Starting phenix.real_space_refine on Mon Jul 6 17:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0y_62728/07_2026/9l0y_62728.cif" } resolution = 3.78 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 321 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 138 5.16 5 C 22021 2.51 5 N 6399 2.21 5 O 7155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35859 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1496 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "2" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1510 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10369 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3977 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 855 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 872 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 65} Chain breaks: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.16 Number of scatterers: 35859 At special positions: 0 Unit cell: (172.7, 216.7, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 146 15.00 O 7155 8.00 N 6399 7.00 C 22021 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: 2.71 Conformation dependent library (CDL) restraints added in 923.9 milliseconds 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7770 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 46 sheets defined 47.5% alpha, 13.1% beta 49 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.713A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.100A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 48 removed outlier: 3.649A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.852A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.190A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 removed outlier: 4.013A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.705A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.565A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.923A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 390 removed outlier: 3.679A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.659A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.068A pdb=" N ILE C 493 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.999A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.678A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.923A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.556A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.944A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.516A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.681A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.125A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1038 removed outlier: 3.662A pdb=" N GLN C1008 " --> pdb=" O ASP C1004 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.641A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.587A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1243 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.671A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 removed outlier: 3.559A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1310 removed outlier: 3.775A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.668A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.632A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.709A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 4.131A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.096A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.538A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 4.653A pdb=" N ARG D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY D 313 " --> pdb=" O ASN D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.771A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.675A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.535A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.538A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.532A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 671 removed outlier: 4.776A pdb=" N GLU D 660 " --> pdb=" O GLU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.063A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.639A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.703A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.614A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 834 through 839' Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.314A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.509A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 removed outlier: 4.510A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.630A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.815A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 4.467A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.533A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.649A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.936A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.915A pdb=" N VAL E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.837A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.564A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 80 removed outlier: 3.755A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 89 removed outlier: 3.680A pdb=" N SER F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.573A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.706A pdb=" N GLY F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.365A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 213 through 237 removed outlier: 4.043A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 Processing helix chain 'F' and resid 262 through 291 removed outlier: 3.606A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.127A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.979A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.322A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 4.084A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 393 removed outlier: 4.315A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 419 removed outlier: 3.508A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.821A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.667A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 4.052A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 removed outlier: 4.185A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 501 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 552 through 564 Processing helix chain 'F' and resid 572 through 578 removed outlier: 3.537A pdb=" N LYS F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 599 Processing helix chain 'F' and resid 604 through 610 removed outlier: 3.932A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 610 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 613 No H-bonds generated for 'chain 'F' and resid 611 through 613' Processing helix chain 'G' and resid 28 through 47 Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 52 through 63 removed outlier: 4.102A pdb=" N ILE G 56 " --> pdb=" O HIS G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.701A pdb=" N ASP G 78 " --> pdb=" O GLY G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 105 through 119 removed outlier: 3.500A pdb=" N LEU G 119 " --> pdb=" O ARG G 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 24 removed outlier: 4.194A pdb=" N ASN J 20 " --> pdb=" O HIS J 17 " (cutoff:3.500A) Proline residue: J 21 - end of helix Processing helix chain 'J' and resid 27 through 47 removed outlier: 3.585A pdb=" N LEU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 52 through 64 removed outlier: 3.935A pdb=" N ILE J 56 " --> pdb=" O HIS J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 