (0.17), residues: 993 sheet: 0.03 (0.27), residues: 383 loop : -1.76 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 77 TYR 0.012 0.001 TYR D 586 PHE 0.016 0.001 PHE C 906 TRP 0.009 0.001 TRP D 223 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00414 (26490) covalent geometry : angle 0.58137 (36350) hydrogen bonds : bond 0.18054 ( 945) hydrogen bonds : angle 6.22094 ( 2557) metal coordination : bond 0.00419 ( 8) metal coordination : angle 3.63185 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 125 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1093 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6657 (p0) outliers start: 165 outliers final: 99 residues processed: 285 average time/residue: 0.5716 time to fit residues: 193.1780 Evaluate side-chains 199 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 99 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 116 LYS 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 236 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1084 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 570 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 803 VAL Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 964 SER Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1033 GLU Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1093 ASP Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1172 SER Chi-restraints excluded: chain D residue 1214 SER Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 102 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 79 ASN A 120 ASN A 124 HIS B 119 HIS C 232 GLN C 323 HIS C 435 GLN C 585 GLN C 610 ASN C 685 ASN C 751 HIS C1066 GLN C1077 GLN C1111 ASN C1129 GLN D 5 ASN D 262 GLN D 352 ASN D 368 ASN D 375 GLN D 396 ASN D 410 GLN D 525 HIS D 533 ASN D 564 ASN D 657 GLN D 852 ASN D 882 GLN D1001 GLN D1133 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1273 GLN E 63 GLN G 21 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.077915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.046436 restraints weight = 72527.286| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.33 r_work: 0.2629 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26498 Z= 0.198 Angle : 0.573 11.014 36362 Z= 0.302 Chirality : 0.044 0.199 4161 Planarity : 0.005 0.085 4407 Dihedral : 16.863 132.499 4749 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 6.92 % Allowed : 30.52 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 3040 helix: 0.20 (0.17), residues: 1025 sheet: 0.07 (0.26), residues: 407 loop : -1.81 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 421 TYR 0.011 0.001 TYR C 314 PHE 0.013 0.001 PHE A 30 TRP 0.009 0.001 TRP D 23 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00478 (26490) covalent geometry : angle 0.56823 (36350) hydrogen bonds : bond 0.05051 ( 945) hydrogen bonds : angle 4.61406 ( 2557) metal coordination : bond 0.00710 ( 8) metal coordination : angle 3.97520 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 109 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: B 70 LYS cc_start: 0.8009 (mppt) cc_final: 0.7512 (mmtt) REVERT: B 185 GLN cc_start: 0.8231 (pm20) cc_final: 0.7964 (tm-30) REVERT: C 109 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8206 (t0) REVERT: C 302 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8134 (ttmm) REVERT: C 661 MET cc_start: 0.8672 (tpp) cc_final: 0.8446 (tpp) REVERT: C 926 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8562 (mpp) REVERT: C 1067 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: D 269 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8184 (p0) REVERT: D 869 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8303 (t0) REVERT: D 1266 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8132 (mtp85) REVERT: G 110 LEU cc_start: 0.9275 (tm) cc_final: 0.9052 (mt) outliers start: 177 outliers final: 69 residues processed: 268 average time/residue: 0.5310 time to fit residues: 167.3005 Evaluate side-chains 179 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 102 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1067 ARG Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 15 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 225 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 476 HIS C 543 GLN C 662 HIS D 22 GLN D 375 GLN D1125 GLN D1133 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.045456 restraints weight = 73271.729| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.31 r_work: 0.2608 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26498 Z= 0.216 Angle : 0.575 10.303 36362 Z= 0.303 Chirality : 0.044 0.223 4161 Planarity : 0.005 0.061 4407 Dihedral : 16.624 131.268 4678 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 5.87 % Allowed : 30.56 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.15), residues: 3040 helix: 0.38 (0.17), residues: 1024 sheet: 0.07 (0.26), residues: 419 loop : -1.77 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.013 0.001 TYR D 586 PHE 0.013 0.001 PHE C 906 TRP 0.009 0.001 TRP D 223 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00521 (26490) covalent geometry : angle 0.57121 (36350) hydrogen bonds : bond 0.04867 ( 945) hydrogen bonds : angle 4.39100 ( 2557) metal coordination : bond 0.00740 ( 8) metal coordination : angle 3.85177 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 107 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 1 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7503 (mpt) REVERT: B 70 LYS cc_start: 0.8139 (mppt) cc_final: 0.7672 (mmtm) REVERT: B 185 GLN cc_start: 0.8302 (pm20) cc_final: 0.8008 (tm-30) REVERT: C 109 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8260 (t0) REVERT: C 201 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7870 (t) REVERT: C 302 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: C 661 MET cc_start: 0.8877 (tpp) cc_final: 0.8531 (tpp) REVERT: C 757 ILE cc_start: 0.9105 (tp) cc_final: 0.8665 (pp) REVERT: C 926 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8593 (mpp) REVERT: C 973 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9169 (p) REVERT: C 1148 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8102 (ppt-90) REVERT: D 205 MET cc_start: 0.7952 (mpm) cc_final: 0.7709 (mmm) REVERT: D 869 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8352 (t0) REVERT: D 1266 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8096 (mtp85) outliers start: 150 outliers final: 69 residues processed: 244 average time/residue: 0.5253 time to fit residues: 152.0571 Evaluate side-chains 180 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 101 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 973 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1148 ARG Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 725 THR 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 846 VAL Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 899 VAL Chi-restraints excluded: chain D residue 985 THR Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 229 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 258 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 407 GLN D 375 GLN D1133 HIS ** 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 = 0.3564 r_free = 0.3564 target = 0.078000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047069 restraints weight = 73161.211| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.25 r_work: 0.2650 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.040 | | 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) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26498 Z= 0.164 Angle : 0.538 11.173 36362 Z= 0.281 Chirality : 0.042 0.219 4161 Planarity : 0.004 0.060 4407 Dihedral : 16.478 131.586 4656 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 4.38 % Allowed : 32.08 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.15), residues: 3040 helix: 0.62 (0.17), residues: 1022 sheet: 0.22 (0.26), residues: 416 loop : -1.69 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 203 TYR 0.009 0.001 TYR C 731 PHE 0.011 0.001 PHE C 906 TRP 0.008 0.001 TRP D 223 HIS 0.004 0.001 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00396 (26490) covalent geometry : angle 0.53431 (36350) hydrogen bonds : bond 0.04228 ( 945) hydrogen bonds : angle 4.16694 ( 2557) metal coordination : bond 0.00544 ( 8) metal coordination : angle 3.35338 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 106 time to evaluate : 1.001 Fit side-chains REVERT: A 30 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: A 131 LYS cc_start: 0.9170 (mtpm) cc_final: 0.8832 (ttmm) REVERT: B 1 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7627 (mpt) REVERT: B 70 LYS cc_start: 0.8281 (mppt) cc_final: 0.7786 (mmtt) REVERT: B 82 SER cc_start: 0.9592 (OUTLIER) cc_final: 0.9237 (p) REVERT: C 201 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8009 (t) REVERT: C 302 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: C 661 MET cc_start: 0.8870 (tpp) cc_final: 0.8598 (tpp) REVERT: C 867 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: C 926 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8596 (mpp) REVERT: D 869 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8386 (t0) REVERT: D 1266 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8114 (mtp85) REVERT: G 107 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8818 (mm-30) outliers start: 112 outliers final: 54 residues processed: 203 average time/residue: 0.5296 time to fit residues: 127.4307 Evaluate side-chains 166 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 102 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 687 CYS 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 D residue 10 LEU Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1208 MET 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 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 265 optimal weight: 0.0030 chunk 143 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN D 505 HIS D1133 HIS ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.045324 restraints weight = 73724.351| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.30 r_work: 0.2605 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26498 