Starting phenix.real_space_refine on Thu Mar 5 13:08:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fn6_29306/03_2026/8fn6_29306.map" } resolution = 3.7 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= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 124 5.16 5 C 13997 2.51 5 N 3921 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22421 Number of models: 1 Model: "" Number of chains: 8 Chain: "g" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 960 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 22} Link IDs: {'rna2p': 5, 'rna3p': 40} Chain breaks: 1 Chain: "1" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain: "2" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3421 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3705 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain: "4" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5790 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain breaks: 1 Chain: "5" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2163 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain: "6" Number of atoms: 3583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3583 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 11, 'TRANS': 440} Chain: "g" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.46, per 1000 atoms: 0.20 Number of scatterers: 22421 At special positions: 0 Unit cell: (115.5, 139.7, 213.4, 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 124 16.00 P 49 15.00 O 4330 8.00 N 3921 7.00 C 13997 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 864.4 milliseconds 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5206 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 10 sheets defined 59.8% alpha, 4.9% beta 18 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain '1' and resid 195 through 217 removed outlier: 4.142A pdb=" N ILE 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) Processing helix chain '1' and resid 245 through 253 Processing helix chain '1' and resid 269 through 274 removed outlier: 3.502A pdb=" N GLN 1 274 " --> pdb=" O LEU 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 277 through 282 Processing helix chain '1' and resid 349 through 356 Processing helix chain '1' and resid 440 through 459 removed outlier: 4.104A pdb=" N VAL 1 444 " --> pdb=" O ASP 1 440 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY 1 445 " --> pdb=" O VAL 1 441 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG 1 454 " --> pdb=" O GLU 1 450 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU 1 455 " --> pdb=" O LEU 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 461 through 466 removed outlier: 4.003A pdb=" N GLU 1 466 " --> pdb=" O ASP 1 462 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 60 Processing helix chain '2' and resid 67 through 78 Processing helix chain '2' and resid 89 through 104 removed outlier: 3.607A pdb=" N LEU 2 93 " --> pdb=" O LYS 2 89 " (cutoff:3.500A) Processing helix chain '2' and resid 134 through 138 removed outlier: 4.183A pdb=" N TYR 2 138 " --> pdb=" O GLU 2 134 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 134 through 138' Processing helix chain '2' and resid 192 through 196 removed outlier: 4.534A pdb=" N LYS 2 195 " --> pdb=" O ASP 2 192 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 236 removed outlier: 3.535A pdb=" N ALA 2 216 " --> pdb=" O ALA 2 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP 2 227 " --> pdb=" O MET 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 259 removed outlier: 3.711A pdb=" N ALA 2 255 " --> pdb=" O ARG 2 252 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS 2 256 " --> pdb=" O SER 2 253 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN 2 257 " --> pdb=" O VAL 2 254 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 275 removed outlier: 3.534A pdb=" N VAL 2 267 " --> pdb=" O PRO 2 263 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 299 removed outlier: 4.540A pdb=" N ALA 2 290 " --> pdb=" O SER 2 286 " (cutoff:3.500A) Processing helix chain '2' and resid 365 through 373 removed outlier: 3.861A pdb=" N ALA 2 369 " --> pdb=" O LYS 2 365 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 384 removed outlier: 3.877A pdb=" N ASP 2 383 " --> pdb=" O SER 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 449 through 453 removed outlier: 3.851A pdb=" N ARG 2 453 " --> pdb=" O GLN 2 450 " (cutoff:3.500A) Processing helix chain '2' and resid 456 through 474 Processing helix chain '3' and resid 4 through 19 Processing helix chain '3' and resid 24 through 36 Processing helix chain '3' and resid 38 through 62 removed outlier: 3.645A pdb=" N LEU 3 42 " --> pdb=" O SER 3 38 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN 3 55 " --> pdb=" O LEU 3 51 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN 3 56 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG 3 57 " --> pdb=" O ALA 3 53 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 101 Processing helix chain '3' and resid 106 through 119 Processing helix chain '3' and resid 124 through 134 Processing helix chain '3' and resid 142 through 158 removed outlier: 3.602A pdb=" N ILE 3 146 " --> pdb=" O GLN 3 142 " (cutoff:3.500A) Proline residue: 3 152 - end of helix removed outlier: 3.703A pdb=" N ARG 3 155 " --> pdb=" O LEU 3 151 