88 removed outlier: 3.907A pdb=" N ASP J 78 " --> pdb=" O GLY J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 103 Processing helix chain 'J' and resid 105 through 119 removed outlier: 3.564A pdb=" N VAL J 109 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU J 119 " --> pdb=" O ARG J 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 24 removed outlier: 4.274A pdb=" N ASN M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) Proline residue: M 21 - end of helix Processing helix chain 'M' and resid 30 through 47 removed outlier: 3.864A pdb=" N GLU M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 52 through 63 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 94 through 103 Processing helix chain 'M' and resid 105 through 119 removed outlier: 3.539A pdb=" N LEU M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 47 Processing helix chain 'N' and resid 51 through 64 removed outlier: 4.130A pdb=" N GLU N 55 " --> pdb=" O ALA N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 90 Processing helix chain 'N' and resid 94 through 102 removed outlier: 3.723A pdb=" N TYR N 102 " --> pdb=" O LEU N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 119 Processing helix chain 'P' and resid 256 through 261 removed outlier: 3.556A pdb=" N ASP P 259 " --> pdb=" O PRO P 256 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 260 " --> pdb=" O VAL P 257 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU P 261 " --> pdb=" O ASP P 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 256 through 261' Processing helix chain 'P' and resid 263 through 274 removed outlier: 4.445A pdb=" N LYS P 271 " --> pdb=" O ALA P 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA P 272 " --> pdb=" O ASN P 268 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU P 273 " --> pdb=" O CYS P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 277 through 284 removed outlier: 3.500A pdb=" N ARG P 284 " --> pdb=" O ASP P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.518A pdb=" N LEU P 289 " --> pdb=" O THR P 285 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU P 290 " --> pdb=" O GLU P 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 285 through 290' Processing helix chain 'P' and resid 303 through 310 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 4.827A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.696A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.634A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 5.046A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.647A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.645A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.425A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.046A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 256 removed outlier: 7.030A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.821A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.696A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.312A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 718 removed outlier: 6.462A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.504A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.728A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.825A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.237A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.530A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.522A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.601A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.704A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.327A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.154A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.574A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.557A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.400A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1025 through 1026 removed outlier: 3.700A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D1107 " --> pdb=" O LEU D1059 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.784A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1186 through 1190 removed outlier: 3.696A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.253A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 68 through 70 removed outlier: 3.511A pdb=" N VAL G 69 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 68 through 69 removed outlier: 3.903A pdb=" N VAL M 69 " --> pdb=" O VAL N 69 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL N 69 " --> pdb=" O VAL M 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 1465 hydrogen bonds defined for protein. 4164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 8.60 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9356 1.33 - 1.45: 6500 1.45 - 1.57: 20317 1.57 - 1.69: 290 1.69 - 1.81: 240 Bond restraints: 36703 Sorted by residual: bond pdb=" C1' DT 1 48 " pdb=" N1 DT 1 48 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" C1' DT 1 47 " pdb=" N1 DT 1 47 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.25e+01 bond pdb=" C3' DT 1 84 " pdb=" O3' DT 1 84 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C5' DA 2 12 " pdb=" C4' DA 2 12 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.13e+01 bond pdb=" C5' DC 2 58 " pdb=" C4' DC 2 58 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.13e+01 ... (remaining 36698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 49007 1.77 - 3.54: 1095 3.54 - 5.31: 72 5.31 - 7.08: 19 7.08 - 8.85: 5 Bond angle restraints: 50198 Sorted by residual: angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 113.71 107.11 6.60 9.50e-01 1.11e+00 4.82e+01 angle pdb=" O4' DT 1 20 " pdb=" C4' DT 1 20 " pdb=" C3' DT 1 20 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.22e+01 angle pdb=" O4' DA 2 38 " pdb=" C4' DA 2 38 " pdb=" C3' DA 2 38 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.36e+01 angle pdb=" N3 DT 1 47 " pdb=" C4 DT 1 47 " pdb=" O4 DT 1 47 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N VAL D1267 " pdb=" CA VAL D1267 " pdb=" C VAL D1267 " ideal model delta sigma weight residual 113.53 108.98 4.55 9.80e-01 1.04e+00 2.16e+01 ... (remaining 50193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 21129 34.60 - 69.19: 1036 69.19 - 103.79: 25 103.79 - 138.38: 1 138.38 - 172.98: 5 Dihedral angle restraints: 22196 sinusoidal: 10150 harmonic: 12046 Sorted by residual: dihedral pdb=" CA CYS G 61 " pdb=" C CYS G 61 " pdb=" N LYS G 62 " pdb=" CA LYS G 62 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA THR A 207 " pdb=" C THR A 207 " pdb=" N ASN A 208 " pdb=" CA ASN A 208 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DA 1 23 " pdb=" C3' DA 1 23 " pdb=" O3' DA 1 23 " pdb=" P DC 1 24 " ideal model delta sinusoidal sigma weight residual -140.00 32.98 -172.98 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 22193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3509 0.032 - 0.063: 1516 0.063 - 0.095: 467 0.095 - 0.127: 213 0.127 - 0.159: 21 Chirality restraints: 5726 Sorted by residual: chirality pdb=" CA PHE G 28 " pdb=" N PHE G 28 " pdb=" C PHE G 28 " pdb=" CB PHE G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" C3' DA 2 30 " pdb=" C4' DA 2 30 " pdb=" O3' DA 2 30 " pdb=" C2' DA 2 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE G 71 " pdb=" N ILE G 71 " pdb=" C ILE G 71 " pdb=" CB ILE G 71 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 5723 not shown) Planarity restraints: 6038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 71 " -0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO N 72 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO N 72 