Starting phenix.real_space_refine on Sat Aug 8 00:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.map" model { file = "/net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mj_75287/08_2026/10mj_75287.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 14735 2.51 5 N 4234 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24190 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 14, 'TRANS': 211} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1775 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "Q" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "P" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 586 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8489 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 61, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9923 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 60, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 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} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14400 SG CYS D 60 111.353 78.845 109.566 1.00132.89 S ATOM 14418 SG CYS D 62 111.893 80.051 112.792 1.00138.88 S ATOM 14527 SG CYS D 75 113.145 77.498 113.381 1.00135.60 S ATOM 14553 SG CYS D 78 109.906 77.586 113.323 1.00127.83 S ATOM 20968 SG CYS D 891 73.422 24.136 87.914 1.00 38.73 S ATOM 21535 SG CYS D 968 72.490 28.023 89.803 1.00 27.49 S ATOM 21577 SG CYS D 975 73.288 26.992 86.291 1.00 28.93 S ATOM 21595 SG CYS D 978 71.155 26.149 86.594 1.00 35.30 S Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 24190 At special positions: 0 Unit cell: (127.897, 133.826, 198.198, 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 87 16.00 P 61 15.00 Mg 1 11.99 O 5070 8.00 N 4234 7.00 C 14735 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " Number of angles added : 12 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5348 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 36 sheets defined 39.3% alpha, 16.1% beta 26 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.597A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) 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 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.297A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.879A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.523A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.918A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.757A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.769A 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 71 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.767A pdb=" N THR C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.565A pdb=" N VAL C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.500A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.632A pdb=" N VAL C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.998A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.609A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.556A pdb=" N GLU C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 406 removed outlier: 3.678A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.949A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 582 through 586 removed outlier: 4.482A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.744A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.897A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 3.592A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.762A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.847A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 926 " --> pdb=" O VAL C 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 921 through 926' Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.684A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 removed outlier: 3.796A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C1080 " --> pdb=" O MET C1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 4.040A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 4.273A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.947A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.546A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (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 140 through 187 removed outlier: 4.063A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.723A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.618A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.637A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.726A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.829A 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 338 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.736A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 484 through 491 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 579 through 589 removed outlier: 3.595A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 removed outlier: 3.953A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 655 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 702 removed outlier: 3.566A pdb=" N GLU D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.506A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.768A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 