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 3 156 " --> pdb=" O PRO 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 161 No H-bonds generated for 'chain '3' and resid 159 through 161' Processing helix chain '3' and resid 162 through 176 removed outlier: 4.404A pdb=" N HIS 3 168 " --> pdb=" O ARG 3 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE 3 176 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 183 through 194 Processing helix chain '3' and resid 199 through 210 removed outlier: 3.866A pdb=" N LEU 3 210 " --> pdb=" O CYS 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 225 removed outlier: 3.809A pdb=" N ALA 3 218 " --> pdb=" O PHE 3 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL 3 225 " --> pdb=" O ILE 3 221 " (cutoff:3.500A) Processing helix chain '3' and resid 225 through 236 Processing helix chain '3' and resid 238 through 257 removed outlier: 3.536A pdb=" N VAL 3 242 " --> pdb=" O ASP 3 238 " (cutoff:3.500A) Processing helix chain '3' and resid 260 through 274 Processing helix chain '3' and resid 279 through 291 removed outlier: 3.668A pdb=" N PHE 3 290 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 297 through 309 removed outlier: 3.826A pdb=" N ALA 3 309 " --> pdb=" O SER 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 316 Processing helix chain '3' and resid 321 through 335 Processing helix chain '3' and resid 340 through 353 removed outlier: 4.402A pdb=" N ASN 3 353 " --> pdb=" O ASN 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 371 removed outlier: 4.017A pdb=" N LEU 3 362 " --> pdb=" O LEU 3 358 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 376 No H-bonds generated for 'chain '3' and resid 374 through 376' Processing helix chain '3' and resid 377 through 385 Processing helix chain '3' and resid 387 through 396 removed outlier: 3.965A pdb=" N HIS 3 395 " --> pdb=" O ARG 3 391 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN 3 396 " --> pdb=" O ARG 3 392 " (cutoff:3.500A) Processing helix chain '3' and resid 399 through 413 Processing helix chain '3' and resid 418 through 435 Proline residue: 3 427 - end of helix Processing helix chain '3' and resid 440 through 457 Processing helix chain '3' and resid 462 through 480 Processing helix chain '4' and resid 337 through 346 Processing helix chain '4' and resid 351 through 360 removed outlier: 3.749A pdb=" N MET 4 355 " --> pdb=" O SER 4 351 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 4 360 " --> pdb=" O PHE 4 356 " (cutoff:3.500A) Processing helix chain '4' and resid 367 through 381 removed outlier: 4.051A pdb=" N GLU 4 380 " --> pdb=" O CYS 4 376 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS 4 381 " --> pdb=" O LEU 4 377 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 395 Processing helix chain '4' and resid 400 through 414 Processing helix chain '4' and resid 439 through 451 Processing helix chain '4' and resid 467 through 487 removed outlier: 3.543A pdb=" N SER 4 471 " --> pdb=" O ASN 4 467 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY 4 487 " --> pdb=" O SER 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 501 Processing helix chain '4' and resid 508 through 522 removed outlier: 3.876A pdb=" N GLY 4 522 " --> pdb=" O ILE 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 525 through 540 Processing helix chain '4' and resid 543 through 565 removed outlier: 3.500A pdb=" N LEU 4 547 " --> pdb=" O TYR 4 543 " (cutoff:3.500A) Proline residue: 4 552 - end of helix removed outlier: 3.602A pdb=" N LEU 4 565 " --> pdb=" O VAL 4 561 " (cutoff:3.500A) Processing helix chain '4' and resid 572 through 590 removed outlier: 3.593A pdb=" N VAL 4 576 " --> pdb=" O ASN 4 572 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU 4 588 " --> pdb=" O THR 4 584 " (cutoff:3.500A) Processing helix chain '4' and resid 595 through 608 removed outlier: 3.616A pdb=" N LYS 4 607 " --> pdb=" O HIS 4 603 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN 4 608 " --> pdb=" O THR 4 604 " (cutoff:3.500A) Processing helix chain '4' and resid 615 through 626 removed outlier: 4.480A pdb=" N SER 4 619 " --> pdb=" O GLU 4 615 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG 4 626 " --> pdb=" O LEU 4 622 " (cutoff:3.500A) Processing helix chain '4' and resid 627 through 633 removed outlier: 6.441A pdb=" N THR 4 630 " --> pdb=" O THR 4 627 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER 4 631 " --> pdb=" O ARG 4 628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA 4 632 " --> pdb=" O ARG 4 629 " (cutoff:3.500A) Processing helix chain '4' and resid 643 through 647 removed outlier: 3.715A pdb=" N GLN 4 646 " --> pdb=" O ASN 4 643 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 4 647 " --> pdb=" O MET 4 644 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 643 through 647' Processing helix chain '4' and resid 648 through 660 removed outlier: 3.852A pdb=" N GLY 4 653 " --> pdb=" O ASP 4 649 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU 4 654 " --> pdb=" O ASP 4 650 " (cutoff:3.500A) Processing helix chain '4' and resid 662 through 666 removed outlier: 3.609A pdb=" N LEU 4 665 " --> pdb=" O THR 4 662 " (cutoff:3.500A) Processing helix chain '4' and resid 667 through 684 Processing helix chain '4' and resid 689 through 704 removed outlier: 3.687A pdb=" N VAL 4 693 " --> pdb=" O PRO 4 689 