Starting phenix.real_space_refine on Sat Feb 7 21:57:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0y_62728/02_2026/9l0y_62728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0y_62728/02_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_62728/02_2026/9l0y_62728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0y_62728/02_2026/9l0y_62728.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0y_62728/02_2026/9l0y_62728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0y_62728/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 7.78, per 1000 atoms: 0.22 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: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.82 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: 10.07 Time building geometry restraints manager: 4.05 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=" C PHE J 28 " pdb=" N PRO J 29 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" CA GLY D 173 " pdb=" C GLY D 173 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.19e+00 bond pdb=" N GLY D 173 " pdb=" CA GLY D 173 " ideal model delta sigma weight residual 1.464 1.449 0.015 1.12e-02 7.97e+03 1.90e+00 bond pdb=" CA LYS F 324 " pdb=" C LYS F 324 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.65e+00 bond pdb=" CB PRO N 72 " pdb=" CG PRO N 72 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.29e+00 ... (remaining 36698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 49283 1.77 - 3.54: 823 3.54 - 5.31: 68 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=" 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 angle pdb=" N SER F 602 " pdb=" CA SER F 602 " pdb=" C SER F 602 " ideal model delta sigma weight residual 114.04 109.13 4.91 1.24e+00 6.50e-01 1.57e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 111.67 107.95 3.72 9.50e-01 1.11e+00 1.53e+01 angle pdb=" N VAL E 4 " pdb=" CA VAL E 4 " pdb=" C VAL E 4 " ideal model delta sigma weight residual 113.42 109.39 4.03 1.17e+00 7.31e-01 1.19e+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: 3625 0.032 - 0.063: 1467 0.063 - 0.095: 423 0.095 - 0.127: 195 0.127 - 0.159: 16 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=" 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 chirality pdb=" CA PRO G 72 " pdb=" N PRO G 72 " pdb=" C PRO G 72 " pdb=" CB PRO G 72 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.21e-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: 1.720 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: 0.110 Set scattering table: 0.100 Process input model: 38.380 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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= 0.127 Angle : 0.557 8.849 50198 Z= 0.314 Chirality : 0.040 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 covalent geometry : bond 0.00253 (36703) covalent geometry : angle 0.55713 (50198) hydrogen bonds : bond 0.14978 ( 1583) hydrogen bonds : angle 6.21585 ( 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 : 1.508 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: 0.2543 time to fit residues: 267.7203 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 : 1.384 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 277 ASN D 419 HIS D 450 HIS D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 461 ASN F 600 HIS N 88 ASN P 276 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.089231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061021 restraints weight = 156149.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062585 restraints weight = 87443.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063605 restraints weight = 60903.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064210 restraints weight = 48938.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064461 restraints weight = 43124.480| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 36703 Z= 0.186 Angle : 0.628 9.078 50198 Z= 0.331 Chirality : 0.043 0.198 5726 Planarity : 0.004 0.064 6038 Dihedral : 18.649 176.466 6270 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 3.43 % Allowed : 14.48 % Favored : 82.09 % 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: -0.48 (0.13), residues: 4148 helix: 0.44 (0.13), residues: 1764 sheet: -0.06 (0.26), residues: 423 loop : -1.04 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1330 TYR 0.019 0.001 TYR C1018 PHE 0.015 0.001 PHE D1274 TRP 0.033 0.002 TRP M 87 HIS 0.013 0.001 HIS P 276 Details of bonding type rmsd covalent geometry : bond 0.00417 (36703) covalent geometry : angle 0.62789 (50198) hydrogen bonds : bond 0.04423 ( 1583) hydrogen bonds : angle 5.04258 ( 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 457 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 335 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.8299 (mmm) cc_final: 0.8042 (mmm) REVERT: A 75 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8568 (tm-30) REVERT: B 10 LYS cc_start: 0.8690 (mmpt) cc_final: 0.7788 (tmtt) REVERT: B 41 ASN cc_start: 0.9177 (t0) cc_final: 0.8834 (t0) REVERT: B 56 VAL cc_start: 0.7231 (OUTLIER) cc_final: 0.6953 (p) REVERT: B 68 TYR cc_start: 0.8360 (m-80) cc_final: 0.7777 (m-80) REVERT: B 202 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.9004 (m) REVERT: C 85 CYS cc_start: 0.8606 (m) cc_final: 0.8256 (m) REVERT: C 207 THR cc_start: 0.8835 (m) cc_final: 0.8511 (p) REVERT: C 448 LEU cc_start: 0.8901 (mt) cc_final: 0.8543 (mt) REVERT: C 667 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9318 (mm) REVERT: C 996 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8461 (mmm160) REVERT: C 1279 GLU cc_start: 0.9058 (pt0) cc_final: 0.8778 (pt0) REVERT: C 1290 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8584 (mmp) REVERT: D 151 MET cc_start: 0.6849 (pmm) cc_final: 0.6260 (pmm) REVERT: D 180 MET cc_start: 0.6933 (mmm) cc_final: 0.6398 (mmm) REVERT: D 301 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8403 (tp30) REVERT: D 304 ASP cc_start: 0.8588 (m-30) cc_final: 0.8376 (m-30) REVERT: D 329 ASP cc_start: 0.8708 (m-30) cc_final: 0.8505 (m-30) REVERT: D 331 ILE cc_start: 0.9289 (tp) cc_final: 0.9082 (tp) REVERT: D 552 ILE cc_start: 0.7949 (mm) cc_final: 0.7713 (mt) REVERT: D 615 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8783 (mtpp) REVERT: D 932 MET cc_start: 0.5281 (mmt) cc_final: 0.4890 (tpp) REVERT: D 999 TYR cc_start: 0.6888 (t80) cc_final: 0.6618 (t80) REVERT: D 1286 