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 72 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC 2 58 " -0.009 2.00e-02 2.50e+03 1.60e-02 5.74e+00 pdb=" N1 DC 2 58 " 0.018 2.00e-02 2.50e+03 pdb=" C2 DC 2 58 " -0.033 2.00e-02 2.50e+03 pdb=" O2 DC 2 58 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC 2 58 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC 2 58 " -0.019 2.00e-02 2.50e+03 pdb=" N4 DC 2 58 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC 2 58 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC 2 58 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS F 600 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO F 601 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 601 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 601 " -0.025 5.00e-02 4.00e+02 ... (remaining 6035 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1465 2.71 - 3.26: 37200 3.26 - 3.81: 61273 3.81 - 4.35: 74172 4.35 - 4.90: 117838 Nonbonded interactions: 291948 Sorted by model distance: nonbonded pdb=" O SER C 788 " pdb=" OG SER C 788 " model vdw 2.165 3.040 nonbonded pdb=" NZ LYS D 650 " pdb=" O THR D 760 " model vdw 2.203 3.120 nonbonded pdb=" O PHE C 812 " pdb=" NE2 GLN D 504 " model vdw 2.211 3.120 nonbonded pdb=" N ASP D 264 " pdb=" OD1 ASP D 264 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR C 563 " pdb=" O ILE C 569 " model vdw 2.221 3.040 ... (remaining 291943 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 6 through 233) selection = chain 'B' } ncs_group { reference = chain 'G' selection = (chain 'J' and resid 27 through 120) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 31.230 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 0.057 36703 Z= 0.252 Angle : 0.593 8.849 50198 Z= 0.409 Chirality : 0.041 0.159 5726 Planarity : 0.004 0.071 6038 Dihedral : 17.032 172.975 14426 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 3.82 % Allowed : 9.22 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.39 (0.13), residues: 4148 helix: 0.53 (0.13), residues: 1680 sheet: 0.11 (0.27), residues: 381 loop : -0.95 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 10 TYR 0.010 0.001 TYR D 679 PHE 0.010 0.001 PHE D 620 TRP 0.019 0.001 TRP G 87 HIS 0.005 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.25 (36703) covalent geometry : angle 0.59277 / 0.41 (50198) hydrogen bonds : bond 0.14978 / 16.11 ( 1583) hydrogen bonds : angle 6.21585 / 7.96 ( 4404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 556 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 137 ASN cc_start: 0.9489 (m-40) cc_final: 0.8936 (m-40) REVERT: B 10 LYS cc_start: 0.8577 (mmpt) cc_final: 0.7688 (tmtt) REVERT: B 41 ASN cc_start: 0.9009 (t0) cc_final: 0.8762 (t0) REVERT: B 51 MET cc_start: 0.9124 (mmp) cc_final: 0.8797 (mmm) REVERT: B 68 TYR cc_start: 0.8743 (m-80) cc_final: 0.8117 (m-80) REVERT: B 202 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8060 (m) REVERT: C 62 TYR cc_start: 0.7832 (m-10) cc_final: 0.7597 (m-10) REVERT: C 85 CYS cc_start: 0.8685 (m) cc_final: 0.8184 (m) REVERT: C 160 ASP cc_start: 0.8079 (m-30) cc_final: 0.7707 (p0) REVERT: C 184 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7262 (tp) REVERT: C 207 THR cc_start: 0.8748 (m) cc_final: 0.8386 (p) REVERT: C 365 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8902 (tm-30) REVERT: C 371 ARG cc_start: 0.8248 (mmt90) cc_final: 0.8037 (mtt-85) REVERT: C 448 LEU cc_start: 0.8317 (mt) cc_final: 0.8046 (mt) REVERT: C 588 GLU cc_start: 0.8543 (pt0) cc_final: 0.7895 (pm20) REVERT: C 779 ARG cc_start: 0.8859 (mtp180) cc_final: 0.8395 (ttm110) REVERT: C 895 LEU cc_start: 0.9185 (mp) cc_final: 0.8716 (mt) REVERT: C 899 GLU cc_start: 0.9019 (pt0) cc_final: 0.8751 (pt0) REVERT: C 930 ASP cc_start: 0.8295 (t0) cc_final: 0.7911 (t0) REVERT: C 1013 GLN cc_start: 0.9287 (mm-40) cc_final: 0.9000 (mt0) REVERT: C 1216 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7957 (mtm180) REVERT: C 1243 MET cc_start: 0.6511 (tpp) cc_final: 0.6176 (tpp) REVERT: C 1259 LEU cc_start: 0.7339 (mp) cc_final: 0.7067 (mt) REVERT: C 1279 GLU cc_start: 0.9086 (pt0) cc_final: 0.8707 (pt0) REVERT: D 28 ASP cc_start: 0.9179 (m-30) cc_final: 0.8481 (p0) REVERT: D 123 ARG cc_start: 0.8580 (mmt-90) cc_final: 0.8182 (mmt-90) REVERT: D 151 MET cc_start: 0.6475 (pmm) cc_final: 0.6202 (pmm) REVERT: D 180 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5528 (mmm) REVERT: D 301 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8532 (tp30) REVERT: D 304 ASP cc_start: 0.8714 (m-30) cc_final: 0.8456 (m-30) REVERT: D 504 GLN cc_start: 0.7993 (pt0) cc_final: 0.7686 (pt0) REVERT: D 695 LYS cc_start: 0.8390 (mmmm) cc_final: 0.8164 (mmmm) REVERT: D 743 MET cc_start: 0.5194 (ppp) cc_final: 0.4914 (ppp) REVERT: D 822 MET cc_start: 0.7291 (tpt) cc_final: 0.6969 (tpp) REVERT: D 915 ILE cc_start: 0.8712 (mt) cc_final: 0.8497 (tp) REVERT: D 922 SER cc_start: 0.8747 (m) cc_final: 0.8542 (p) REVERT: D 932 MET cc_start: 0.5475 (mmp) cc_final: 0.4983 (tpp) REVERT: D 999 TYR cc_start: 0.7689 (t80) cc_final: 0.6412 (t80) REVERT: E 7 GLN cc_start: 0.8102 (mp-120) cc_final: 0.7897 (pm20) REVERT: E 35 LYS cc_start: 0.8651 (mptt) cc_final: 0.8355 (mmtp) REVERT: E 43 ASN cc_start: 0.8352 (t0) cc_final: 0.7623 (t0) REVERT: E 60 ASN cc_start: 0.8293 (t0) cc_final: 0.7999 (t0) REVERT: F 100 MET cc_start: 0.8430 (ppp) cc_final: 0.8184 (ptp) REVERT: F 273 MET cc_start: 0.8914 (tpt) cc_final: 0.8341 (tpt) REVERT: F 276 MET cc_start: 0.8909 (ppp) cc_final: 0.8526 (ppp) REVERT: F 277 MET cc_start: 0.8466 (tpt) cc_final: 0.7967 (tpt) REVERT: F 288 MET cc_start: 0.4965 (mpp) cc_final: 0.4105 (mpp) REVERT: F 294 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7481 (mp10) REVERT: F 379 MET cc_start: 0.9173 (tmm) cc_final: 0.8528 (tmm) REVERT: F 425 TYR cc_start: 0.8993 (m-80) cc_final: 0.8585 (m-80) REVERT: F 455 HIS cc_start: 0.7701 (t-90) cc_final: 0.7198 (t70) REVERT: F 458 GLU cc_start: 0.9004 (pp20) cc_final: 0.8738 (pp20) REVERT: F 507 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8432 (mmm) REVERT: F 527 THR cc_start: 0.9514 (t) cc_final: 0.9305 (p) REVERT: F 528 LEU cc_start: 0.8559 (mt) cc_final: 0.8244 (tp) REVERT: G 39 LEU cc_start: 0.9384 (mp) cc_final: 0.9177 (mt) REVERT: G 61 CYS cc_start: 0.9573 (t) cc_final: 0.9329 (m) REVERT: G 117 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8291 (tpt90) REVERT: J 34 GLU cc_start: 0.8967 (tt0) cc_final: 0.8612 (tt0) REVERT: N 63 HIS cc_start: 0.8768 (t-90) cc_final: 0.8526 (t-90) outliers start: 136 outliers final: 29 residues processed: 665 average time/residue: 0.2188 time to fit residues: 231.6325 Evaluate side-chains 349 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain F residue 506 SER Chi-restraints excluded: chain F residue 507 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain N residue 70 TYR Chi-restraints excluded: chain N residue 107 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 93 GLN B 66 HIS B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 554 HIS C 684 ASN C 686 GLN C1314 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 450 HIS D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 ASN F 600 HIS G 88 ASN N 88 ASN P 276 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.090020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062525 restraints weight = 158457.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064498 restraints weight = 94013.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064548 restraints weight = 60818.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065002 restraints weight = 48798.