762 " --> pdb=" O LYS D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.688A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 881 removed outlier: 4.933A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.725A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 removed outlier: 3.623A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1126 Processing helix chain 'D' and resid 1126 through 1146 removed outlier: 3.870A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.106A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 removed outlier: 3.976A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1215 removed outlier: 3.595A pdb=" N ALA D1213 " --> pdb=" O GLY D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1227 removed outlier: 3.644A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (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 sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 6.585A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 99 removed outlier: 7.526A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 99 removed outlier: 4.162A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 15 removed outlier: 6.479A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL B 196 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL B 22 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 173 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.708A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 54 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.616A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 104 through 107 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.596A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.473A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 135 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 137 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 150 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.444A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.319A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 216 " --> pdb=" O HIS C 200 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.974A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 568 through 571 removed outlier: 3.531A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.495A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.977A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.658A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 749 through 760 removed outlier: 4.042A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.788A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1136 through 1137 Processing sheet with id=AD2, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.350A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.660A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 329 through 330 removed outlier: 3.793A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD6, first strand: chain 'D' and resid 897 through 900 Processing sheet with id=AD7, first strand: chain 'D' and resid 902 through 903 Processing sheet with id=AD8, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 4.878A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D1103 " --> pdb=" O VAL D1053 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.486A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7422 1.34 - 1.45: 3261 1.45 - 1.57: 13394 1.57 - 1.69: 118 1.69 - 1.81: 153 Bond restraints: 24348 Sorted by residual: bond pdb=" C3' DT P 31 " pdb=" C2' DT P 31 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.53e+00 bond pdb=" C3' DC P 33 " pdb=" C2' DC P 33 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.64e+00 bond pdb=" N THR D1011 " pdb=" CA THR D1011 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.44e+00 bond pdb=" N MET D1012 " pdb=" CA MET D1012 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.38e+00 bond pdb=" C3' DC Q 32 " pdb=" C2' DC Q 32 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.19e+00 ... (remaining 24343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 32354 1.44 - 2.88: 771 2.88 - 4.31: 98 4.31 - 5.75: 19 5.75 - 7.19: 7 Bond angle restraints: 33249 Sorted by residual: angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT Q 39 " pdb=" C4 DT Q 39 " pdb=" O4 DT Q 39 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT P 31 " pdb=" C4 DT P 31 " pdb=" O4 DT P 31 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT Q 44 " pdb=" C4 DT Q 44 " pdb=" O4 DT Q 44 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 33244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 14368 32.93 - 65.86: 386 65.86 - 98.80: 8 98.80 - 131.73: 0 131.73 - 164.66: 1 Dihedral angle restraints: 14763 sinusoidal: 6442 harmonic: 8321 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual -128.00 36.66 -164.66 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" CA GLU C 767 " pdb=" C GLU C 767 " pdb=" N GLU C 768 " pdb=" CA GLU C 768 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 24 " pdb=" C GLU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta harmonic sigma weight residual 180.00 -158.27 -21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 