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8438 (mtpt) REVERT: E 5 THR cc_start: 0.5086 (p) cc_final: 0.4134 (p) REVERT: E 35 LYS cc_start: 0.8839 (mptt) cc_final: 0.8593 (mmtp) REVERT: E 52 ARG cc_start: 0.8951 (mtp85) cc_final: 0.8634 (mtp85) REVERT: F 273 MET cc_start: 0.8892 (tpt) cc_final: 0.8142 (tpt) REVERT: F 276 MET cc_start: 0.8899 (ppp) cc_final: 0.8472 (ppp) REVERT: F 277 MET cc_start: 0.8735 (tpt) cc_final: 0.8278 (tpt) REVERT: F 288 MET cc_start: 0.4771 (mpp) cc_final: 0.3969 (mpp) REVERT: F 455 HIS cc_start: 0.7170 (t-90) cc_final: 0.6486 (t70) REVERT: F 470 MET cc_start: 0.8443 (mmp) cc_final: 0.7945 (mmt) outliers start: 122 outliers final: 58 residues processed: 437 average time/residue: 0.2448 time to fit residues: 172.4664 Evaluate side-chains 317 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 254 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP 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 202 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 30 ILE 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 481 LEU 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 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 1077 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1287 LEU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1322 SER 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 307 LEU 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 501 VAL 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 918 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 1243 LEU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 460 ILE 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 Chi-restraints excluded: chain P residue 270 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 343 optimal weight: 5.9990 chunk 149 optimal weight: 0.0040 chunk 112 optimal weight: 0.9980 chunk 374 optimal weight: 7.9990 chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 ASN ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1129 ASN C1313 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 HIS ** D1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 52 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.088907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061350 restraints weight = 157417.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063298 restraints weight = 91301.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063491 restraints weight = 56247.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063759 restraints weight = 47118.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063834 restraints weight = 46526.308| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36703 Z= 0.162 Angle : 0.600 9.754 50198 Z= 0.315 Chirality : 0.042 0.194 5726 Planarity : 0.004 0.069 6038 Dihedral : 18.576 178.895 6255 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 3.51 % Allowed : 16.02 % Favored : 80.46 % 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: -0.42 (0.13), residues: 4148 helix: 0.53 (0.13), residues: 1763 sheet: -0.20 (0.25), residues: 428 loop : -1.01 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 247 TYR 0.021 0.001 TYR P 277 PHE 0.012 0.001 PHE C 505 TRP 0.029 0.002 TRP M 87 HIS 0.008 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00366 (36703) covalent geometry : angle 0.60025 (50198) hydrogen bonds : bond 0.03901 ( 1583) hydrogen bonds : angle 4.82457 ( 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 407 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 282 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 10 LYS cc_start: 0.8703 (mmpt) cc_final: 0.7912 (tmtt) REVERT: B 41 ASN cc_start: 0.9194 (t0) cc_final: 0.8882 (t0) REVERT: B 56 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6874 (p) REVERT: B 68 TYR cc_start: 0.8522 (m-80) cc_final: 0.8089 (m-80) REVERT: C 85 CYS cc_start: 0.8587 (m) cc_final: 0.8250 (m) REVERT: C 207 THR cc_start: 0.8858 (m) cc_final: 0.8470 (p) REVERT: C 246 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6059 (pt) REVERT: C 369 MET cc_start: 0.9054 (tmm) cc_final: 0.8851 (tmm) REVERT: C 465 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7778 (ttm-80) REVERT: C 667 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9365 (mm) REVERT: C 1119 MET cc_start: 0.9190 (tpp) cc_final: 0.8896 (tpp) REVERT: C 1279 GLU cc_start: 0.9052 (pt0) cc_final: 0.8810 (pt0) REVERT: D 151 MET cc_start: 0.6812 (pmm) cc_final: 0.6194 (pmm) REVERT: D 180 MET cc_start: 0.6902 (mmm) cc_final: 0.6376 (mmm) REVERT: D 301 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8393 (tp30) REVERT: D 348 ASP cc_start: 0.8811 (t0) cc_final: 0.8322 (t70) REVERT: D 743 MET cc_start: 0.6510 (ppp) cc_final: 0.6183 (ppp) REVERT: D 932 MET cc_start: 0.4921 (mmt) cc_final: 0.4559 (tpp) REVERT: E 43 ASN cc_start: 0.7166 (t0) cc_final: 0.6934 (t0) REVERT: F 273 MET cc_start: 0.8912 (tpt) cc_final: 0.8483 (tpt) REVERT: F 538 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 40 ARG cc_start: 0.8433 (ptp-110) cc_final: 0.8179 (ptp-110) REVERT: N 78 ASP cc_start: 0.9378 (t0) cc_final: 0.8829 (m-30) outliers start: 125 outliers final: 68 residues processed: 385 average time/residue: 0.2270 time to fit residues: 144.4368 Evaluate side-chains 319 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 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 135 THR 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 453 ILE Chi-restraints excluded: chain C residue 465 ARG 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 878 THR Chi-restraints excluded: chain C residue 1013 GLN 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 C residue 1322 SER 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 307 LEU 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 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL 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 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 494 ILE 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 J residue 69 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain M residue 31 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 256 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 366 optimal weight: 0.0980 chunk 324 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 399 optimal weight: 10.0000 chunk 295 optimal weight: 0.0170 chunk 173 optimal weight: 7.