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065020 restraints weight = 45949.107| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 36703 Z= 0.189 Angle : 0.657 9.487 50198 Z= 0.351 Chirality : 0.045 0.266 5726 Planarity : 0.005 0.063 6038 Dihedral : 18.701 167.856 6270 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 3.26 % Allowed : 14.39 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4148 helix: 0.39 (0.13), residues: 1754 sheet: 0.01 (0.26), residues: 405 loop : -1.07 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 731 TYR 0.016 0.002 TYR P 277 PHE 0.017 0.001 PHE C1025 TRP 0.024 0.002 TRP M 87 HIS 0.014 0.001 HIS P 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (36703) covalent geometry : angle 0.65654 / 0.35 (50198) hydrogen bonds : bond 0.04727 / 5.07 ( 1583) hydrogen bonds : angle 5.24790 / 6.74 ( 4404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 329 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8395 (mmm) cc_final: 0.8143 (mmm) REVERT: A 75 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8553 (tm-30) REVERT: B 10 LYS cc_start: 0.8672 (mmpt) cc_final: 0.7739 (tmtt) REVERT: B 41 ASN cc_start: 0.9171 (t0) cc_final: 0.8824 (t0) REVERT: B 56 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6856 (p) REVERT: B 68 TYR cc_start: 0.8450 (m-80) cc_final: 0.7851 (m-80) REVERT: B 202 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.9003 (m) REVERT: C 85 CYS cc_start: 0.8664 (m) cc_final: 0.8163 (m) REVERT: C 207 THR cc_start: 0.8803 (m) cc_final: 0.8503 (p) REVERT: C 369 MET cc_start: 0.8839 (tmm) cc_final: 0.8600 (tmm) REVERT: C 448 LEU cc_start: 0.8897 (mt) cc_final: 0.8560 (mt) REVERT: C 653 MET cc_start: 0.8251 (tpp) cc_final: 0.8018 (tpt) REVERT: C 667 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9340 (mm) REVERT: C 1013 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8989 (mt0) REVERT: C 1025 PHE cc_start: 0.8418 (t80) cc_final: 0.7950 (m-80) REVERT: C 1250 SER cc_start: 0.9037 (p) cc_final: 0.8357 (p) REVERT: C 1279 GLU cc_start: 0.9079 (pt0) cc_final: 0.8807 (pt0) REVERT: D 28 ASP cc_start: 0.8473 (m-30) cc_final: 0.8041 (p0) REVERT: D 151 MET cc_start: 0.6816 (pmm) cc_final: 0.6259 (pmm) REVERT: D 180 MET cc_start: 0.7067 (mmm) cc_final: 0.6556 (mmm) REVERT: D 301 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8352 (tp30) REVERT: D 304 ASP cc_start: 0.8584 (m-30) cc_final: 0.8351 (m-30) REVERT: D 615 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: D 932 MET cc_start: 0.5025 (mmp) cc_final: 0.4680 (tpp) REVERT: D 999 TYR cc_start: 0.6878 (t80) cc_final: 0.6601 (t80) REVERT: D 1189 MET cc_start: 0.9131 (tpp) cc_final: 0.8580 (tpt) REVERT: E 5 THR cc_start: 0.5107 (p) cc_final: 0.4021 (p) REVERT: E 35 LYS cc_start: 0.8867 (mptt) cc_final: 0.8650 (mmtp) REVERT: E 43 ASN cc_start: 0.7507 (t0) cc_final: 0.7275 (t0) REVERT: F 100 MET cc_start: 0.8436 (ppp) cc_final: 0.8172 (ptp) REVERT: F 273 MET cc_start: 0.8953 (tpt) cc_final: 0.8260 (tpt) REVERT: F 276 MET cc_start: 0.8881 (ppp) cc_final: 0.8562 (ppp) REVERT: F 288 MET cc_start: 0.4731 (mpp) cc_final: 0.4036 (mpp) REVERT: F 379 MET cc_start: 0.9141 (tmm) cc_final: 0.8929 (tpp) REVERT: F 455 HIS cc_start: 0.6940 (t-90) cc_final: 0.6272 (t70) REVERT: F 470 MET cc_start: 0.8397 (mmp) cc_final: 0.7618 (mmt) REVERT: F 473 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: F 567 MET cc_start: 0.7985 (mpp) cc_final: 0.7774 (mpp) REVERT: G 35 LEU cc_start: 0.9547 (mt) cc_final: 0.9178 (pp) REVERT: G 117 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8323 (tpt90) REVERT: N 63 HIS cc_start: 0.9165 (t-90) cc_final: 0.8539 (t-90) outliers start: 116 outliers final: 60 residues processed: 423 average time/residue: 0.2106 time to fit residues: 145.2637 Evaluate side-chains 329 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 264 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 615 LYS Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1106 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 87 TRP Chi-restraints excluded: chain N residue 70 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 343 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 112 optimal weight: 0.0770 chunk 374 optimal weight: 0.0000 chunk 300 optimal weight: 50.0000 chunk 269 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.090544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063073 restraints weight = 158066.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065070 restraints weight = 92526.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065300 restraints weight = 56646.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065601 restraints weight = 46980.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065665 restraints weight = 45654.837| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36703 Z= 0.133 Angle : 0.605 10.881 50198 Z= 0.322 Chirality : 0.044 0.341 5726 Planarity : 0.004 0.061 6038 Dihedral : 18.640 170.076 6256 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 3.32 % Allowed : 15.13 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.51 (0.13), residues: 4148 helix: 0.45 (0.13), residues: 1754 sheet: -0.09 (0.26), residues: 404 loop : -1.07 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 779 TYR 0.034 0.001 TYR P 277 PHE 0.011 0.001 PHE C 505 TRP 0.028 0.002 TRP M 87 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (36703) covalent geometry : angle 0.60550 / 0.32 (50198) hydrogen bonds : bond 0.04150 / 4.43 ( 1583) hydrogen bonds : angle 4.97601 / 6.41 ( 4404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 293 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 10 LYS cc_start: 0.8676 (mmpt) cc_final: 0.7750 (tmtt) REVERT: B 41 ASN cc_start: 0.9145 (t0) cc_final: 0.8801 (t0) REVERT: B 56 VAL cc_start: 0.6905 (OUTLIER) cc_final: 0.6655 (p) REVERT: B 68 TYR cc_start: 0.8445 (m-80) cc_final: 0.8001 (m-80) REVERT: B 142 MET cc_start: 0.8361 (pmm) cc_final: 0.8040 (pmm) REVERT: C 32 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8861 (mm) REVERT: C 85 CYS cc_start: 0.8601 (m) cc_final: 0.8275 (m) REVERT: C 246 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6125 (pt) REVERT: C 448 LEU cc_start: 0.8863 (mt) cc_final: 0.8507 (mt) REVERT: C 667 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9320 (mm) REVERT: C 1013 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9027 (mp10) REVERT: C 1025 PHE cc_start: 0.8303 (t80) cc_final: 0.7877 (m-80) REVERT: C 1279 GLU cc_start: 0.9068 (pt0) cc_final: 0.8820 (pt0) REVERT: D 28 ASP cc_start: 0.8495 (m-30) cc_final: 0.8004 (p0) REVERT: D 151 MET cc_start: 0.6824 (pmm) cc_final: 0.6186 (pmm) REVERT: D 180 MET cc_start: 0.6877 (mmm) cc_final: 0.6411 (mmm) REVERT: D 301 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8351 (tp30) REVERT: D 304 ASP cc_start: 0.8561 (m-30) cc_final: 0.8337 (m-30) REVERT: D 348 ASP cc_start: 0.8718 (t0) cc_final: 0.8331 (t0) REVERT: D 743 MET cc_start: 0.6225 (ppp) cc_final: 0.5897 (ppp) REVERT: D 932 MET cc_start: 0.4966 (mmt) cc_final: 0.4667 (tpp) REVERT: D 1189 MET cc_start: 0.9162 (tpp) cc_final: 0.8581 (tpt) REVERT: E 35 LYS cc_start: 0.8873 (mptt) cc_final: 0.8612 (mmtp) REVERT: E 43 ASN cc_start: 0.7520 (t0) cc_final: 0.7303 (t0) REVERT: F 100 MET cc_start: 0.8441 (ppp) cc_final: 0.8132 (ptp) REVERT: F 273 MET cc_start: 0.8933 (tpt) cc_final: 0.8151 (tpt) REVERT: F 276 MET cc_start: 0.8921 (ppp) cc_final: 0.8569 (ppp) REVERT: F 379 MET cc_start: 0.9162 (tmm) cc_final: 0.8951 (tpp) REVERT: F 470 MET cc_start: 0.8373 (mmp) cc_final: 0.7538 (mmt) REVERT: F 473 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: G 34 GLU cc_start: 0.8922 (tp30) cc_final: 0.8509 (pt0) REVERT: G 35 LEU cc_start: 0.9564 (mt) cc_final: 0.9204 (pp) REVERT: G 117 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8356 (tpt90) outliers start: 118 outliers final: 56 residues processed: 395 average time/residue: 0.2033 time to fit residues: 133.4903 Evaluate side-chains 318 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 923 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1106 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 87 TRP Chi-restraints excluded: chain N residue 70 TYR Chi-restraints excluded: chain N residue 110 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 256 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 25 optimal weight: 0.1980 chunk 1 optimal weight: 50.0000 chunk 73 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 399 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN C1313 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN N 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.089116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060796 restraints weight = 156317.