Z= 0.260 Angle : 0.597 11.029 36362 Z= 0.313 Chirality : 0.045 0.218 4161 Planarity : 0.005 0.060 4407 Dihedral : 16.557 130.460 4648 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 5.71 % Allowed : 31.14 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.15), residues: 3040 helix: 0.56 (0.17), residues: 1031 sheet: 0.15 (0.26), residues: 415 loop : -1.76 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 56 TYR 0.015 0.001 TYR D 586 PHE 0.015 0.001 PHE C 906 TRP 0.010 0.001 TRP D 656 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00628 (26490) covalent geometry : angle 0.59273 (36350) hydrogen bonds : bond 0.05089 ( 945) hydrogen bonds : angle 4.29258 ( 2557) metal coordination : bond 0.00903 ( 8) metal coordination : angle 3.76364 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 102 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: A 131 LYS cc_start: 0.9260 (mtpm) cc_final: 0.8993 (ttmm) REVERT: B 1 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7634 (mpt) REVERT: B 70 LYS cc_start: 0.8305 (mppt) cc_final: 0.7724 (mmtt) REVERT: B 82 SER cc_start: 0.9582 (OUTLIER) cc_final: 0.9225 (p) REVERT: B 185 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 109 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8337 (t0) REVERT: C 201 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7948 (t) REVERT: C 302 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: C 352 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8456 (mp10) REVERT: C 661 MET cc_start: 0.8869 (tpp) cc_final: 0.8571 (tpp) REVERT: C 666 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8154 (p) REVERT: C 867 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: C 926 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8601 (mpp) REVERT: D 279 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9153 (t70) REVERT: D 506 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8216 (ttp-170) REVERT: D 869 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8363 (t0) REVERT: D 957 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9060 (pp) REVERT: D 1131 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: D 1266 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8140 (mtp85) REVERT: E 87 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9011 (tm) REVERT: G 4 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7410 (p0) REVERT: G 107 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8836 (mm-30) outliers start: 146 outliers final: 72 residues processed: 235 average time/residue: 0.5125 time to fit residues: 143.1938 Evaluate side-chains 190 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 99 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 352 GLN 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 402 GLU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 687 CYS 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 973 SER Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN 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 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 51 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 228 optimal weight: 0.0050 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 134 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 200 HIS C 545 ASN D1133 HIS ** 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 = 0.3591 r_free = 0.3591 target = 0.079039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048201 restraints weight = 73446.442| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.34 r_work: 0.2675 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26498 Z= 0.103 Angle : 0.511 12.923 36362 Z= 0.264 Chirality : 0.041 0.218 4161 Planarity : 0.004 0.061 4407 Dihedral : 16.416 132.410 4647 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 3.17 % Allowed : 33.53 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 3040 helix: 0.82 (0.17), residues: 1025 sheet: 0.45 (0.27), residues: 391 loop : -1.55 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 401 TYR 0.011 0.001 TYR D1062 PHE 0.008 0.001 PHE C 153 TRP 0.010 0.001 TRP D 23 HIS 0.004 0.000 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00233 (26490) covalent geometry : angle 0.50807 (36350) hydrogen bonds : bond 0.03342 ( 945) hydrogen bonds : angle 3.92373 ( 2557) metal coordination : bond 0.00281 ( 8) metal coordination : angle 2.89089 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 103 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: A 131 LYS cc_start: 0.9081 (mtpm) cc_final: 0.8780 (ttmm) REVERT: A 223 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8142 (ptm160) REVERT: B 1 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7675 (mpt) REVERT: B 70 LYS cc_start: 0.8254 (mppt) cc_final: 0.7799 (mptt) REVERT: B 123 MET cc_start: 0.8606 (ttm) cc_final: 0.8398 (ttm) REVERT: B 185 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7910 (tm-30) REVERT: C 109 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8351 (t0) REVERT: C 302 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8382 (ttmm) REVERT: C 661 MET cc_start: 0.8822 (tpp) cc_final: 0.8486 (tpp) REVERT: C 867 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: D 145 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8875 (p-80) REVERT: D 216 LEU cc_start: 0.8859 (mm) cc_final: 0.8469 (pp) REVERT: D 279 ASP cc_start: 0.9342 (OUTLIER) cc_final: 0.9075 (p0) REVERT: D 767 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6594 (t70) REVERT: D 1131 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: D 1266 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8083 (mtp85) REVERT: E 87 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9056 (tm) outliers start: 81 outliers final: 40 residues processed: 176 average time/residue: 0.5784 time to fit residues: 119.7744 Evaluate side-chains 153 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 753 GLU 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 D residue 10 LEU Chi-restraints excluded: chain D residue 29 LYS 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 160 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU 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 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 105 optimal weight: 0.9980 chunk 266 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 270 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1133 HIS ** 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 = 0.3559 r_free = 0.3559 target = 0.077603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.046738 restraints weight = 73800.383| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.25 r_work: 0.2650 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26498 Z= 0.168 Angle : 0.538 15.191 36362 Z= 0.278 Chirality : 0.043 0.347 4161 Planarity : 0.004 0.065 4407 Dihedral : 16.373 130.926 4634 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 3.64 % Allowed : 33.10 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 3040 helix: 0.93 (0.17), residues: 1026 sheet: 0.35 (0.26), residues: 414 loop : -1.52 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.012 0.001 TYR D1062 PHE 0.012 0.001 PHE C 906 TRP 0.010 0.001 TRP D 656 HIS 0.003 0.001 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00403 (26490) covalent geometry : angle 0.53501 (36350) hydrogen bonds : bond 0.04117 ( 945) hydrogen bonds : angle 3.96552 ( 2557) metal coordination : bond 0.00573 ( 8) metal coordination : angle 3.04026 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 102 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: A 131 LYS cc_start: 0.9166 (mtpm) cc_final: 0.8901 (ttmm) REVERT: A 223 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8128 (ptm160) REVERT: B 1 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7682 (mpt) REVERT: B 70 LYS cc_start: 0.8290 (mppt) cc_final: 0.7807 (mmtt) REVERT: B 185 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 62 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: C 109 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8350 (t0) REVERT: C 302 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8421 (ttmm) REVERT: C 661 MET cc_start: 0.8834 (tpp) cc_final: 0.8526 (tpp) REVERT: C 666 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8051 (p) REVERT: C 867 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: D 216 LEU cc_start: 0.8855 (mm) cc_final: 0.8458 (pp) REVERT: D 279 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.9023 (p0) REVERT: D 869 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8364 (t0) REVERT: D 957 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9084 (pp) REVERT: D 1131 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: D 1266 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: E 87 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9057 (tm) REVERT: G 4 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7302 (p0) REVERT: G 107 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8778 (mm-30) REVERT: G 110 LEU cc_start: 0.9291 (tm) cc_final: 0.9078 (mt) outliers start: 93 outliers final: 51 residues processed: 185 average time/residue: 0.5590 time to fit residues: 121.2779 Evaluate side-chains 169 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 102 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 150 VAL 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 109 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 753 GLU 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 D residue 10 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 987 LYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU 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 44 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 107 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.0670 chunk 199 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 227 optimal weight: 0.2980 chunk 224 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1133 HIS ** 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 = 0.3596 r_free = 0.3596 target = 0.079378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.048630 restraints weight = 73585.022| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.30 r_work: 