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 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** F 131 GLN P 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.089924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061605 restraints weight = 155285.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063209 restraints weight = 85331.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064262 restraints weight = 59063.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064768 restraints weight = 47283.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065247 restraints weight = 42136.499| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2747 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= 0.118 Angle : 0.572 14.079 50198 Z= 0.297 Chirality : 0.041 0.189 5726 Planarity : 0.004 0.060 6038 Dihedral : 18.464 177.347 6252 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 3.15 % Allowed : 16.64 % Favored : 80.21 % 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: -0.28 (0.13), residues: 4148 helix: 0.68 (0.13), residues: 1765 sheet: -0.04 (0.26), residues: 408 loop : -0.98 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 996 TYR 0.020 0.001 TYR P 277 PHE 0.023 0.001 PHE F 256 TRP 0.027 0.002 TRP M 87 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00259 (36703) covalent geometry : angle 0.57191 (50198) hydrogen bonds : bond 0.03417 ( 1583) hydrogen bonds : angle 4.57050 ( 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 399 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 287 time to evaluate : 1.311 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: A 51 MET cc_start: 0.8020 (mmp) cc_final: 0.7770 (mmm) REVERT: A 75 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 10 LYS cc_start: 0.8696 (mmpt) cc_final: 0.7947 (tmtt) REVERT: B 41 ASN cc_start: 0.9125 (t0) cc_final: 0.8833 (t0) REVERT: B 56 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.7105 (p) REVERT: B 68 TYR cc_start: 0.8332 (m-80) cc_final: 0.7824 (m-80) REVERT: B 185 TYR cc_start: 0.9280 (p90) cc_final: 0.8896 (p90) REVERT: C 85 CYS cc_start: 0.8539 (m) cc_final: 0.8220 (m) REVERT: C 246 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5595 (pt) REVERT: C 369 MET cc_start: 0.9114 (tmm) cc_final: 0.8901 (tmm) REVERT: C 448 LEU cc_start: 0.8751 (mt) cc_final: 0.8520 (mt) REVERT: C 465 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7820 (ttm-80) REVERT: C 667 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9356 (mm) REVERT: C 996 ARG cc_start: 0.8409 (mmm160) cc_final: 0.8204 (mmm160) REVERT: C 1023 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7532 (p-80) REVERT: C 1119 MET cc_start: 0.9095 (tpp) cc_final: 0.8714 (tpp) REVERT: C 1279 GLU cc_start: 0.8958 (pt0) cc_final: 0.8750 (pt0) REVERT: D 136 GLU cc_start: 0.8278 (tp30) cc_final: 0.7871 (tm-30) REVERT: D 151 MET cc_start: 0.6742 (pmm) cc_final: 0.6091 (pmm) REVERT: D 180 MET cc_start: 0.6927 (mmm) cc_final: 0.6438 (mmm) REVERT: D 301 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8320 (tp30) REVERT: D 615 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8477 (ptpp) REVERT: D 738 ARG cc_start: 0.8188 (tmm-80) cc_final: 0.7978 (tmm-80) REVERT: D 743 MET cc_start: 0.6520 (ppp) cc_final: 0.6271 (ppp) REVERT: D 929 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7487 (tm-30) REVERT: D 932 MET cc_start: 0.4702 (mmt) cc_final: 0.4450 (tpp) REVERT: D 999 TYR cc_start: 0.6988 (t80) cc_final: 0.6763 (t80) REVERT: D 1040 MET cc_start: 0.5834 (mtp) cc_final: 0.5606 (ptm) REVERT: F 273 MET cc_start: 0.9011 (tpt) cc_final: 0.8766 (tpt) REVERT: F 276 MET cc_start: 0.9088 (ppp) cc_final: 0.8725 (ppp) REVERT: F 538 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8105 (tm-30) REVERT: P 260 LEU cc_start: 0.8697 (mm) cc_final: 0.8092 (tp) REVERT: P 277 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7675 (t80) outliers start: 112 outliers final: 62 residues processed: 378 average time/residue: 0.2114 time to fit residues: 131.6211 Evaluate side-chains 327 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE 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 B residue 205 MET Chi-restraints excluded: chain C residue 28 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 465 ARG 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 877 VAL Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 1023 HIS 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 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER 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 421 VAL Chi-restraints excluded: chain D residue 453 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 615 LYS Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 844 THR 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 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 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 N residue 70 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 140 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 263 optimal weight: 0.3980 chunk 360 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.088247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060634 restraints weight = 156358.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062661 restraints weight = 89191.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062989 restraints weight = 53677.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063196 restraints weight = 43992.