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062394 restraints weight = 85718.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063437 restraints weight = 59202.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064090 restraints weight = 47365.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064425 restraints weight = 41588.663| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36703 Z= 0.169 Angle : 0.612 10.218 50198 Z= 0.324 Chirality : 0.043 0.255 5726 Planarity : 0.004 0.062 6038 Dihedral : 18.640 172.081 6250 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 3.32 % Allowed : 16.31 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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 (0.13), residues: 4148 helix: 0.54 (0.13), residues: 1750 sheet: -0.11 (0.27), residues: 394 loop : -1.09 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG G 118 TYR 0.046 0.001 TYR P 277 PHE 0.024 0.001 PHE C 230 TRP 0.025 0.002 TRP M 87 HIS 0.008 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (36703) covalent geometry : angle 0.61224 / 0.32 (50198) hydrogen bonds : bond 0.04021 / 4.29 ( 1583) hydrogen bonds : angle 4.84091 / 6.21 ( 4404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 275 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8242 (mmp) cc_final: 0.8030 (mmm) REVERT: A 75 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 10 LYS cc_start: 0.8686 (mmpt) cc_final: 0.7883 (tmtt) REVERT: B 41 ASN cc_start: 0.9149 (t0) cc_final: 0.8845 (t0) REVERT: B 56 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.7045 (p) REVERT: B 68 TYR cc_start: 0.8338 (m-80) cc_final: 0.7938 (m-80) REVERT: C 32 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 85 CYS cc_start: 0.8606 (m) cc_final: 0.8265 (m) REVERT: C 246 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5963 (pt) REVERT: C 465 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7834 (ttm-80) REVERT: C 667 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9334 (mm) REVERT: C 996 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8453 (mmm160) REVERT: D 151 MET cc_start: 0.6799 (pmm) cc_final: 0.6174 (pmm) REVERT: D 180 MET cc_start: 0.6945 (mmm) cc_final: 0.6512 (mmm) REVERT: D 301 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8373 (tp30) REVERT: D 414 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: D 423 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8930 (mp) REVERT: D 743 MET cc_start: 0.6518 (ppp) cc_final: 0.6230 (ppp) REVERT: D 932 MET cc_start: 0.5091 (mmt) cc_final: 0.4741 (tpp) REVERT: E 35 LYS cc_start: 0.8805 (mptt) cc_final: 0.8561 (mmtp) REVERT: F 100 MET cc_start: 0.8472 (ppp) cc_final: 0.8182 (ptp) REVERT: F 273 MET cc_start: 0.8924 (tpt) cc_final: 0.8045 (tpt) REVERT: F 276 MET cc_start: 0.8945 (ppp) cc_final: 0.8454 (ppp) REVERT: F 277 MET cc_start: 0.8730 (tpt) cc_final: 0.8214 (tpt) REVERT: F 470 MET cc_start: 0.8302 (mmp) cc_final: 0.7186 (mmt) REVERT: F 473 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: F 561 MET cc_start: 0.9140 (tpt) cc_final: 0.8934 (tpt) REVERT: G 117 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8220 (tpt90) REVERT: N 78 ASP cc_start: 0.9350 (t0) cc_final: 0.8765 (m-30) REVERT: P 277 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7379 (t80) outliers start: 118 outliers final: 74 residues processed: 372 average time/residue: 0.1992 time to fit residues: 124.1767 Evaluate side-chains 329 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 87 TRP Chi-restraints excluded: chain N residue 70 TYR Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 140 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 271 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 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 = 0.3834 r_free = 0.3834 target = 0.089164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061817 restraints weight = 154927.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063519 restraints weight = 92422.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063904 restraints weight = 58772.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064540 restraints weight = 46854.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064437 restraints weight = 44257.818| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36703 Z= 0.149 Angle : 0.603 12.004 50198 Z= 0.317 Chirality : 0.043 0.254 5726 Planarity : 0.004 0.056 6038 Dihedral : 18.620 171.719 6250 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 3.26 % Allowed : 16.73 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.43 (0.13), residues: 4148 helix: 0.61 (0.13), residues: 1749 sheet: -0.13 (0.26), residues: 397 loop : -1.10 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 247 TYR 0.025 0.001 TYR P 277 PHE 0.013 0.001 PHE C 505 TRP 0.029 0.002 TRP M 87 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (36703) covalent geometry : angle 0.60309 / 0.32 (50198) hydrogen bonds : bond 0.03838 / 4.07 ( 1583) hydrogen bonds : angle 4.76117 / 6.11 ( 4404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 273 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8539 (tm-30) REVERT: B 10 LYS cc_start: 0.8690 (mmpt) cc_final: 0.7894 (tmtt) REVERT: B 41 ASN cc_start: 0.9196 (t0) cc_final: 0.8874 (t0) REVERT: B 56 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6981 (p) REVERT: B 68 TYR cc_start: 0.8492 (m-80) cc_final: 0.8056 (m-80) REVERT: C 32 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 85 CYS cc_start: 0.8618 (m) cc_final: 0.8240 (m) REVERT: C 246 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6116 (pt) REVERT: C 448 LEU cc_start: 0.8800 (mt) cc_final: 0.8558 (mt) REVERT: C 465 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7790 (ttm-80) REVERT: C 667 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9353 (mm) REVERT: C 996 ARG cc_start: 0.8966 (mmm160) cc_final: 0.8634 (mmm160) REVERT: C 1119 MET cc_start: 0.9170 (tpp) cc_final: 0.8925 (tpp) REVERT: D 151 MET cc_start: 0.6858 (pmm) cc_final: 0.6151 (pmm) REVERT: D 180 MET cc_start: 0.6953 (mmm) cc_final: 0.6525 (mmm) REVERT: D 301 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8391 (tp30) REVERT: D 348 ASP cc_start: 0.8749 (t0) cc_final: 0.8213 (t0) REVERT: D 743 MET cc_start: 0.6380 (ppp) cc_final: 0.6065 (ppp) REVERT: D 929 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 932 MET cc_start: 0.5000 (mmt) cc_final: 0.4684 (tpp) REVERT: D 1025 MET cc_start: 0.8315 (mmm) cc_final: 0.8108 (mmp) REVERT: E 35 LYS cc_start: 0.8864 (mptt) cc_final: 0.8600 (mmtp) REVERT: F 100 MET cc_start: 0.8560 (ppp) cc_final: 0.8230 (ptp) REVERT: F 273 MET cc_start: 0.8928 (tpt) cc_final: 0.8575 (tpt) REVERT: F 458 GLU cc_start: 0.8282 (pp20) cc_final: 0.8033 (pp20) REVERT: F 470 MET cc_start: 0.8387 (mmp) cc_final: 0.7924 (mmp) REVERT: F 561 MET cc_start: 0.9230 (tpt) cc_final: 0.8909 (tpt) REVERT: G 117 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8184 (tpt90) REVERT: J 40 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.8273 (ptp-110) REVERT: N 63 HIS cc_start: 0.9241 (t-90) cc_final: 0.8625 (t-90) REVERT: P 277 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7256 (t80) outliers start: 116 outliers final: 71 residues processed: 371 average time/residue: 0.2125 time to fit residues: 132.0799 Evaluate side-chains 327 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 250 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain N residue 70 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 277 optimal weight: 0.6980 chunk 300 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 422 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 322 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 264 optimal weight: 30.0000 chunk 298 optimal weight: 40.