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN 4 703 " --> pdb=" O VAL 4 699 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY 4 704 " --> pdb=" O TRP 4 700 " (cutoff:3.500A) Processing helix chain '4' and resid 705 through 707 No H-bonds generated for 'chain '4' and resid 705 through 707' Processing helix chain '4' and resid 711 through 720 Processing helix chain '4' and resid 721 through 725 Processing helix chain '4' and resid 726 through 737 Processing helix chain '4' and resid 744 through 751 Processing helix chain '4' and resid 753 through 761 removed outlier: 3.890A pdb=" N LEU 4 758 " --> pdb=" O PRO 4 755 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU 4 759 " --> pdb=" O ARG 4 756 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 4 760 " --> pdb=" O ARG 4 757 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU 4 761 " --> pdb=" O LEU 4 758 " (cutoff:3.500A) Processing helix chain '4' and resid 762 through 773 Processing helix chain '4' and resid 775 through 781 removed outlier: 3.814A pdb=" N MET 4 779 " --> pdb=" O GLU 4 775 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 799 removed outlier: 4.024A pdb=" N LEU 4 787 " --> pdb=" O LEU 4 783 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL 4 788 " --> pdb=" O SER 4 784 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA 4 789 " --> pdb=" O HIS 4 785 " (cutoff:3.500A) Processing helix chain '4' and resid 805 through 818 Processing helix chain '4' and resid 824 through 833 removed outlier: 3.567A pdb=" N THR 4 832 " --> pdb=" O ASN 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 834 through 836 No H-bonds generated for 'chain '4' and resid 834 through 836' Processing helix chain '4' and resid 848 through 857 Processing helix chain '4' and resid 862 through 876 Processing helix chain '4' and resid 884 through 894 removed outlier: 3.746A pdb=" N ARG 4 890 " --> pdb=" O LEU 4 886 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY 4 891 " --> pdb=" O LEU 4 887 " (cutoff:3.500A) Processing helix chain '4' and resid 899 through 913 removed outlier: 3.803A pdb=" N TYR 4 903 " --> pdb=" O ASN 4 899 " (cutoff:3.500A) Processing helix chain '4' and resid 918 through 933 removed outlier: 3.599A pdb=" N PHE 4 929 " --> pdb=" O LEU 4 925 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU 4 932 " --> pdb=" O SER 4 928 " (cutoff:3.500A) Processing helix chain '4' and resid 936 through 950 removed outlier: 4.047A pdb=" N SER 4 945 " --> pdb=" O SER 4 941 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER 4 946 " --> pdb=" O ARG 4 942 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE 4 947 " --> pdb=" O MET 4 943 " (cutoff:3.500A) Processing helix chain '4' and resid 951 through 954 Processing helix chain '4' and resid 956 through 970 removed outlier: 4.088A pdb=" N ALA 4 960 " --> pdb=" O ASP 4 956 " (cutoff:3.500A) Processing helix chain '4' and resid 977 through 990 removed outlier: 4.247A pdb=" N ALA 4 981 " --> pdb=" O ASP 4 977 " (cutoff:3.500A) Processing helix chain '4' and resid 995 through 1010 Processing helix chain '4' and resid 1013 through 1030 removed outlier: 4.083A pdb=" N VAL 41017 " --> pdb=" O HIS 41013 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN 41030 " --> pdb=" O ARG 41026 " (cutoff:3.500A) Processing helix chain '4' and resid 1034 through 1049 Processing helix chain '4' and resid 1052 through 1059 removed outlier: 3.815A pdb=" N ASN 41058 " --> pdb=" O GLY 41054 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 41059 " --> pdb=" O ALA 41055 " (cutoff:3.500A) Processing helix chain '4' and resid 1059 through 1068 removed outlier: 3.681A pdb=" N SER 41065 " --> pdb=" O ALA 41061 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE 41066 " --> pdb=" O LEU 41062 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 41067 " --> pdb=" O GLY 41063 " (cutoff:3.500A) Processing helix chain '4' and resid 1074 through 1085 Processing helix chain '5' and resid 34 through 52 removed outlier: 3.580A pdb=" N LEU 5 38 " --> pdb=" O ASN 5 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL 5 39 " --> pdb=" O ARG 5 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG 5 43 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP 5 44 " --> pdb=" O HIS 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 71 removed outlier: 3.684A pdb=" N ARG 5 71 " --> pdb=" O GLU 5 68 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 109 removed outlier: 3.601A pdb=" N GLU 5 100 " --> pdb=" O THR 5 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG 5 103 " --> pdb=" O MET 5 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA 5 108 " --> pdb=" O TYR 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 120 Processing helix chain '5' and resid 147 through 158 removed outlier: 3.760A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 185 removed outlier: 4.082A pdb=" N TYR 5 184 " --> pdb=" O PRO 5 180 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE 5 185 " --> pdb=" O LEU 5 181 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 180 through 185' Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 212 through 216 removed outlier: 4.006A pdb=" N GLU 5 216 " --> pdb=" O PRO 5 213 " (cutoff:3.500A) Processing helix chain '5' and resid 246 through 255 removed outlier: 4.385A pdb=" N MET 5 250 " --> pdb=" O TYR 5 246 