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063299 restraints weight = 43967.609| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3074 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= 0.166 Angle : 0.598 14.349 50198 Z= 0.310 Chirality : 0.042 0.202 5726 Planarity : 0.004 0.059 6038 Dihedral : 18.476 177.413 6248 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Rotamer: Outliers : 3.23 % Allowed : 17.68 % Favored : 79.08 % 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: -0.22 (0.13), residues: 4148 helix: 0.75 (0.13), residues: 1767 sheet: -0.10 (0.26), residues: 410 loop : -0.94 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 476 TYR 0.018 0.001 TYR P 277 PHE 0.012 0.001 PHE C 505 TRP 0.028 0.002 TRP M 87 HIS 0.016 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00373 (36703) covalent geometry : angle 0.59801 (50198) hydrogen bonds : bond 0.03655 ( 1583) hydrogen bonds : angle 4.57782 ( 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: 115 poor density : 274 time to evaluate : 1.377 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: 0.8993 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 10 LYS cc_start: 0.8659 (mmpt) cc_final: 0.7959 (tmtt) REVERT: B 41 ASN cc_start: 0.9174 (t0) cc_final: 0.8929 (t0) REVERT: B 68 TYR cc_start: 0.8500 (m-80) cc_final: 0.7949 (m-80) REVERT: C 85 CYS cc_start: 0.8599 (m) cc_final: 0.8213 (m) REVERT: C 177 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9353 (pt) REVERT: C 207 THR cc_start: 0.8793 (m) cc_final: 0.8453 (p) REVERT: C 246 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5893 (pt) REVERT: C 369 MET cc_start: 0.9226 (tmm) cc_final: 0.8945 (tmm) REVERT: C 465 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7802 (ttm-80) REVERT: C 667 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9374 (mm) REVERT: C 800 MET cc_start: 0.8676 (pmm) cc_final: 0.8024 (ptp) REVERT: C 996 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8434 (mmm160) REVERT: C 1119 MET cc_start: 0.9084 (tpp) cc_final: 0.8679 (tpp) REVERT: D 151 MET cc_start: 0.6874 (pmm) cc_final: 0.6161 (pmm) REVERT: D 180 MET cc_start: 0.6982 (mmm) cc_final: 0.6522 (mmm) REVERT: D 301 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8376 (tp30) REVERT: D 579 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8707 (tm) REVERT: D 653 ILE cc_start: 0.7865 (mm) cc_final: 0.7634 (mm) REVERT: D 738 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.8105 (tmm-80) REVERT: D 743 MET cc_start: 0.6534 (ppp) cc_final: 0.6239 (ppp) REVERT: D 790 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8423 (p) REVERT: D 929 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 930 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8453 (pp) REVERT: D 932 MET cc_start: 0.5062 (mmt) cc_final: 0.4716 (tpp) REVERT: F 273 MET cc_start: 0.8952 (tpt) cc_final: 0.8617 (tpt) REVERT: F 538 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8168 (tm-30) REVERT: N 34 GLU cc_start: 0.7826 (tp30) cc_final: 0.7450 (mm-30) REVERT: P 260 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8211 (tp) REVERT: P 277 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7679 (t80) outliers start: 115 outliers final: 70 residues processed: 372 average time/residue: 0.2141 time to fit residues: 133.5721 Evaluate side-chains 327 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 177 ILE 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 479 LEU 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 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 1046 VAL 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 1268 GLN Chi-restraints excluded: chain C residue 1313 HIS Chi-restraints excluded: chain C residue 1322 SER 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 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 501 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL 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 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 E residue 49 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 386 LEU 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 69 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain P residue 260 LEU 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: 10.0000 chunk 300 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 422 optimal weight: 8.9990 chunk 318 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 322 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 264 optimal weight: 20.0000 chunk 298 optimal weight: 40.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1313 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 488 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN J 68 GLN P 294 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.086570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059278 restraints weight = 156318.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060413 restraints weight = 102196.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061072 restraints weight = 62162.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061200 restraints weight = 51044.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061274 restraints weight = 48523.239| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36703 Z= 0.227 Angle : 0.652 11.895 50198 Z= 0.341 Chirality : 0.043 0.279 5726 Planarity : 0.004 0.056 6038 Dihedral : 18.630 177.183 6246 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 3.65 % Allowed : 17.74 % Favored : 78.61 % 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: -0.31 (0.13), residues: 4148 helix: 0.69 (0.13), residues: 1769 sheet: -0.34 (0.25), residues: 435 loop : -0.98 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 371 TYR 0.016 0.001 TYR P 277 PHE 0.014 0.001 PHE C 405 TRP 0.049 0.002 TRP J 87 HIS 0.056 0.002 HIS C1313 Details of bonding type rmsd covalent geometry : bond 0.00509 (36703) covalent geometry : angle 0.65191 (50198) hydrogen bonds : bond 0.04031 ( 1583) hydrogen bonds : angle 4.70573 ( 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 383 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 253 time to evaluate : 1.472 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: 0.8219 (mmp) cc_final: 0.7917 (mmm) REVERT: A 75 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 10 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8047 (tmtt) REVERT: B 41 ASN cc_start: 0.9164 (t0) cc_final: 0.8920 (t0) REVERT: B 56 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6625 (p) REVERT: B 68 TYR cc_start: 0.8535 (m-80) cc_final: 0.7982 (m-80) REVERT: C 85 CYS cc_start: 0.8686 (m) cc_final: 0.8289 (m) REVERT: C 177 ILE cc_start: 0.9571 (OUTLIER) cc_final: 0.9321 (pt) REVERT: C 207 THR cc_start: 0.8840 (m) cc_final: 0.8536 (p) REVERT: C 246 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5902 (pt) REVERT: C 369 MET cc_start: 0.9363 (tmm) cc_final: 0.9100 (tmm) REVERT: C 371 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7701 (mtt90) REVERT: C 465 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7810 (ttm-80) REVERT: C 667 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9351 (mm) REVERT: C 800 MET cc_start: 0.8602 (pmm) cc_final: 0.8127 (ptp) REVERT: C 1119 MET cc_start: 0.9092 (tpp) cc_final: 0.8722 (tpp) REVERT: C 1232 MET cc_start: 0.8504 (mmm) cc_final: 0.8173 (mtp) REVERT: D 151 MET cc_start: 0.6825 (pmm) cc_final: 0.6071 (pmm) REVERT: D 180 MET cc_start: 0.7127 (mmm) cc_final: 0.6696 (mmm) REVERT: D 301 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8430 (tp30) REVERT: D 423 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8826 (mp) REVERT: D 579 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8887 (tm) REVERT: D 604 MET cc_start: 0.9288 (ppp) cc_final: 0.9062 (ppp) REVERT: D 738 ARG cc_start: 0.8342 (tmm-80) cc_final: 0.8027 (tmm-80) REVERT: D 822 MET cc_start: 0.8632 (tpp) cc_final: 0.8390 (tpp) REVERT: D 929 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7626 (tm-30) REVERT: D 930 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8522 (pp) REVERT: D 932 MET cc_start: 0.5178 (mmt) cc_final: 0.4691 (tpp) REVERT: D 1040 MET cc_start: 0.5785 (mtp) cc_final: 0.5501 (ptm) REVERT: D 1074 LEU cc_start: 0.1518 (OUTLIER) cc_final: 0.1161 (mt) REVERT: D 1189 MET cc_start: 0.9129 (tpp) cc_final: 0.8846 (tpp) REVERT: F 273 MET cc_start: 0.9021 (tpt) cc_final: 0.8803 (tpt) REVERT: F 538 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8139 (tm-30) REVERT: P 277 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7845 (t80) outliers start: 130 outliers final: 79 residues processed: 361 average time/residue: 0.2229 time to fit residues: 133.3607 Evaluate side-chains 323 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 234 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 140 ILE 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 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 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 448 LEU Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU 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 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 935 THR Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1211 ARG Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 29 MET 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 312 ARG 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 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 839 VAL 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 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 E residue 49 ILE Chi-restraints excluded: chain E residue 56 GLU 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 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 69 VAL Chi-restraints excluded: chain J residue 114 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 289 optimal weight: 0.0030 chunk 266 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 395 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 300 optimal weight: 30.0000 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** 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 294 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN F 406 GLN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.087702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059030 restraints weight = 157921.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060586 restraints weight = 87707.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061620 restraints weight = 61300.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062246 restraints weight = 49475.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062525 restraints weight = 43673.910| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36703 Z= 0.140 Angle : 0.609 13.077 50198 Z= 0.315 Chirality : 0.042 0.274 5726 Planarity : 0.004 0.055 6038 Dihedral : 18.610 177.065 6246 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 3.09 % Allowed : 19.12 % Favored : 77.79 % 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: -0.22 (0.13), residues: 4148 helix: 0.73 (0.13), residues: 1779 sheet: -0.10 (0.27), residues: 393 loop : -0.93 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 731 TYR 0.017 0.001 TYR P 277 PHE 0.011 0.001 PHE D1319 TRP 0.047 0.002 TRP J 87 HIS 0.011 0.001 HIS F 455 Details of bonding type rmsd covalent geometry : bond 0.00315 (36703) covalent geometry : angle 0.60903 (50198) hydrogen bonds : bond 0.03552 ( 1583) hydrogen bonds : angle 4.56753 ( 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 364 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 254 time to evaluate : 1.404 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: A 51 MET cc_start: 0.8352 (mmp) cc_final: 0.8044 (mmm) REVERT: A 75 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 10 LYS cc_start: 0.8731 (mmpt) cc_final: 0.8051 (tmtt) REVERT: B 41 ASN cc_start: 0.9213 (t0) cc_final: 0.8953 (t0) REVERT: B 56 VAL cc_start: 0.7092 (OUTLIER) cc_final: 0.6838 (p) REVERT: B 68 TYR cc_start: 0.8506 (m-80) cc_final: 0.7989 (m-80) REVERT: C 85 CYS cc_start: 0.8663 (m) cc_final: 0.8237 (m) REVERT: C 246 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5797 (pt) REVERT: C 315 MET cc_start: 0.7865 (mtp) cc_final: 0.7662 (ptp) REVERT: C 369 MET cc_start: 0.9401 (tmm) cc_final: 0.9145 (tmm) REVERT: C 465 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7839 (ttm-80) REVERT: C 667 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9378 (mm) REVERT: C 800 MET cc_start: 0.8631 (pmm) cc_final: 0.8233 (ptp) REVERT: C 1119 MET cc_start: 0.9184 (tpp) cc_final: 0.8671 (tpp) REVERT: C 1232 MET cc_start: 0.8649 (mmm) cc_final: 0.8390 (mtp) REVERT: D 151 MET cc_start: 0.6724 (pmm) cc_final: 0.5985 (pmm) REVERT: D 164 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8351 (pp30) REVERT: D 180 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6558 (mmm) REVERT: D 301 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8371 (tp30) REVERT: D 312 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8786 (ttt-90) REVERT: D 579 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8916 (tm) REVERT: D 604 MET cc_start: 0.9338 (ppp) cc_final: 0.8888 (tmm) REVERT: D 790 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8433 (p) REVERT: D 929 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 930 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8427 (pp) REVERT: D 932 MET cc_start: 0.5056 (mmt) cc_final: 0.4608 (tpp) REVERT: D 1074 LEU cc_start: 0.1834 (OUTLIER) cc_final: 0.1387 (mt) REVERT: D 1189 MET cc_start: 0.9138 (tpp) cc_final: 0.8891 (tpp) REVERT: F 273 MET cc_start: 0.9017 (tpt) cc_final: 0.8754 (tpt) REVERT: F 538 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8233 (tm-30) REVERT: J 62 LYS cc_start: 0.9338 (tttt) cc_final: 0.8994 (tmtt) REVERT: N 78 ASP cc_start: 0.9271 (t0) cc_final: 0.8777 (m-30) REVERT: P 277 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7812 (t80) outliers start: 110 outliers final: 74 residues processed: 346 average time/residue: 0.2121 time to fit residues: 122.1304 Evaluate side-chains 326 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 240 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 B residue 205 MET 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 384 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 582 ASN 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 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 878 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 374 LEU 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 790 THR 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 839 VAL 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 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 1256 ILE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 56 GLU 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 17 HIS Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 115 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 259 optimal weight: 6.9990 chunk 426 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 401 optimal weight: 0.9980 chunk 371 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 266 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** 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 690 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.087716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060108 restraints weight = 155505.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062132 restraints weight = 88284.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062366 restraints weight = 53536.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062563 restraints weight = 44219.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062614 restraints weight = 44295.581| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36703 Z= 0.134 Angle : 0.605 12.738 50198 Z= 0.311 Chirality : 0.041 0.172 5726 Planarity : 0.004 0.055 6038 Dihedral : 18.587 179.396 6246 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 2.84 % Allowed : 19.68 % Favored : 77.48 % 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: -0.15 (0.13), residues: 4148 helix: 0.80 (0.13), residues: 1779 sheet: -0.01 (0.27), residues: 387 loop : -0.91 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1106 TYR 0.016 0.001 TYR P 277 PHE 0.009 0.001 PHE C 505 TRP 0.042 0.002 TRP J 87 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00301 (36703) covalent geometry : angle 0.60471 (50198) hydrogen bonds : bond 0.03454 ( 1583) hydrogen bonds : angle 4.49328 ( 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 367 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 266 time to evaluate : 1.391 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 75 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 10 LYS cc_start: 0.8711 (mmpt) cc_final: 0.8076 (tmtt) REVERT: B 41 ASN cc_start: 0.9156 (t0) cc_final: 0.8935 (t0) REVERT: B 68 TYR cc_start: 0.8548 (m-80) cc_final: 0.8021 (m-80) REVERT: B 85 LEU cc_start: 0.9430 (pp) cc_final: 0.9201 (tt) REVERT: B 196 THR cc_start: 0.8048 (p) cc_final: 0.7826 (m) REVERT: C 85 CYS cc_start: 0.8634 (m) cc_final: 0.8222 (m) REVERT: C 246 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5905 (pt) REVERT: C 315 MET cc_start: 0.7812 (mtp) cc_final: 0.7598 (ptp) REVERT: C 369 MET cc_start: 0.9367 (tmm) cc_final: 0.9027 (tmm) REVERT: C 465 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7776 (ttm-80) REVERT: C 667 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9390 (mm) REVERT: C 800 MET cc_start: 0.8543 (pmm) cc_final: 0.8120 (ptp) REVERT: C 1119 MET cc_start: 0.9116 (tpp) cc_final: 0.8645 (tpp) REVERT: C 1232 MET cc_start: 0.8581 (mmm) cc_final: 0.8298 (mtp) REVERT: D 151 MET cc_start: 0.6838 (pmm) cc_final: 0.6125 (pmm) REVERT: D 164 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8346 (pp30) REVERT: D 180 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6547 (mmm) REVERT: D 301 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8301 (tp30) REVERT: D 374 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8979 (tt) REVERT: D 579 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8884 (tm) REVERT: D 604 MET cc_start: 0.9291 (ppp) cc_final: 0.8816 (tmm) REVERT: D 743 MET cc_start: 0.6222 (ppp) cc_final: 0.5758 (tmm) REVERT: D 790 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8437 (p) REVERT: D 929 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7648 (tm-30) REVERT: D 932 MET cc_start: 0.5121 (mmt) cc_final: 0.4674 (tpp) REVERT: D 1040 MET cc_start: 0.5245 (ptm) cc_final: 0.4097 (ptp) REVERT: D 1074 LEU cc_start: 0.1657 (OUTLIER) cc_final: 0.1304 (mt) REVERT: D 1189 MET cc_start: 0.9146 (tpp) cc_final: 0.8845 (tpp) REVERT: E 44 ASP cc_start: 0.6817 (m-30) cc_final: 0.6266 (m-30) REVERT: F 273 MET cc_start: 0.9023 (tpt) cc_final: 0.8745 (tpt) REVERT: F 538 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 608 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8497 (mtm-85) REVERT: J 62 LYS cc_start: 0.9343 (tttt) cc_final: 0.8994 (tmtt) REVERT: N 34 GLU cc_start: 0.7899 (tp30) cc_final: 0.7534 (mm-30) REVERT: N 78 ASP cc_start: 0.9257 (t0) cc_final: 0.8780 (m-30) REVERT: P 277 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (t80) outliers start: 101 outliers final: 70 residues processed: 350 average time/residue: 0.2170 time to fit residues: 126.0744 Evaluate side-chains 322 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 241 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 203 ILE 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 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 445 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 465 ARG 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 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 1046 VAL Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 400 MET 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 790 THR 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 839 VAL 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 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 1256 ILE Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 608 ARG 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 27 ARG Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain J residue 115 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 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: 3.9990 chunk 411 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 276 optimal weight: 0.9980 chunk 325 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 GLN ** 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** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 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 = 0.3795 r_free = 0.3795 target = 0.087309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058917 restraints weight = 155888.