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 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 = 0.3811 r_free = 0.3811 target = 0.087997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059330 restraints weight = 156215.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060819 restraints weight = 87449.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061845 restraints weight = 61360.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062476 restraints weight = 49599.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062733 restraints weight = 43799.107| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36703 Z= 0.195 Angle : 0.634 11.437 50198 Z= 0.335 Chirality : 0.044 0.258 5726 Planarity : 0.004 0.055 6038 Dihedral : 18.650 171.606 6250 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 3.43 % Allowed : 17.21 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.45 (0.13), residues: 4148 helix: 0.62 (0.13), residues: 1752 sheet: -0.39 (0.25), residues: 436 loop : -1.09 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 85 TYR 0.026 0.001 TYR P 277 PHE 0.014 0.001 PHE C 505 TRP 0.063 0.002 TRP J 87 HIS 0.009 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (36703) covalent geometry : angle 0.63409 / 0.33 (50198) hydrogen bonds : bond 0.04052 / 4.32 ( 1583) hydrogen bonds : angle 4.76665 / 6.16 ( 4404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 259 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 10 LYS cc_start: 0.8695 (mmpt) cc_final: 0.7967 (tmtt) REVERT: B 41 ASN cc_start: 0.9143 (t0) cc_final: 0.8885 (t0) REVERT: B 68 TYR cc_start: 0.8373 (m-80) cc_final: 0.7869 (m-80) REVERT: C 85 CYS cc_start: 0.8605 (m) cc_final: 0.8267 (m) REVERT: C 177 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9340 (pt) REVERT: C 465 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7784 (ttm-80) REVERT: C 667 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9366 (mm) REVERT: C 996 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8458 (mmm160) REVERT: C 1119 MET cc_start: 0.9089 (tpp) cc_final: 0.8869 (tpp) REVERT: D 151 MET cc_start: 0.6866 (pmm) cc_final: 0.6188 (pmm) REVERT: D 180 MET cc_start: 0.7104 (mmm) cc_final: 0.6668 (mmm) REVERT: D 301 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8338 (tp30) REVERT: D 423 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 743 MET cc_start: 0.6576 (ppp) cc_final: 0.6304 (ppp) REVERT: D 929 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7556 (tm-30) REVERT: D 930 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (pp) REVERT: D 932 MET cc_start: 0.4751 (mmt) cc_final: 0.4449 (tpp) REVERT: D 1189 MET cc_start: 0.9141 (tpp) cc_final: 0.8655 (tpt) REVERT: E 44 ASP cc_start: 0.5486 (m-30) cc_final: 0.5072 (m-30) REVERT: F 100 MET cc_start: 0.8518 (ppp) cc_final: 0.8228 (ptp) REVERT: F 273 MET cc_start: 0.9110 (tpt) cc_final: 0.8818 (tpt) REVERT: F 379 MET cc_start: 0.9307 (tpp) cc_final: 0.9059 (tpp) REVERT: F 474 MET cc_start: 0.7762 (mtm) cc_final: 0.7560 (mtp) REVERT: F 538 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8100 (tm-30) REVERT: G 35 LEU cc_start: 0.9510 (mt) cc_final: 0.9123 (pp) REVERT: J 40 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8296 (ptp-110) REVERT: P 277 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 122 outliers final: 81 residues processed: 366 average time/residue: 0.2009 time to fit residues: 122.1703 Evaluate side-chains 329 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain N residue 70 TYR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 289 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 395 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.087217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059355 restraints weight = 157876.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061295 restraints weight = 91441.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.061510 restraints weight = 56632.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061661 restraints weight = 46145.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061728 restraints weight = 47106.633| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36703 Z= 0.207 Angle : 0.645 12.050 50198 Z= 0.340 Chirality : 0.044 0.274 5726 Planarity : 0.004 0.058 6038 Dihedral : 18.710 171.246 6250 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 3.74 % Allowed : 17.68 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.44 (0.13), residues: 4148 helix: 0.62 (0.13), residues: 1755 sheet: -0.29 (0.25), residues: 430 loop : -1.11 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.023 0.001 TYR P 277 PHE 0.026 0.001 PHE F 256 TRP 0.047 0.002 TRP J 87 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (36703) covalent geometry : angle 0.64506 / 0.34 (50198) hydrogen bonds : bond 0.04048 / 4.29 ( 1583) hydrogen bonds : angle 4.78921 / 6.20 ( 4404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 255 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 10 LYS cc_start: 0.8686 (mmpt) cc_final: 0.7983 (tmtt) REVERT: B 41 ASN cc_start: 0.9160 (t0) cc_final: 0.8896 (t0) REVERT: B 68 TYR cc_start: 0.8480 (m-80) cc_final: 0.7920 (m-80) REVERT: C 85 CYS cc_start: 0.8663 (m) cc_final: 0.8306 (m) REVERT: C 246 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6241 (pt) REVERT: C 465 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7824 (ttm-80) REVERT: C 667 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9361 (mm) REVERT: C 800 MET cc_start: 0.8660 (pmm) cc_final: 0.8102 (ptp) REVERT: C 996 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8625 (mmm160) REVERT: C 1066 MET cc_start: 0.8097 (mtp) cc_final: 0.7872 (mtp) REVERT: C 1304 MET cc_start: 0.8706 (tpp) cc_final: 0.8459 (ttm) REVERT: D 151 MET cc_start: 0.6872 (pmm) cc_final: 0.6160 (pmm) REVERT: D 180 MET cc_start: 0.7131 (mmm) cc_final: 0.6724 (mmm) REVERT: D 301 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8348 (tp30) REVERT: D 423 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8820 (mp) REVERT: D 929 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 930 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8505 (pp) REVERT: D 932 MET cc_start: 0.4880 (mmt) cc_final: 0.4503 (tpp) REVERT: D 1040 MET cc_start: 0.5486 (ptm) cc_final: 0.4506 (ptp) REVERT: D 1074 LEU cc_start: 0.1546 (OUTLIER) cc_final: 0.1067 (mt) REVERT: D 1189 MET cc_start: 0.9165 (tpp) cc_final: 0.8753 (tpt) REVERT: F 100 MET cc_start: 0.8485 (ppp) cc_final: 0.8167 (ptp) REVERT: F 105 MET cc_start: 0.8864 (ppp) cc_final: 0.8652 (tmm) REVERT: F 273 MET cc_start: 0.9058 (tpt) cc_final: 0.8757 (tpt) REVERT: F 379 MET cc_start: 0.9394 (tpp) cc_final: 0.9176 (tpp) REVERT: F 538 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8114 (tm-30) REVERT: F 561 MET cc_start: 0.9216 (tpt) cc_final: 0.8920 (tpt) REVERT: G 64 LEU cc_start: 0.8869 (mt) cc_final: 0.8661 (mt) REVERT: J 40 ARG cc_start: 0.8629 (ptp-110) cc_final: 0.8419 (ptp-110) REVERT: P 277 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7542 (t80) outliers start: 133 outliers final: 94 residues processed: 371 average time/residue: 0.1940 time to fit residues: 120.7626 Evaluate side-chains 337 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 236 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1074 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 259 optimal weight: 20.0000 chunk 426 optimal weight: 0.0050 chunk 230 optimal weight: 0.5980 chunk 401 optimal weight: 9.9990 chunk 371 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN F 406 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.088880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060256 restraints weight = 156268.