14760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3694 0.107 - 0.214: 101 0.214 - 0.321: 0 0.321 - 0.428: 0 0.428 - 0.534: 3 Chirality restraints: 3798 Sorted by residual: chirality pdb=" P C R 11 " pdb=" OP1 C R 11 " pdb=" OP2 C R 11 " pdb=" O5' C R 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.14e+00 chirality pdb=" P G R 13 " pdb=" OP1 G R 13 " pdb=" OP2 G R 13 " pdb=" O5' G R 13 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" P G R 12 " pdb=" OP1 G R 12 " pdb=" OP2 G R 12 " pdb=" O5' G R 12 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.39e+00 ... (remaining 3795 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D1013 " -0.643 9.50e-02 1.11e+02 2.88e-01 5.06e+01 pdb=" NE ARG D1013 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D1013 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D1013 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D1013 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 444 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO C 445 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 507 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO C 508 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 508 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 508 " 0.023 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6929 2.83 - 3.35: 21589 3.35 - 3.87: 37378 3.87 - 4.38: 43500 4.38 - 4.90: 77042 Nonbonded interactions: 186438 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.318 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.386 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.530 2.170 nonbonded pdb=" O5' G R 18 " pdb=" O4' G R 18 " model vdw 2.534 2.432 nonbonded pdb=" C THR C 288 " pdb=" OG1 THR C 288 " model vdw 2.554 2.616 ... (remaining 186433 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 183 or (resid 184 and (name N or name \ CA or name C or name O or name CB )) or resid 185 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.610 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.003 0.044 24356 Z= 0.202 Angle : 0.737 49.063 33261 Z= 0.359 Chirality : 0.045 0.534 3798 Planarity : 0.006 0.288 4164 Dihedral : 13.162 164.658 9415 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.26 % Allowed : 5.90 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2894 helix: 1.19 (0.17), residues: 1026 sheet: 0.12 (0.28), residues: 367 loop : -0.88 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 6 TYR 0.011 0.001 TYR A 168 PHE 0.011 0.001 PHE C 439 TRP 0.008 0.001 TRP C 938 HIS 0.003 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.20 (24348) covalent geometry : angle 0.54165 / 0.35 (33249) hydrogen bonds : bond 0.15162 / 9.95 ( 993) hydrogen bonds : angle 5.30035 / 3.72 ( 2742) metal coordination : bond 0.02316 / 1.16 ( 8) metal coordination : angle 26.32325 / 13.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 296 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8790 (m) REVERT: C 672 MET cc_start: 0.8822 (mmp) cc_final: 0.8438 (mmt) REVERT: D 244 LEU cc_start: 0.8840 (mm) cc_final: 0.8378 (mm) REVERT: D 290 LEU cc_start: 0.8845 (tp) cc_final: 0.8597 (mt) REVERT: D 477 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 104 outliers final: 25 residues processed: 386 average time/residue: 0.2008 time to fit residues: 114.6542 Evaluate side-chains 198 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 200 ASN E 69 ASN E 70 GLN E 88 GLN C 388 GLN C 889 HIS D 207 GLN D 653 HIS D 854 HIS D1009 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058449 restraints weight = 62616.547| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.44 r_work: 0.2733 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24356 Z= 0.194 Angle : 0.608 18.060 33261 Z= 0.313 Chirality : 0.043 0.179 3798 Planarity : 0.005 0.057 4164 Dihedral : 13.697 167.475 3917 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.07 % Allowed : 8.60 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2894 helix: 1.44 (0.17), residues: 1049 sheet: 0.13 (0.28), residues: 368 loop : -0.91 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 401 TYR 0.014 0.001 TYR D 251 PHE 0.015 0.001 PHE D 252 TRP 0.011 0.001 TRP D1220 HIS 0.026 0.001 HIS D 653 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (24348) covalent geometry : angle 0.58192 / 0.31 (33249) hydrogen bonds : bond 0.04831 / 3.20 ( 993) hydrogen bonds : angle 4.36382 / 3.08 ( 2742) metal coordination : bond 0.01576 / 0.69 ( 8) metal coordination : angle 9.28747 / 4.