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060500 restraints weight = 85166.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061526 restraints weight = 58755.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062161 restraints weight = 47037.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062441 restraints weight = 41324.334| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36703 Z= 0.151 Angle : 0.629 13.461 50198 Z= 0.322 Chirality : 0.042 0.180 5726 Planarity : 0.004 0.068 6038 Dihedral : 18.593 176.457 6243 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 2.73 % Allowed : 20.02 % Favored : 77.26 % 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: -0.16 (0.13), residues: 4148 helix: 0.79 (0.13), residues: 1775 sheet: -0.09 (0.26), residues: 409 loop : -0.91 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1106 TYR 0.015 0.001 TYR P 277 PHE 0.011 0.001 PHE C 505 TRP 0.039 0.002 TRP J 87 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00343 (36703) covalent geometry : angle 0.62894 (50198) hydrogen bonds : bond 0.03535 ( 1583) hydrogen bonds : angle 4.49313 ( 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 349 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 252 time to evaluate : 1.328 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 75 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 10 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8106 (tmtt) REVERT: B 68 TYR cc_start: 0.8421 (m-80) cc_final: 0.7979 (m-80) REVERT: B 85 LEU cc_start: 0.9362 (pp) cc_final: 0.9087 (tt) REVERT: B 196 THR cc_start: 0.8148 (p) cc_final: 0.7946 (m) REVERT: C 85 CYS cc_start: 0.8581 (m) cc_final: 0.8191 (m) REVERT: C 246 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5750 (pt) REVERT: C 369 MET cc_start: 0.9317 (tmm) cc_final: 0.8964 (tmm) REVERT: C 465 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7787 (ttm-80) REVERT: C 667 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9357 (mm) REVERT: C 800 MET cc_start: 0.8471 (pmm) cc_final: 0.8091 (ptp) REVERT: C 1119 MET cc_start: 0.9071 (tpp) cc_final: 0.8654 (tpp) REVERT: C 1232 MET cc_start: 0.8478 (mmm) cc_final: 0.8175 (mtp) REVERT: D 151 MET cc_start: 0.6849 (pmm) cc_final: 0.6134 (pmm) REVERT: D 164 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8154 (pp30) REVERT: D 180 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6920 (mmm) REVERT: D 301 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8253 (tp30) REVERT: D 485 MET cc_start: 0.8654 (tpp) cc_final: 0.8403 (tpp) REVERT: D 579 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8832 (tm) REVERT: D 790 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8428 (p) REVERT: D 929 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7651 (tm-30) REVERT: D 932 MET cc_start: 0.4834 (mmt) cc_final: 0.4470 (tpp) REVERT: D 1074 LEU cc_start: 0.1869 (OUTLIER) cc_final: 0.1518 (mt) REVERT: D 1189 MET cc_start: 0.9111 (tpp) cc_final: 0.8813 (tpp) REVERT: D 1273 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8084 (t0) REVERT: E 44 ASP cc_start: 0.7023 (m-30) cc_final: 0.6389 (m-30) REVERT: F 273 MET cc_start: 0.8951 (tpt) cc_final: 0.8709 (tpt) REVERT: F 276 MET cc_start: 0.9135 (ppp) cc_final: 0.8861 (ptm) REVERT: F 277 MET cc_start: 0.8664 (tpt) cc_final: 0.8216 (tpt) REVERT: F 538 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8072 (tm-30) REVERT: J 62 LYS cc_start: 0.9328 (tttt) cc_final: 0.8937 (tmtt) REVERT: N 34 GLU cc_start: 0.7761 (tp30) cc_final: 0.7491 (mm-30) REVERT: N 78 ASP cc_start: 0.9182 (t0) cc_final: 0.8726 (m-30) REVERT: P 277 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 97 outliers final: 75 residues processed: 330 average time/residue: 0.2145 time to fit residues: 118.7939 Evaluate side-chains 321 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 236 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 203 ILE 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 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 445 ILE Chi-restraints excluded: chain C residue 448 LEU 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 655 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 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1268 GLN 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 180 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 453 VAL 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 790 THR 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 839 VAL 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 D residue 1256 ILE Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 56 GLU 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 95 VAL Chi-restraints excluded: chain J residue 17 HIS Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain J residue 115 ARG 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: 0.7980 chunk 93 optimal weight: 0.6980 chunk 368 optimal weight: 4.9990 chunk 285 optimal weight: 9.9990 chunk 342 optimal weight: 40.0000 chunk 421 optimal weight: 10.0000 chunk 294 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 292 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** 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 716 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.086274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.058086 restraints weight = 157167.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060029 restraints weight = 85127.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.060306 restraints weight = 56417.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060859 restraints weight = 43995.