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061860 restraints weight = 86776.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062905 restraints weight = 60419.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063481 restraints weight = 48711.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063750 restraints weight = 43123.723| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36703 Z= 0.118 Angle : 0.624 13.278 50198 Z= 0.323 Chirality : 0.043 0.268 5726 Planarity : 0.004 0.058 6038 Dihedral : 18.671 170.387 6248 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 2.92 % Allowed : 18.50 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.37 (0.13), residues: 4148 helix: 0.66 (0.13), residues: 1756 sheet: -0.14 (0.26), residues: 408 loop : -1.07 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 33 TYR 0.022 0.001 TYR P 277 PHE 0.022 0.001 PHE F 256 TRP 0.039 0.002 TRP J 87 HIS 0.056 0.001 HIS C1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (36703) covalent geometry : angle 0.62389 / 0.32 (50198) hydrogen bonds : bond 0.03655 / 3.88 ( 1583) hydrogen bonds : angle 4.60501 / 5.97 ( 4404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 274 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 10 LYS cc_start: 0.8677 (mmpt) cc_final: 0.7955 (tmtt) REVERT: B 41 ASN cc_start: 0.9201 (t0) cc_final: 0.8816 (t0) REVERT: B 56 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6519 (p) REVERT: B 68 TYR cc_start: 0.8468 (m-80) cc_final: 0.7929 (m-80) REVERT: B 185 TYR cc_start: 0.9291 (p90) cc_final: 0.8863 (p90) REVERT: C 85 CYS cc_start: 0.8632 (m) cc_final: 0.8226 (m) REVERT: C 246 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.5911 (pt) REVERT: C 465 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7772 (ttm-80) REVERT: C 667 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9346 (mm) REVERT: C 800 MET cc_start: 0.8623 (pmm) cc_final: 0.7918 (ptp) REVERT: C 996 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8468 (mmm160) REVERT: C 1066 MET cc_start: 0.8068 (mtp) cc_final: 0.7849 (mtp) REVERT: D 151 MET cc_start: 0.6772 (pmm) cc_final: 0.6054 (pmm) REVERT: D 180 MET cc_start: 0.7094 (mmm) cc_final: 0.6701 (mmm) REVERT: D 301 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8306 (tp30) REVERT: D 579 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8794 (tm) REVERT: D 604 MET cc_start: 0.9351 (ppp) cc_final: 0.8958 (tmm) REVERT: D 929 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7631 (tm-30) REVERT: D 932 MET cc_start: 0.4725 (mmt) cc_final: 0.4420 (tpp) REVERT: D 1040 MET cc_start: 0.5138 (ptm) cc_final: 0.4469 (ptp) REVERT: D 1074 LEU cc_start: 0.1946 (OUTLIER) cc_final: 0.1465 (mt) REVERT: D 1189 MET cc_start: 0.9152 (tpp) cc_final: 0.8723 (tpt) REVERT: E 44 ASP cc_start: 0.5231 (m-30) cc_final: 0.4965 (m-30) REVERT: F 100 MET cc_start: 0.8529 (ppp) cc_final: 0.8168 (ptp) REVERT: F 273 MET cc_start: 0.9094 (tpt) cc_final: 0.8828 (tpt) REVERT: F 379 MET cc_start: 0.9460 (tpp) cc_final: 0.9233 (tpp) REVERT: F 456 MET cc_start: 0.8324 (mmp) cc_final: 0.7858 (mmp) REVERT: F 538 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8202 (tm-30) REVERT: F 561 MET cc_start: 0.9172 (tpt) cc_final: 0.8816 (tpt) REVERT: G 35 LEU cc_start: 0.9509 (mt) cc_final: 0.9150 (pp) REVERT: G 64 LEU cc_start: 0.8916 (mt) cc_final: 0.8705 (mt) REVERT: J 62 LYS cc_start: 0.9349 (tttt) cc_final: 0.9041 (tmtt) REVERT: P 277 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7546 (t80) outliers start: 104 outliers final: 73 residues processed: 360 average time/residue: 0.1977 time to fit residues: 119.5393 Evaluate side-chains 327 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 247 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1074 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 110 TYR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 327 optimal weight: 4.9990 chunk 411 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 chunk 276 optimal weight: 0.0270 chunk 325 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 404 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 716 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.087257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058821 restraints weight = 155972.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060350 restraints weight = 87434.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.061344 restraints weight = 61181.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061940 restraints weight = 49437.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062293 restraints weight = 43721.693| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36703 Z= 0.183 Angle : 0.663 17.363 50198 Z= 0.342 Chirality : 0.044 0.290 5726 Planarity : 0.004 0.076 6038 Dihedral : 18.697 175.904 6246 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 2.50 % Allowed : 19.51 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.35 (0.13), residues: 4148 helix: 0.66 (0.13), residues: 1762 sheet: -0.23 (0.26), residues: 415 loop : -1.03 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 40 TYR 0.022 0.001 TYR P 277 PHE 0.026 0.001 PHE C1025 TRP 0.035 0.002 TRP J 87 HIS 0.010 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (36703) covalent geometry : angle 0.66303 / 0.34 (50198) hydrogen bonds : bond 0.03950 / 4.27 ( 1583) hydrogen bonds : angle 4.69403 / 6.12 ( 4404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 255 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8208 (mmp) cc_final: 0.7946 (mmm) REVERT: A 75 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 136 GLU cc_start: 0.8134 (pm20) cc_final: 0.7922 (pm20) REVERT: B 10 LYS cc_start: 0.8707 (mmpt) cc_final: 0.8005 (tmtt) REVERT: B 41 ASN cc_start: 0.9124 (t0) cc_final: 0.8879 (t0) REVERT: B 56 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6873 (p) REVERT: B 68 TYR cc_start: 0.8377 (m-80) cc_final: 0.7897 (m-80) REVERT: C 85 CYS cc_start: 0.8609 (m) cc_final: 0.8262 (m) REVERT: C 177 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9329 (pt) REVERT: C 246 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6209 (pt) REVERT: C 465 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7859 (ttm-80) REVERT: C 667 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9375 (mm) REVERT: C 800 MET cc_start: 0.8628 (pmm) cc_final: 0.8069 (ptp) REVERT: C 996 ARG cc_start: 0.8765 (mmm160) cc_final: 0.8375 (mmm160) REVERT: C 1119 MET cc_start: 0.9121 (tpp) cc_final: 0.8912 (tpp) REVERT: D 136 GLU cc_start: 0.8247 (tp30) cc_final: 0.7970 (tm-30) REVERT: D 151 MET cc_start: 0.6703 (pmm) cc_final: 0.5953 (pmm) REVERT: D 180 MET cc_start: 0.7272 (mmm) cc_final: 0.6862 (mmm) REVERT: D 301 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8384 (tm-30) REVERT: D 579 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8829 (tm) REVERT: D 743 MET cc_start: 0.6530 (ppp) cc_final: 0.6292 (ppp) REVERT: D 929 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 932 MET cc_start: 0.4757 (mmt) cc_final: 0.4429 (tpp) REVERT: D 1074 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.1128 (mt) REVERT: D 1189 MET cc_start: 0.9115 (tpp) cc_final: 0.8700 (tpt) REVERT: F 100 MET cc_start: 0.8456 (ppp) cc_final: 0.8171 (ptp) REVERT: F 273 MET cc_start: 0.9073 (tpt) cc_final: 0.8790 (tpt) REVERT: F 379 MET cc_start: 0.9412 (tpp) cc_final: 0.9199 (tpp) REVERT: F 538 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8064 (tm-30) REVERT: F 561 MET cc_start: 0.9127 (tpt) cc_final: 0.8737 (tpt) REVERT: J 62 LYS cc_start: 0.9376 (tttt) cc_final: 0.9072 (tmtt) REVERT: N 34 GLU cc_start: 0.7872 (tp30) cc_final: 0.7474 (mm-30) REVERT: P 277 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7588 (t80) outliers start: 89 outliers final: 71 residues processed: 329 average time/residue: 0.1975 time to fit residues: 108.1574 Evaluate side-chains 326 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 247 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1074 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 73 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 368 optimal weight: 0.6980 chunk 285 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 421 optimal weight: 0.5980 chunk 294 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 292 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN P 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.088645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060020 restraints weight = 156823.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061592 restraints weight = 86812.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062621 restraints weight = 60512.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063250 restraints weight = 48832.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063538 restraints weight = 43131.326| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36703 Z= 0.121 Angle : 0.649 19.629 50198 Z= 0.333 Chirality : 0.043 0.316 5726 Planarity : 0.004 0.052 6038 Dihedral : 18.673 179.007 6246 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.14 % Allowed : 20.10 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.33 (0.13), residues: 4148 helix: 0.66 (0.13), residues: 1762 sheet: 0.00 (0.27), residues: 381 loop : -1.04 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 82 TYR 0.021 0.001 TYR P 277 PHE 0.018 0.001 PHE F 256 TRP 0.034 0.002 TRP J 87 HIS 0.011 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (36703) covalent geometry : angle 0.64913 / 0.33 (50198) hydrogen bonds : bond 0.03606 / 3.86 ( 1583) hydrogen bonds : angle 4.57950 / 5.96 ( 4404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8296 Ramachandran restraints generated. 4148 Oldfield, 0 Emsley, 4148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 10 LYS cc_start: 0.8713 (mmpt) cc_final: 0.8002 (tmtt) REVERT: B 41 ASN cc_start: 0.9182 (t0) cc_final: 0.8846 (t0) REVERT: B 68 TYR cc_start: 0.8468 (m-80) cc_final: 0.7938 (m-80) REVERT: B 185 TYR cc_start: 0.9307 (p90) cc_final: 0.8867 (p90) REVERT: C 85 CYS cc_start: 0.8647 (m) cc_final: 0.8247 (m) REVERT: C 246 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5876 (pt) REVERT: C 465 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7789 (ttm-80) REVERT: C 667 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9346 (mm) REVERT: C 800 MET cc_start: 0.8658 (pmm) cc_final: 0.8019 (ptp) REVERT: C 996 ARG cc_start: 0.8823 (mmm160) cc_final: 0.8425 (mmm160) REVERT: C 1119 MET cc_start: 0.9212 (tpp) cc_final: 0.8619 (tpp) REVERT: D 136 GLU cc_start: 0.8344 (tp30) cc_final: 0.7990 (tm-30) REVERT: D 151 MET cc_start: 0.6681 (pmm) cc_final: 0.5886 (pmm) REVERT: D 180 MET cc_start: 0.7174 (mmm) cc_final: 0.6732 (mmm) REVERT: D 301 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8270 (tp30) REVERT: D 579 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8737 (tm) REVERT: D 604 MET cc_start: 0.9346 (ppp) cc_final: 0.8964 (tmm) REVERT: D 743 MET cc_start: 0.6330 (ppp) cc_final: 0.6007 (ppp) REVERT: D 929 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7629 (tm-30) REVERT: D 932 MET cc_start: 0.4748 (mmt) cc_final: 0.4431 (tpp) REVERT: D 1040 MET cc_start: 0.5415 (ptm) cc_final: 0.4823 (ptp) REVERT: D 1074 LEU cc_start: 0.1806 (OUTLIER) cc_final: 0.1356 (mt) REVERT: E 44 ASP cc_start: 0.6720 (m-30) cc_final: 0.6464 (m-30) REVERT: F 100 MET cc_start: 0.8536 (ppp) cc_final: 0.8187 (ptp) REVERT: F 273 MET cc_start: 0.9081 (tpt) cc_final: 0.8815 (tpt) REVERT: F 379 MET cc_start: 0.9489 (tpp) cc_final: 0.9271 (tpp) REVERT: F 472 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7188 (mp10) REVERT: F 538 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8195 (tm-30) REVERT: F 561 MET cc_start: 0.9172 (tpt) cc_final: 0.8816 (tpt) REVERT: G 64 LEU cc_start: 0.8899 (mt) cc_final: 0.8636 (mt) REVERT: J 40 ARG cc_start: 0.8826 (mtt180) cc_final: 0.8607 (mtm180) REVERT: J 62 LYS cc_start: 0.9350 (tttt) cc_final: 0.9041 (tmtt) REVERT: N 34 GLU cc_start: 0.7806 (tp30) cc_final: 0.7435 (mm-30) REVERT: P 277 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7571 (t80) outliers start: 76 outliers final: 66 residues processed: 327 average time/residue: 0.2100 time to fit residues: 115.4129 Evaluate side-chains 328 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1105 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 844 THR Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1074 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain N residue 71 ILE Chi-restraints excluded: chain N residue 91 ASN Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 277 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 290 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 82 optimal weight: 0.1980 chunk 140 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 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 = 0.3822 r_free = 0.3822 target = 0.088616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059898 restraints weight = 154389.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061567 restraints weight = 81686.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062651 restraints weight = 55561.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063252 restraints weight = 44114.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063680 restraints weight = 38753.492| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36703 Z= 0.124 Angle : 0.649 18.615 50198 Z= 0.332 Chirality : 0.043 0.325 5726 Planarity : 0.004 0.060 6038 Dihedral : 18.664 177.668 6245 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 20.35 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4148 helix: 0.67 (0.13), residues: 1767 sheet: 0.04 (0.27), residues: 381 loop : -1.02 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 117 TYR 0.020 0.001 TYR P 277 PHE 0.026 0.001 PHE C 230 TRP 0.066 0.002 TRP G 87 HIS 0.011 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (36703) covalent geometry : angle 0.64936 / 0.33 (50198) hydrogen bonds : bond 0.03581 / 3.85 ( 1583) hydrogen bonds : angle 4.54865 / 5.92 ( 4404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7272.99 seconds wall clock time: 125 minutes 54.07 seconds (7554.07 seconds total)