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7833 (mp10) cc_final: 0.7632 (mp10) REVERT: A 141 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: B 151 GLN cc_start: 0.8777 (tp40) cc_final: 0.8296 (tm-30) REVERT: C 232 GLN cc_start: 0.7794 (mt0) cc_final: 0.7273 (mp10) REVERT: C 467 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7948 (mtt-85) REVERT: C 867 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 902 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8695 (pt0) REVERT: D 244 LEU cc_start: 0.9315 (mm) cc_final: 0.8993 (mm) REVERT: D 256 MET cc_start: 0.7436 (ttm) cc_final: 0.7161 (mmm) REVERT: D 310 MET cc_start: 0.8585 (tpp) cc_final: 0.8285 (tpp) REVERT: D 663 MET cc_start: 0.8968 (mmt) cc_final: 0.8638 (mmp) REVERT: D 866 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8387 (mmt90) REVERT: D 1012 MET cc_start: 0.7453 (ttp) cc_final: 0.7248 (tmm) outliers start: 75 outliers final: 50 residues processed: 232 average time/residue: 0.1418 time to fit residues: 53.4653 Evaluate side-chains 201 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1009 GLN Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 84 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 GLN E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056135 restraints weight = 64067.692| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.57 r_work: 0.2680 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24356 Z= 0.231 Angle : 0.587 10.662 33261 Z= 0.308 Chirality : 0.044 0.177 3798 Planarity : 0.004 0.044 4164 Dihedral : 13.798 170.118 3911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.03 % Allowed : 9.46 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2894 helix: 1.50 (0.17), residues: 1050 sheet: -0.02 (0.28), residues: 371 loop : -0.94 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 208 TYR 0.017 0.001 TYR A 168 PHE 0.016 0.001 PHE D1226 TRP 0.012 0.001 TRP D1220 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (24348) covalent geometry : angle 0.57616 / 0.31 (33249) hydrogen bonds : bond 0.05018 / 3.33 ( 993) hydrogen bonds : angle 4.23661 / 2.99 ( 2742) metal coordination : bond 0.01356 / 0.60 ( 8) metal coordination : angle 6.03916 / 2.94 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 156 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7986 (mp10) cc_final: 0.7753 (mp10) REVERT: E 66 ASP cc_start: 0.9133 (t0) cc_final: 0.8854 (t70) REVERT: C 467 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7877 (mtt-85) REVERT: C 902 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8680 (pt0) REVERT: C 985 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8828 (tt) REVERT: D 216 LEU cc_start: 0.8798 (mm) cc_final: 0.8173 (tp) REVERT: D 244 LEU cc_start: 0.9449 (mm) cc_final: 0.9075 (mm) REVERT: D 256 MET cc_start: 0.7665 (ttm) cc_final: 0.7295 (mmm) REVERT: D 310 MET cc_start: 0.8690 (tpp) cc_final: 0.8324 (tpp) REVERT: D 427 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.7298 (ttm-80) REVERT: D 866 ARG cc_start: 0.8904 (mmt-90) cc_final: 0.8376 (mmt90) REVERT: D 1147 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8819 (m) outliers start: 74 outliers final: 49 residues processed: 223 average time/residue: 0.1668 time to fit residues: 59.9754 Evaluate side-chains 194 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1087 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.0030 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 152 ASN E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057777 restraints weight = 62265.531| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.47 r_work: 0.2716 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24356 Z= 0.131 Angle : 0.514 7.533 33261 Z= 0.273 Chirality : 0.042 0.169 3798 Planarity : 0.004 0.040 4164 Dihedral : 13.773 172.878 3910 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.46 % Allowed : 11.14 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2894 helix: 1.73 (0.17), residues: 1040 sheet: 0.18 (0.28), residues: 365 loop : -0.78 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 37 TYR 0.012 0.001 TYR A 168 PHE 0.008 0.001 PHE C 439 TRP 0.009 0.001 TRP C 70 HIS 0.002 0.000 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24348) covalent geometry : angle 0.50751 / 0.27 (33249) hydrogen bonds : bond 0.04026 / 2.68 ( 993) hydrogen bonds : angle 4.00147 / 2.83 ( 2742) metal coordination : bond 0.00816 / 0.35 ( 8) metal coordination : angle 4.26223 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8046 (mp10) cc_final: 0.7798 (mp10) REVERT: B 152 ASN cc_start: 0.7951 (t0) cc_final: 0.6915 (t0) REVERT: E 66 ASP cc_start: 0.9092 (t0) cc_final: 0.8757 (t70) REVERT: C 232 GLN cc_start: 0.7956 (mt0) cc_final: 0.7398 (mp10) REVERT: C 467 ARG cc_start: 0.8378 (mtt180) cc_final: 0.7890 (mtt180) REVERT: C 713 MET cc_start: 0.9311 (mmt) cc_final: 0.8888 (mmt) REVERT: C 902 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8696 (pt0) REVERT: D 114 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 205 MET cc_start: 0.7454 (mmp) cc_final: 0.7129 (mmp) REVERT: D 216 LEU cc_start: 0.8744 (mm) cc_final: 0.8119 (tp) REVERT: D 244 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9104 (mm) REVERT: D 256 MET cc_start: 0.7724 (ttm) cc_final: 0.7427 (mmm) REVERT: D 310 MET cc_start: 0.8625 (tpp) cc_final: 0.8229 (tpp) REVERT: D 427 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7487 (ttm-80) REVERT: D 477 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8834 (tp30) REVERT: D 663 MET cc_start: 0.9018 (mmt) cc_final: 0.8634 (mmp) REVERT: D 866 ARG cc_start: 0.8899 (mmt-90) cc_final: 0.8631 (mmt-90) REVERT: D 1012 MET cc_start: 0.6767 (tmm) cc_final: 0.6537 (tmm) REVERT: D 1013 ARG cc_start: 0.8091 (mpt180) cc_final: 0.7121 (mtm-85) outliers start: 60 outliers final: 44 residues processed: 207 average time/residue: 0.1587 time to fit residues: 53.9316 Evaluate side-chains 190 