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP 5 251 " --> pdb=" O GLU 5 247 " (cutoff:3.500A) Processing helix chain '5' and resid 265 through 272 Processing helix chain '5' and resid 274 through 279 removed outlier: 3.811A pdb=" N VAL 5 279 " --> pdb=" O MET 5 275 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 81 removed outlier: 3.811A pdb=" N GLY 6 81 " --> pdb=" O HIS 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 97 removed outlier: 4.049A pdb=" N ALA 6 87 " --> pdb=" O ASN 6 83 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR 6 97 " --> pdb=" O VAL 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 removed outlier: 3.512A pdb=" N VAL 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 6 112 " --> pdb=" O SER 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 133 removed outlier: 3.614A pdb=" N ASP 6 133 " --> pdb=" O ARG 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 154 removed outlier: 3.509A pdb=" N VAL 6 150 " --> pdb=" O VAL 6 146 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 175 removed outlier: 3.636A pdb=" N VAL 6 165 " --> pdb=" O ASP 6 161 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE 6 166 " --> pdb=" O ALA 6 162 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 6 167 " --> pdb=" O ARG 6 163 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 6 175 " --> pdb=" O GLN 6 171 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 196 removed outlier: 3.946A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY 6 196 " --> pdb=" O PHE 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 Processing helix chain '6' and resid 222 through 235 removed outlier: 4.078A pdb=" N ILE 6 226 " --> pdb=" O ALA 6 222 " (cutoff:3.500A) Processing helix chain '6' and resid 238 through 252 Processing helix chain '6' and resid 257 through 270 Proline residue: 6 263 - end of helix Processing helix chain '6' and resid 278 through 287 removed outlier: 3.509A pdb=" N THR 6 284 " --> pdb=" O LYS 6 280 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 309 removed outlier: 3.593A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 324 removed outlier: 3.775A pdb=" N VAL 6 324 " --> pdb=" O THR 6 320 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 328 removed outlier: 4.555A pdb=" N ASP 6 328 " --> pdb=" O GLU 6 325 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 325 through 328' Processing helix chain '6' and resid 334 through 346 removed outlier: 3.549A pdb=" N THR 6 338 " --> pdb=" O TYR 6 334 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE 6 342 " --> pdb=" O THR 6 338 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN 6 343 " --> pdb=" O LEU 6 339 " (cutoff:3.500A) Processing helix chain '6' and resid 349 through 359 removed outlier: 3.820A pdb=" N PHE 6 353 " --> pdb=" O ASN 6 349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 6 359 " --> pdb=" O ASN 6 355 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 381 removed outlier: 4.101A pdb=" N HIS 6 381 " --> pdb=" O THR 6 377 " (cutoff:3.500A) Processing helix chain '6' and resid 386 through 401 removed outlier: 3.814A pdb=" N ARG 6 392 " --> pdb=" O GLU 6 388 " (cutoff:3.500A) Processing helix chain '6' and resid 405 through 420 Processing helix chain '6' and resid 423 through 435 removed outlier: 4.257A pdb=" N VAL 6 435 " --> pdb=" O SER 6 431 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 457 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 479 Processing helix chain '6' and resid 484 through 496 Processing helix chain '6' and resid 500 through 509 Processing sheet with id=AA1, first strand: chain '1' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain '1' and resid 221 through 229 removed outlier: 3.604A pdb=" N LYS 1 229 " --> pdb=" O VAL 1 262 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 1 262 " --> pdb=" O LYS 1 229 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 262 through 263 current: chain '1' and resid 304 through 309 removed outlier: 7.575A pdb=" N GLN 1 304 " --> pdb=" O SER 1 320 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER 1 320 " --> pdb=" O GLN 1 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N HIS 1 306 " --> pdb=" O VAL 1 318 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL 1 318 " --> pdb=" O HIS 1 306 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP 1 308 " --> pdb=" O LEU 1 316 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 315 through 320 current: chain '1' and resid 400 through 412 Processing sheet with id=AA3, first strand: chain '1' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain '1' and resid 362 through 364 Processing sheet with id=AA5, first strand: chain '2' and resid 175 through 179 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 175 through 179 current: chain '2' and resid 277 through 280 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 277 through 280 current: chain '2' and resid 323 through 325 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 323 through 325 current: chain '2' and resid 353 through 360 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 353 through 360 current: chain '2' and resid 418 through 429 Processing sheet with id=AA6, first strand: chain '5' and resid 57 through 61 removed outlier: 6.969A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 76 through 78 