0.2698 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26498 Z= 0.096 Angle : 0.498 15.115 36362 Z= 0.256 Chirality : 0.041 0.322 4161 Planarity : 0.004 0.067 4407 Dihedral : 16.271 131.855 4634 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 2.82 % Allowed : 33.84 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.15), residues: 3040 helix: 1.02 (0.17), residues: 1032 sheet: 0.59 (0.27), residues: 389 loop : -1.42 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 401 TYR 0.014 0.001 TYR D 251 PHE 0.009 0.001 PHE C 153 TRP 0.008 0.001 TRP D 23 HIS 0.004 0.000 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00220 (26490) covalent geometry : angle 0.49630 (36350) hydrogen bonds : bond 0.03091 ( 945) hydrogen bonds : angle 3.74546 ( 2557) metal coordination : bond 0.00204 ( 8) metal coordination : angle 2.43288 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 103 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: A 128 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 131 LYS cc_start: 0.9052 (mtpm) cc_final: 0.8749 (ttmm) REVERT: B 1 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7697 (mpt) REVERT: B 70 LYS cc_start: 0.8359 (mppt) cc_final: 0.7940 (mptt) REVERT: B 123 MET cc_start: 0.8631 (ttm) cc_final: 0.8380 (ttm) REVERT: C 62 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: C 109 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8381 (t0) REVERT: C 302 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8442 (ttmm) REVERT: C 661 MET cc_start: 0.8869 (tpp) cc_final: 0.8587 (tpp) REVERT: C 753 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: D 216 LEU cc_start: 0.8884 (mm) cc_final: 0.8491 (pp) REVERT: D 279 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.9031 (p0) REVERT: D 1131 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: D 1266 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8112 (mtp85) REVERT: E 87 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (tm) REVERT: G 4 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7330 (p0) REVERT: G 31 MET cc_start: 0.8762 (mpm) cc_final: 0.7944 (mtm) REVERT: G 109 ILE cc_start: 0.9032 (tp) cc_final: 0.8795 (tt) REVERT: G 110 LEU cc_start: 0.9274 (tm) cc_final: 0.9070 (mt) outliers start: 72 outliers final: 39 residues processed: 170 average time/residue: 0.7052 time to fit residues: 139.8298 Evaluate side-chains 152 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 150 VAL 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 109 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 753 GLU 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 D residue 10 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 171 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 273 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1133 HIS ** 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 = 0.3568 r_free = 0.3568 target = 0.078018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.047219 restraints weight = 73498.250| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.24 r_work: 0.2664 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26498 Z= 0.150 Angle : 0.527 14.410 36362 Z= 0.272 Chirality : 0.042 0.325 4161 Planarity : 0.004 0.071 4407 Dihedral : 16.280 131.162 4626 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.82 % Allowed : 33.72 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3040 helix: 1.04 (0.17), residues: 1033 sheet: 0.52 (0.26), residues: 412 loop : -1.41 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.012 0.001 TYR D1062 PHE 0.011 0.001 PHE C 906 TRP 0.010 0.001 TRP D 656 HIS 0.003 0.001 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00362 (26490) covalent geometry : angle 0.52482 (36350) hydrogen bonds : bond 0.03873 ( 945) hydrogen bonds : angle 3.82350 ( 2557) metal coordination : bond 0.00483 ( 8) metal coordination : angle 2.74059 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 104 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: A 128 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8673 (pp) REVERT: A 131 LYS cc_start: 0.9146 (mtpm) cc_final: 0.8894 (ttmm) REVERT: B 1 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7682 (mpt) REVERT: B 70 LYS cc_start: 0.8343 (mppt) cc_final: 0.7905 (mptt) REVERT: B 123 MET cc_start: 0.8578 (ttm) cc_final: 0.8354 (ttm) REVERT: C 62 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (mm-30) REVERT: C 109 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8341 (t0) REVERT: C 302 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8566 (ttmm) REVERT: C 661 MET cc_start: 0.8823 (tpp) cc_final: 0.8490 (tpp) REVERT: C 753 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8453 (mt-10) REVERT: C 867 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: D 216 LEU cc_start: 0.8870 (mm) cc_final: 0.8480 (pp) REVERT: D 767 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6695 (t70) REVERT: D 1131 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: D 1266 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8189 (mtp85) REVERT: E 87 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9096 (tm) REVERT: G 4 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7204 (p0) outliers start: 72 outliers final: 47 residues processed: 171 average time/residue: 0.6561 time to fit residues: 132.4193 Evaluate side-chains 161 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 101 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 105 VAL 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 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 753 GLU 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 1009 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 916 ILE Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 3 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1133 HIS ** 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 = 0.3555 r_free = 0.3555 target = 0.077365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.046559 restraints weight = 73373.587| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.23 r_work: 0.2643 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26498 Z= 0.190 Angle : 0.560 14.546 36362 Z= 0.289 Chirality : 0.043 0.344 4161 Planarity : 0.004 0.066 4407 Dihedral : 16.324 130.998 4626 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 2.62 % Allowed : 33.96 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.15), residues: 3040 helix: 0.99 (0.17), residues: 1033 sheet: 0.48 (0.26), residues: 406 loop : -1.44 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 305 TYR 0.012 0.001 TYR D1062 PHE 0.013 0.001 PHE C 906 TRP 0.011 0.001 TRP D 656 HIS 0.003 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00463 (26490) covalent geometry : angle 0.55750 (36350) hydrogen bonds : bond 0.04246 ( 945) hydrogen bonds : angle 3.94389 ( 2557) metal coordination : bond 0.00639 ( 8) metal coordination : angle 3.02651 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 100 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: A 128 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8860 (pp) REVERT: A 131 LYS cc_start: 0.9199 (mtpm) cc_final: 0.8912 (ttmm) REVERT: B 1 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7695 (mpt) REVERT: B 70 LYS cc_start: 0.8382 (mppt) cc_final: 0.7946 (mptt) REVERT: C 62 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8722 (mm-30) REVERT: C 109 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8389 (t0) REVERT: C 352 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8456 (OUTLIER) REVERT: C 666 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8249 (p) REVERT: D 216 LEU cc_start: 0.8867 (mm) cc_final: 0.8465 (pp) REVERT: D 279 ASP cc_start: 0.9342 (OUTLIER) cc_final: 0.9082 (p0) REVERT: D 1131 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: D 1266 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8182 (mtp85) REVERT: E 87 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9092 (tm) REVERT: G 4 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7378 (p0) REVERT: G 31 MET cc_start: 0.8753 (mpp) cc_final: 0.7883 (mtm) outliers start: 67 outliers final: 45 residues processed: 164 average time/residue: 0.6358 time to fit residues: 123.0289 Evaluate side-chains 156 residues out of total 2577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL 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 109 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 352 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 753 GLU Chi-restraints excluded: chain C residue 867 GLU Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 1008 THR Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1131 GLN Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1266 ARG Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain G residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 264 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 219 optimal weight: 0.0060 chunk 245 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1133 HIS ** 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 = 0.3585 r_free = 0.3585 target = 0.078828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048034 restraints weight = 73261.986| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.26 r_work: 0.2673 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26498 Z= 0.102 Angle : 0.519 17.179 36362 Z= 0.265 Chirality : 0.041 0.371 4161 Planarity : 0.004 0.068 4407 Dihedral : 16.239 132.274 4624 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.84 % Allowed : 34.66 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3040 helix: 1.12 (0.17), residues: 1032 sheet: 0.63 (0.27), residues: 392 loop : -1.34 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.012 0.001 TYR D1062 PHE 0.009 0.001 PHE C 153 TRP 0.008 0.001 TRP D 656 HIS 0.004 0.000 HIS D 606 Details of bonding type rmsd covalent geometry : bond 0.00238 (26490) covalent geometry : angle 0.51665 (36350) hydrogen bonds : bond 0.03273 ( 945) hydrogen bonds : angle 3.75766 ( 2557) metal coordination : bond 0.00238 ( 8) metal coordination : angle 2.53425 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9017.30 seconds wall clock time: 154 minutes 5.83 seconds (9245.83 seconds total)