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 195 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 261 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN E 69 ASN E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.058075 restraints weight = 62102.950| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.42 r_work: 0.2727 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24356 Z= 0.111 Angle : 0.489 9.919 33261 Z= 0.259 Chirality : 0.041 0.174 3798 Planarity : 0.004 0.041 4164 Dihedral : 13.718 174.307 3908 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.74 % Allowed : 11.31 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2894 helix: 1.87 (0.17), residues: 1042 sheet: 0.24 (0.28), residues: 362 loop : -0.71 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 37 TYR 0.011 0.001 TYR C 731 PHE 0.008 0.001 PHE C 153 TRP 0.008 0.001 TRP C 70 HIS 0.002 0.000 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (24348) covalent geometry : angle 0.48440 / 0.26 (33249) hydrogen bonds : bond 0.03706 / 2.47 ( 993) hydrogen bonds : angle 3.89322 / 2.75 ( 2742) metal coordination : bond 0.00668 / 0.29 ( 8) metal coordination : angle 3.66026 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8090 (mp10) cc_final: 0.7814 (mp10) REVERT: A 185 GLN cc_start: 0.8670 (pm20) cc_final: 0.8399 (pm20) REVERT: E 66 ASP cc_start: 0.9077 (t0) cc_final: 0.8782 (t70) REVERT: C 232 GLN cc_start: 0.7943 (mt0) cc_final: 0.7423 (mp10) REVERT: C 467 ARG cc_start: 0.8341 (mtt180) cc_final: 0.7852 (mtt180) REVERT: C 713 MET cc_start: 0.9278 (mmt) cc_final: 0.8872 (mmt) REVERT: D 114 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8685 (tt) REVERT: D 216 LEU cc_start: 0.8760 (mm) cc_final: 0.8162 (tp) REVERT: D 244 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9113 (mm) REVERT: D 256 MET cc_start: 0.7734 (ttm) cc_final: 0.7432 (mmm) REVERT: D 310 MET cc_start: 0.8589 (tpp) cc_final: 0.8197 (tpp) REVERT: D 427 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7307 (ttm-80) REVERT: D 477 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8830 (tp30) REVERT: D 663 MET cc_start: 0.9010 (mmt) cc_final: 0.8626 (mmp) REVERT: D 1012 MET cc_start: 0.6692 (tmm) cc_final: 0.6416 (tmm) REVERT: D 1147 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8742 (m) outliers start: 67 outliers final: 47 residues processed: 210 average time/residue: 0.1596 time to fit residues: 55.2212 Evaluate side-chains 194 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 238 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.056064 restraints weight = 63487.639| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.55 r_work: 0.2684 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24356 Z= 0.164 Angle : 0.517 7.643 33261 Z= 0.273 Chirality : 0.042 0.178 3798 Planarity : 0.004 0.042 4164 Dihedral : 13.746 175.136 3908 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.54 % Allowed : 11.55 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2894 helix: 1.87 (0.17), residues: 1044 sheet: 0.18 (0.27), residues: 374 loop : -0.73 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 37 TYR 0.025 0.001 TYR D 251 PHE 0.012 0.001 PHE D1226 TRP 0.008 0.001 TRP C 243 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (24348) covalent geometry : angle 0.51253 / 0.27 (33249) hydrogen bonds : bond 0.04195 / 2.79 ( 993) hydrogen bonds : angle 3.89687 / 2.75 ( 2742) metal coordination : bond 0.00856 / 0.39 ( 8) metal coordination : angle 3.60998 / 1.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8166 (mp10) cc_final: 0.7892 (mp10) REVERT: B 151 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8876 (tp40) REVERT: E 66 ASP cc_start: 0.9127 (t0) cc_final: 0.8791 (t70) REVERT: C 467 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7896 (mtt180) REVERT: C 630 MET cc_start: 0.9002 (tpt) cc_final: 0.8776 (tpp) REVERT: C 713 MET cc_start: 0.9272 (mmt) cc_final: 0.8897 (mmt) REVERT: D 114 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8703 (tt) REVERT: D 216 LEU cc_start: 0.8802 (mm) cc_final: 0.8202 (tp) REVERT: D 244 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9143 (mm) REVERT: D 310 MET cc_start: 0.8638 (tpp) cc_final: 0.8225 (tpp) REVERT: D 427 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.7345 (ttm-80) REVERT: D 477 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8852 (tp30) REVERT: D 866 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8501 (mmt-90) REVERT: D 1012 MET cc_start: 0.6710 (tmm) cc_final: 0.6441 (tmm) REVERT: D 1147 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8760 (m) outliers start: 62 outliers final: 47 residues processed: 201 average time/residue: 0.1544 time to fit residues: 51.3519 Evaluate side-chains 192 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 54 optimal weight: 30.0000 chunk 114 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055522 restraints weight = 62296.708| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.44 r_work: 0.2664 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24356 Z= 0.196 Angle : 0.545 7.181 33261 Z= 0.287 Chirality : 0.043 0.176 3798 Planarity : 0.004 0.040 4164 Dihedral : 13.800 174.637 3908 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.42 % Allowed : 12.17 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2894 helix: 1.85 (0.17), residues: 1043 sheet: 0.12 (0.28), residues: 372 loop : -0.79 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 37 TYR 0.018 0.001 TYR D 134 PHE 0.013 0.001 PHE D1226 TRP 0.010 0.001 TRP D1220 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (24348) covalent geometry : angle 0.54068 / 0.29 (33249) hydrogen bonds : bond 0.04532 / 3.02 ( 993) hydrogen bonds : angle 3.97710 / 2.81 ( 2742) metal coordination : bond 0.00984 / 0.45 ( 8) metal coordination : angle 3.56410 / 1.