Processing sheet with id=AA8, first strand: chain '5' and resid 131 through 134 Processing sheet with id=AA9, first strand: chain '5' and resid 192 through 196 removed outlier: 6.210A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '5' and resid 228 through 229 1019 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7318 1.34 - 1.46: 4084 1.46 - 1.58: 11244 1.58 - 1.70: 95 1.70 - 1.82: 191 Bond restraints: 22932 Sorted by residual: bond pdb=" C4 ATP g 201 " pdb=" C5 ATP g 201 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C5 ATP g 201 " pdb=" C6 ATP g 201 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C8 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 2.07e+01 bond pdb=" C5 ATP g 201 " pdb=" N7 ATP g 201 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 1.374 1.332 0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 22927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 31147 3.66 - 7.32: 123 7.32 - 10.98: 18 10.98 - 14.64: 1 14.64 - 18.30: 1 Bond angle restraints: 31290 Sorted by residual: angle pdb=" PB ATP g 201 " pdb=" O3B ATP g 201 " pdb=" PG ATP g 201 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP g 201 " pdb=" O3A ATP g 201 " pdb=" PB ATP g 201 " ideal model delta sigma weight residual 136.83 124.25 12.58 1.00e+00 1.00e+00 1.58e+02 angle pdb=" C5 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" N3 ATP g 201 " pdb=" C4 ATP g 201 " pdb=" N9 ATP g 201 " ideal model delta sigma weight residual 127.04 135.03 -7.99 1.15e+00 7.59e-01 4.84e+01 angle pdb=" N1 ATP g 201 " pdb=" C2 ATP g 201 " pdb=" N3 ATP g 201 " ideal model delta sigma weight residual 128.69 123.63 5.06 1.00e+00 1.00e+00 2.56e+01 ... (remaining 31285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.43: 12745 25.43 - 50.85: 1076 50.85 - 76.28: 136 76.28 - 101.70: 27 101.70 - 127.13: 2 Dihedral angle restraints: 13986 sinusoidal: 5992 harmonic: 7994 Sorted by residual: dihedral pdb=" O4' A g 5 " pdb=" C1' A g 5 " pdb=" N9 A g 5 " pdb=" C4 A g 5 " ideal model delta sinusoidal sigma weight residual -106.00 -167.61 61.61 1 1.70e+01 3.46e-03 1.74e+01 dihedral pdb=" CA ASP 4 862 " pdb=" C ASP 4 862 " pdb=" N LYS 4 863 " pdb=" CA LYS 4 863 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN 5 75 " pdb=" C GLN 5 75 " pdb=" N MET 5 76 " pdb=" CA MET 5 76 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3024 0.051 - 0.103: 523 0.103 - 0.154: 80 0.154 - 0.205: 6 0.205 - 0.256: 2 Chirality restraints: 3635 Sorted by residual: chirality pdb=" CB VAL 4 501 " pdb=" CA VAL 4 501 " pdb=" CG1 VAL 4 501 " pdb=" CG2 VAL 4 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL 1 372 " pdb=" CA VAL 1 372 " pdb=" CG1 VAL 1 372 " pdb=" CG2 VAL 1 372 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE 4 366 " pdb=" N ILE 4 366 " pdb=" C ILE 4 366 " pdb=" CB ILE 4 366 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3632 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 492 " -0.020 2.00e-02 2.50e+03 2.13e-02 7.93e+00 pdb=" CG PHE 6 492 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 492 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 492 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 492 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 492 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE 6 492 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 6 489 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C GLU 6 489 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU 6 489 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU 6 490 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 4 361 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C GLU 4 361 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU 4 361 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN 4 362 " 0.012 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1706 2.74 - 3.28: 23417 3.28 - 3.82: 37118 3.82 - 4.36: 40715 4.36 - 4.90: 68598 Nonbonded interactions: 171554 Sorted by model distance: nonbonded pdb=" OG SER 4 525 " pdb=" OE1 GLU 4 528 " model vdw 2.196 3.040 nonbonded pdb=" O LEU 3 370 " pdb=" OG SER 3 374 " model vdw 2.200 3.040 nonbonded pdb=" O ARG 6 281 " pdb=" OG1 THR 6 284 " model vdw 2.235 3.040 nonbonded pdb=" O ARG 41056 " pdb=" OG SER 41060 " model vdw 2.240 3.040 nonbonded pdb=" OD2 ASP 2 124 " pdb=" NH2 ARG 6 235 " model vdw 2.249 3.120 ... (remaining 171549 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 0.080 22933 Z= 0.164 Angle : 0.652 18.302 31290 Z= 0.362 Chirality : 0.040 0.256 3635 Planarity : 0.004 0.043 3880 Dihedral : 17.575 127.130 8780 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.91 % Rotamer: Outliers : 0.60 % Allowed : 26.07 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2711 helix: 0.91 (0.14), residues: 1502 sheet: 0.02 (0.36), residues: 217 loop : -1.84 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 415 TYR 0.015 0.001 TYR 4 341 PHE 0.048 0.001 PHE 6 492 TRP 0.025 0.002 TRP 2 443 HIS 0.005 0.001 HIS 6 475 Details of bonding type rmsd covalent geometry : bond 0.00281 (22932) covalent geometry : angle 0.65163 (31290) hydrogen bonds : bond 0.14385 ( 1055) hydrogen bonds : angle 5.54177 ( 3048) Misc. bond : bond 0.03971 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 103 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7429 (mmt90) REVERT: 5 167 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: 5 265 TRP cc_start: 0.7608 (t-100) cc_final: 0.6314 (m-90) outliers start: 14 outliers final: 5 residues processed: 259 average time/residue: 0.1532 time to fit residues: 62.6898 Evaluate side-chains 235 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 275 LEU Chi-restraints excluded: chain 4 residue 494 LEU Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 6 residue 402 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 254 GLN ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 140 HIS ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 922 GLN 4 950 ASN 41052 HIS 5 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.176175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.141590 restraints weight = 44700.