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060936 restraints weight = 41057.199| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36703 Z= 0.170 Angle : 0.640 15.233 50198 Z= 0.328 Chirality : 0.042 0.185 5726 Planarity : 0.004 0.057 6038 Dihedral : 18.635 176.432 6243 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 2.59 % Allowed : 20.07 % Favored : 77.34 % 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: -0.16 (0.13), residues: 4148 helix: 0.80 (0.13), residues: 1777 sheet: -0.19 (0.26), residues: 420 loop : -0.90 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1106 TYR 0.017 0.001 TYR D 631 PHE 0.012 0.001 PHE C 405 TRP 0.034 0.002 TRP J 87 HIS 0.006 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00387 (36703) covalent geometry : angle 0.64015 (50198) hydrogen bonds : bond 0.03667 ( 1583) hydrogen bonds : angle 4.54777 ( 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 332 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 240 time to evaluate : 1.469 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: A 51 MET cc_start: 0.8431 (mmp) cc_final: 0.8059 (mmm) REVERT: A 75 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 10 LYS cc_start: 0.8671 (mmpt) cc_final: 0.8138 (tmtt) REVERT: B 68 TYR cc_start: 0.8679 (m-80) cc_final: 0.8117 (m-80) REVERT: C 85 CYS cc_start: 0.8760 (m) cc_final: 0.8316 (m) REVERT: C 246 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6003 (pt) REVERT: C 369 MET cc_start: 0.9387 (tmm) cc_final: 0.9025 (tmm) REVERT: C 465 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7843 (ttm-80) REVERT: C 667 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9315 (mm) REVERT: C 800 MET cc_start: 0.8614 (pmm) cc_final: 0.8384 (ptp) REVERT: C 805 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8545 (ptm) REVERT: C 1119 MET cc_start: 0.9244 (tpp) cc_final: 0.8673 (tpp) REVERT: C 1232 MET cc_start: 0.8763 (mmm) cc_final: 0.8529 (mtp) REVERT: D 151 MET cc_start: 0.6971 (pmm) cc_final: 0.6267 (pmm) REVERT: D 180 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6743 (mmm) REVERT: D 301 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8377 (tp30) REVERT: D 485 MET cc_start: 0.8943 (tpp) cc_final: 0.8511 (tpp) REVERT: D 579 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9023 (tm) REVERT: D 929 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 932 MET cc_start: 0.5229 (mmt) cc_final: 0.4749 (tpp) REVERT: D 1074 LEU cc_start: 0.2237 (OUTLIER) cc_final: 0.1947 (mt) REVERT: D 1189 MET cc_start: 0.9176 (tpp) cc_final: 0.8884 (tpp) REVERT: D 1273 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8204 (t0) REVERT: E 30 MET cc_start: 0.8677 (tpp) cc_final: 0.8189 (mpp) REVERT: F 105 MET cc_start: 0.9101 (tmm) cc_final: 0.8838 (tmm) REVERT: F 273 MET cc_start: 0.9028 (tpt) cc_final: 0.8776 (tpt) REVERT: F 297 MET cc_start: 0.4688 (mmm) cc_final: 0.3677 (ttt) REVERT: F 470 MET cc_start: 0.8622 (mmp) cc_final: 0.8420 (mmt) REVERT: F 538 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8264 (tm-30) REVERT: F 608 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8489 (mtm-85) REVERT: J 62 LYS cc_start: 0.9371 (tttt) cc_final: 0.8990 (tmtt) REVERT: N 34 GLU cc_start: 0.7812 (tp30) cc_final: 0.7527 (mm-30) REVERT: N 78 ASP cc_start: 0.9275 (t0) cc_final: 0.8807 (m-30) REVERT: P 277 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7943 (t80) outliers start: 92 outliers final: 76 residues processed: 316 average time/residue: 0.2155 time to fit residues: 114.6933 Evaluate side-chains 319 residues out of total 3582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 203 ILE 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 183 ILE Chi-restraints excluded: chain B residue 205 MET 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 445 ILE Chi-restraints excluded: chain C residue 448 LEU 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 655 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 802 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1268 GLN 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 180 MET Chi-restraints excluded: chain D residue 212 THR 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 428 THR 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 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL 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 D residue 1273 ASP Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 56 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 497 VAL Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 608 ARG 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 J residue 27 ARG Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain J residue 115 ARG 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 290 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 297 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN ** C 120 GLN ** 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 690 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.086503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.057585 restraints weight = 156272.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059286 restraints weight = 81420.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060386 restraints weight = 54657.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 76)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061057 restraints weight = 43027.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061364 restraints weight = 37448.812| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36703 Z= 0.151 Angle : 0.631 14.867 50198 Z= 0.322 Chirality : 0.042 0.172 5726 Planarity : 0.004 0.078 6038 Dihedral : 18.635 176.560 6243 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 2.59 % Allowed : 20.19 % Favored : 77.23 % 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: -0.14 (0.13), residues: 4148 helix: 0.83 (0.13), residues: 1770 sheet: -0.10 (0.26), residues: 398 loop : -0.91 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 996 TYR 0.016 0.001 TYR D 631 PHE 0.010 0.001 PHE C 505 TRP 0.036 0.002 TRP J 87 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd covalent geometry : bond 0.00342 (36703) covalent geometry : angle 0.63063 (50198) hydrogen bonds : bond 0.03548 ( 1583) hydrogen bonds : angle 4.49525 ( 4404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7719.80 seconds wall clock time: 133 minutes 36.68 seconds (8016.68 seconds total)