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8226 (mp10) cc_final: 0.7948 (mp10) REVERT: B 151 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8838 (tp40) REVERT: E 66 ASP cc_start: 0.9160 (t0) cc_final: 0.8880 (t70) REVERT: E 78 TYR cc_start: 0.8240 (m-80) cc_final: 0.8011 (m-80) REVERT: C 467 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7844 (mtt180) REVERT: C 985 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8798 (tt) REVERT: D 205 MET cc_start: 0.7334 (mmp) cc_final: 0.6961 (mmp) REVERT: D 216 LEU cc_start: 0.8803 (mm) cc_final: 0.8334 (tp) REVERT: D 244 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9168 (mm) REVERT: D 256 MET cc_start: 0.7241 (mmm) cc_final: 0.6637 (mmm) REVERT: D 310 MET cc_start: 0.8705 (tpp) cc_final: 0.8289 (tpp) REVERT: D 427 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.7327 (ttm-80) REVERT: D 443 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8915 (mp) REVERT: D 477 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8846 (tp30) REVERT: D 1147 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8808 (m) outliers start: 59 outliers final: 47 residues processed: 196 average time/residue: 0.1531 time to fit residues: 49.4582 Evaluate side-chains 191 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 94 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056575 restraints weight = 63429.286| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.55 r_work: 0.2698 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24356 Z= 0.106 Angle : 0.492 12.976 33261 Z= 0.263 Chirality : 0.041 0.251 3798 Planarity : 0.004 0.042 4164 Dihedral : 13.733 175.168 3908 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.25 % Allowed : 12.86 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2894 helix: 1.95 (0.17), residues: 1043 sheet: 0.25 (0.28), residues: 369 loop : -0.71 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 37 TYR 0.017 0.001 TYR D 251 PHE 0.009 0.001 PHE C 153 TRP 0.009 0.001 TRP C 70 HIS 0.002 0.000 HIS C 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (24348) covalent geometry : angle 0.48903 / 0.26 (33249) hydrogen bonds : bond 0.03649 / 2.44 ( 993) hydrogen bonds : angle 3.83047 / 2.71 ( 2742) metal coordination : bond 0.00546 / 0.23 ( 8) metal coordination : angle 3.06776 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 148 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8295 (mp10) cc_final: 0.8024 (mp10) REVERT: B 151 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8844 (tp40) REVERT: E 66 ASP cc_start: 0.9119 (t0) cc_final: 0.8870 (t70) REVERT: C 467 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7823 (mtt180) REVERT: C 630 MET cc_start: 0.8980 (tpt) cc_final: 0.8725 (tpp) REVERT: D 114 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8735 (tt) REVERT: D 216 LEU cc_start: 0.8731 (mm) cc_final: 0.8284 (tp) REVERT: D 244 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9170 (mm) REVERT: D 256 MET cc_start: 0.7250 (mmm) cc_final: 0.6562 (mmm) REVERT: D 427 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7340 (ttm-80) REVERT: D 477 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8848 (tp30) REVERT: D 1147 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8767 (m) outliers start: 55 outliers final: 45 residues processed: 196 average time/residue: 0.1439 time to fit residues: 45.7527 Evaluate side-chains 193 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 134 optimal weight: 5.9990 chunk 240 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 269 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057271 restraints weight = 62172.135| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.46 r_work: 0.2712 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24356 Z= 0.108 Angle : 0.492 11.253 33261 Z= 0.260 Chirality : 0.041 0.228 3798 Planarity : 0.004 0.042 4164 Dihedral : 13.685 175.655 3908 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.13 % Allowed : 12.90 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2894 helix: 2.02 (0.17), residues: 1042 sheet: 0.28 (0.28), residues: 369 loop : -0.67 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1231 TYR 0.017 0.001 TYR D 251 PHE 0.014 0.001 PHE D 252 TRP 0.008 0.001 TRP C 70 HIS 0.003 0.000 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (24348) covalent geometry : angle 0.48835 / 0.26 (33249) hydrogen bonds : bond 0.03497 / 2.33 ( 993) hydrogen bonds : angle 3.77146 / 2.66 ( 2742) metal coordination : bond 0.00542 / 0.23 ( 8) metal coordination : angle 3.02526 / 1.