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141154 restraints weight = 55916.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142463 restraints weight = 48020.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144105 restraints weight = 31132.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.144337 restraints weight = 27890.004| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22933 Z= 0.150 Angle : 0.581 8.906 31290 Z= 0.297 Chirality : 0.039 0.177 3635 Planarity : 0.004 0.051 3880 Dihedral : 10.476 128.837 3671 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.09 % Allowed : 24.40 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2711 helix: 1.18 (0.14), residues: 1508 sheet: 0.11 (0.36), residues: 216 loop : -1.90 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 2 438 TYR 0.015 0.001 TYR 5 184 PHE 0.021 0.001 PHE 4 473 TRP 0.021 0.002 TRP 2 443 HIS 0.008 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00340 (22932) covalent geometry : angle 0.58094 (31290) hydrogen bonds : bond 0.04557 ( 1055) hydrogen bonds : angle 4.40715 ( 3048) Misc. bond : bond 0.00385 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 250 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 276 GLN cc_start: 0.5928 (OUTLIER) cc_final: 0.5663 (pp30) REVERT: 2 258 ASN cc_start: 0.7768 (t0) cc_final: 0.7432 (t0) REVERT: 2 300 MET cc_start: 0.5291 (mmp) cc_final: 0.4824 (mmm) REVERT: 3 170 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7155 (mt) REVERT: 3 173 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (mm) REVERT: 4 564 MET cc_start: 0.8131 (tpp) cc_final: 0.7832 (tpp) REVERT: 4 652 ILE cc_start: 0.8333 (mm) cc_final: 0.8056 (mt) REVERT: 5 103 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7560 (mmt90) REVERT: 5 167 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: 5 265 TRP cc_start: 0.7764 (t-100) cc_final: 0.6505 (m-90) REVERT: 5 273 ILE cc_start: 0.6679 (mm) cc_final: 0.6423 (mm) REVERT: 6 164 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6577 (tm-30) REVERT: 6 470 ARG cc_start: 0.8099 (tpt-90) cc_final: 0.7885 (tpt-90) REVERT: 6 495 TYR cc_start: 0.7308 (m-80) cc_final: 0.7103 (m-10) REVERT: 6 505 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8330 (mp10) outliers start: 72 outliers final: 35 residues processed: 307 average time/residue: 0.1332 time to fit residues: 67.0716 Evaluate side-chains 272 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 353 VAL Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 980 VAL Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 114 LEU Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 238 ASP Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 400 ILE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 505 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 107 optimal weight: 0.6980 chunk 0 optimal weight: 10.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 8 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 242 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 HIS 3 277 GLN ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN 6 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.176159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.141669 restraints weight = 44769.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.141617 restraints weight = 57124.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143268 restraints weight = 48066.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.143457 restraints weight = 31853.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144850 restraints weight = 29137.816| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22933 Z= 0.127 Angle : 0.552 9.553 31290 Z= 0.281 Chirality : 0.039 0.319 3635 Planarity : 0.004 0.062 3880 Dihedral : 10.234 127.437 3663 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.99 % Allowed : 24.31 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2711 helix: 1.25 (0.14), residues: 1501 sheet: 0.03 (0.35), residues: 216 loop : -1.90 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 151 TYR 0.023 0.001 TYR 4 341 PHE 0.026 0.001 PHE 6 492 TRP 0.022 0.001 TRP 2 443 HIS 0.007 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00292 (22932) covalent geometry : angle 0.55221 (31290) hydrogen bonds : bond 0.03810 ( 1055) hydrogen bonds : angle 4.19021 ( 3048) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 248 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 258 ASN cc_start: 0.7749 (t0) cc_final: 0.7359 (t0) REVERT: 3 128 MET cc_start: 0.8326 (ttm) cc_final: 0.8120 (ttm) REVERT: 3 170 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7010 (mt) REVERT: 3 173 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8239 (mm) REVERT: 3 183 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6263 (pp) REVERT: 4 564 MET cc_start: 0.8045 (tpp) cc_final: 0.7735 (tpp) REVERT: 4 652 ILE cc_start: 0.8377 (mm) cc_final: 0.8058 (mt) REVERT: 4 778 ASP cc_start: 0.6529 (t70) cc_final: 0.6281 (t0) REVERT: 5 167 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5981 (m-80) REVERT: 5 265 TRP cc_start: 0.7725 (t-100) cc_final: 0.6376 (m-90) REVERT: 6 130 GLU cc_start: 0.8076 (tp30) cc_final: 0.7871 (tp30) REVERT: 6 164 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6417 (tm-30) REVERT: 6 307 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6738 (t80) REVERT: 6 470 ARG cc_start: 0.8020 (tpt-90) cc_final: 0.7732 (tpt-90) outliers start: 93 outliers final: 49 residues processed: 325 average time/residue: 0.1382 time to fit residues: 73.5267 Evaluate side-chains 285 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 255 VAL Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 287 ASN Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 168 HIS Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 173 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 400 ILE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 441 LEU Chi-restraints excluded: chain 6 residue 449 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 99 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 218 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 167 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.177246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143204 restraints weight = 44901.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144787 restraints weight = 58898.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145751 restraints weight = 41706.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146511 restraints weight = 28329.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146954 restraints weight = 26547.797| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22933 Z= 0.107 Angle : 0.546 12.724 31290 Z= 0.273 Chirality : 0.039 0.268 3635 Planarity : 0.004 0.057 3880 Dihedral : 10.076 126.655 3659 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.31 % Allowed : 24.57 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2711 helix: 1.32 (0.14), residues: 1504 sheet: -0.12 (0.35), residues: 209 loop : -1.83 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 1 465 TYR 0.013 0.001 TYR 3 393 PHE 0.027 0.001 PHE 6 492 TRP 0.018 0.001 TRP 2 443 HIS 0.018 0.001 HIS 3 168 Details of bonding type rmsd covalent geometry : bond 0.00236 (22932) covalent geometry : angle 0.54570 (31290) hydrogen bonds : bond 0.03392 ( 1055) hydrogen bonds : angle 4.06526 ( 3048) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 100 TYR cc_start: 0.7253 (t80) cc_final: 0.6888 (t80) REVERT: 3 128 MET cc_start: 0.8261 (ttm) cc_final: 0.8030 (ttm) REVERT: 3 133 TYR cc_start: 0.5926 (m-80) cc_final: 0.5721 (t80) REVERT: 3 170 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7144 (mt) REVERT: 3 183 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6370 (pp) REVERT: 4 348 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: 4 564 MET cc_start: 0.7889 (tpp) cc_final: 0.7613 (tpp) REVERT: 4 652 ILE cc_start: 0.8299 (mm) cc_final: 0.7935 (mt) REVERT: 4 836 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6671 (m-70) REVERT: 5 167 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5695 (m-80) REVERT: 5 265 TRP cc_start: 0.7623 (t-100) cc_final: 0.6447 (m-90) REVERT: 6 164 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6328 (tm-30) REVERT: 6 307 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6702 (t80) REVERT: 6 470 ARG cc_start: 0.7967 (tpt-90) cc_final: 0.7519 (tpt-90) outliers start: 77 outliers final: 49 residues processed: 306 average time/residue: 0.1279 time to fit residues: 64.6226 Evaluate side-chains 281 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 209 TRP Chi-restraints excluded: chain 1 residue 276 GLN Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 287 ASN Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 670 LEU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 258 VAL Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 404 PHE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 204 optimal weight: 0.3980 chunk 207 optimal weight: 0.0970 chunk 253 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 274 optimal weight: 0.0270 chunk 262 optimal weight: 8.9990 chunk 246 optimal weight: 0.5980 chunk 259 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 174 ASN ** 1 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.179588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.146786 restraints weight = 44521.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.147580 restraints weight = 61117.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.148871 restraints weight = 48570.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.149481 restraints weight = 31498.