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8277 (mp10) cc_final: 0.8008 (mp10) REVERT: E 66 ASP cc_start: 0.9111 (t0) cc_final: 0.8872 (t70) REVERT: C 467 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7838 (mtt180) REVERT: C 630 MET cc_start: 0.8983 (tpt) cc_final: 0.8708 (tpp) REVERT: D 124 ASP cc_start: 0.9327 (m-30) cc_final: 0.8937 (p0) REVERT: D 216 LEU cc_start: 0.8708 (mm) cc_final: 0.8292 (tp) REVERT: D 244 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9174 (mm) REVERT: D 256 MET cc_start: 0.7297 (mmm) cc_final: 0.6601 (mmm) REVERT: D 427 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: D 477 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8849 (tp30) REVERT: D 1012 MET cc_start: 0.7158 (tmm) cc_final: 0.6799 (tmm) REVERT: D 1025 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7446 (t) REVERT: D 1147 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8737 (m) outliers start: 52 outliers final: 41 residues processed: 193 average time/residue: 0.1611 time to fit residues: 51.4135 Evaluate side-chains 189 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 198 optimal weight: 6.9990 chunk 273 optimal weight: 0.2980 chunk 201 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.056649 restraints weight = 62267.015| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.42 r_work: 0.2699 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24356 Z= 0.135 Angle : 0.513 11.754 33261 Z= 0.269 Chirality : 0.042 0.305 3798 Planarity : 0.004 0.042 4164 Dihedral : 13.663 175.828 3906 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.93 % Allowed : 13.11 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2894 helix: 2.03 (0.17), residues: 1043 sheet: 0.26 (0.28), residues: 380 loop : -0.68 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1231 TYR 0.016 0.001 TYR D 251 PHE 0.009 0.001 PHE C 153 TRP 0.008 0.001 TRP C 243 HIS 0.003 0.000 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (24348) covalent geometry : angle 0.51001 / 0.27 (33249) hydrogen bonds : bond 0.03717 / 2.48 ( 993) hydrogen bonds : angle 3.78039 / 2.67 ( 2742) metal coordination : bond 0.00667 / 0.30 ( 8) metal coordination : angle 2.97452 / 1.43 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5788 Ramachandran restraints generated. 2894 Oldfield, 0 Emsley, 2894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8290 (mp10) cc_final: 0.8024 (mp10) REVERT: E 66 ASP cc_start: 0.9108 (t0) cc_final: 0.8874 (t70) REVERT: C 232 GLN cc_start: 0.8058 (mt0) cc_final: 0.7513 (mp10) REVERT: C 467 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7847 (mtt180) REVERT: C 630 MET cc_start: 0.8987 (tpt) cc_final: 0.8720 (tpp) REVERT: C 985 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8744 (tt) REVERT: D 124 ASP cc_start: 0.9334 (m-30) cc_final: 0.8958 (p0) REVERT: D 143 MET cc_start: 0.8601 (ptm) cc_final: 0.8306 (tmm) REVERT: D 216 LEU cc_start: 0.8731 (mm) cc_final: 0.8326 (tp) REVERT: D 244 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9193 (mm) REVERT: D 256 MET cc_start: 0.7307 (mmm) cc_final: 0.6674 (mmm) REVERT: D 427 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.7436 (ttm-80) REVERT: D 477 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8834 (tp30) REVERT: D 1147 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (m) outliers start: 47 outliers final: 43 residues processed: 187 average time/residue: 0.1580 time to fit residues: 48.4612 Evaluate side-chains 192 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 243 TRP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 427 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 1025 THR Chi-restraints excluded: chain D residue 1061 PHE Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1217 THR Chi-restraints excluded: chain D residue 1238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 216 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 63 optimal weight: 0.0070 chunk 253 optimal weight: 6.9990 chunk 255 optimal weight: 0.6980 chunk 159 optimal weight: 7.9990 chunk 285 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.089827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057898 restraints weight = 63238.893| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.45 r_work: 0.2739 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24356 Z= 0.103 Angle : 0.496 10.661 33261 Z= 0.260 Chirality : 0.041 0.216 3798 Planarity : 0.004 0.048 4164 Dihedral : 13.618 176.112 3906 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.13 % Allowed : 12.95 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 2894 helix: 2.05 (0.17), residues: 1044 sheet: 0.38 (0.29), residues: 357 loop : -0.65 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1231 TYR 0.016 0.001 TYR D 251 PHE 0.013 0.001 PHE D 252 TRP 0.009 0.001 TRP C 938 HIS 0.002 0.000 HIS C 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (24348) covalent geometry : angle 0.49328 / 0.26 (33249) hydrogen bonds : bond 0.03311 / 2.22 ( 993) hydrogen bonds : angle 3.72299 / 2.63 ( 2742) metal coordination : bond 0.00492 / 0.21 ( 8) metal coordination : angle 2.79932 / 1.33 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.73 seconds wall clock time: 96 minutes 37.02 seconds (5797.02 seconds total)