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.150024 restraints weight = 29712.436| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22933 Z= 0.101 Angle : 0.532 9.150 31290 Z= 0.268 Chirality : 0.038 0.262 3635 Planarity : 0.004 0.058 3880 Dihedral : 9.948 125.534 3659 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.57 % Allowed : 24.31 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2711 helix: 1.39 (0.14), residues: 1502 sheet: -0.04 (0.35), residues: 209 loop : -1.78 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 151 TYR 0.014 0.001 TYR 6 504 PHE 0.029 0.001 PHE 6 492 TRP 0.019 0.001 TRP 2 443 HIS 0.005 0.001 HIS 41013 Details of bonding type rmsd covalent geometry : bond 0.00218 (22932) covalent geometry : angle 0.53226 (31290) hydrogen bonds : bond 0.03142 ( 1055) hydrogen bonds : angle 3.95771 ( 3048) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 241 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 128 MET cc_start: 0.8324 (ttm) cc_final: 0.8097 (ttm) REVERT: 3 170 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.6908 (mt) REVERT: 3 183 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6009 (pp) REVERT: 3 327 ILE cc_start: 0.8205 (mt) cc_final: 0.7914 (tp) REVERT: 4 348 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: 4 564 MET cc_start: 0.7853 (tpp) cc_final: 0.7622 (tpp) REVERT: 4 652 ILE cc_start: 0.8124 (mm) cc_final: 0.7858 (mt) REVERT: 4 778 ASP cc_start: 0.6464 (t70) cc_final: 0.5965 (t0) REVERT: 4 836 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6654 (m-70) REVERT: 5 103 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7562 (mmm-85) REVERT: 5 167 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: 5 265 TRP cc_start: 0.7618 (t-100) cc_final: 0.6547 (t-100) REVERT: 6 164 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6283 (tm-30) REVERT: 6 307 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6563 (t80) REVERT: 6 470 ARG cc_start: 0.7916 (tpt-90) cc_final: 0.7641 (tpt-90) outliers start: 83 outliers final: 49 residues processed: 311 average time/residue: 0.1396 time to fit residues: 70.2280 Evaluate side-chains 284 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 320 SER Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 348 GLN Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 670 LEU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 170 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 404 PHE Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 148 optimal weight: 0.5980 chunk 217 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 232 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 276 GLN ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.179000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.144791 restraints weight = 44464.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145528 restraints weight = 52817.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146721 restraints weight = 46007.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.147065 restraints weight = 28980.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.147763 restraints weight = 26815.963| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22933 Z= 0.104 Angle : 0.549 14.406 31290 Z= 0.273 Chirality : 0.039 0.264 3635 Planarity : 0.004 0.059 3880 Dihedral : 9.871 125.039 3659 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.91 % Allowed : 24.57 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2711 helix: 1.42 (0.14), residues: 1503 sheet: -0.00 (0.35), residues: 209 loop : -1.75 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 151 TYR 0.015 0.001 TYR 3 393 PHE 0.029 0.001 PHE 6 492 TRP 0.019 0.001 TRP 2 443 HIS 0.006 0.001 HIS 41013 Details of bonding type rmsd covalent geometry : bond 0.00233 (22932) covalent geometry : angle 0.54851 (31290) hydrogen bonds : bond 0.03108 ( 1055) hydrogen bonds : angle 3.92788 ( 3048) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 240 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 419 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8498 (pp20) REVERT: 2 257 GLN cc_start: 0.6546 (tp40) cc_final: 0.6253 (tp40) REVERT: 3 128 MET cc_start: 0.8327 (ttm) cc_final: 0.8098 (ttm) REVERT: 3 170 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7063 (mt) REVERT: 3 327 ILE cc_start: 0.8287 (mt) cc_final: 0.7953 (tp) REVERT: 4 564 MET cc_start: 0.7804 (tpp) cc_final: 0.7417 (tpp) REVERT: 4 778 ASP cc_start: 0.6503 (t70) cc_final: 0.5938 (t0) REVERT: 4 836 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6721 (m-70) REVERT: 5 103 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7566 (mmm-85) REVERT: 5 167 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: 5 265 TRP cc_start: 0.7651 (t-100) cc_final: 0.6513 (t-100) REVERT: 6 164 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6284 (tm-30) REVERT: 6 307 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.6633 (t80) REVERT: 6 470 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.7866 (mmp80) outliers start: 91 outliers final: 58 residues processed: 318 average time/residue: 0.1385 time to fit residues: 71.7570 Evaluate side-chains 294 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 230 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 320 SER Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 332 THR Chi-restraints excluded: chain 2 residue 351 MET Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 670 LEU Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 1083 LEU Chi-restraints excluded: chain 5 residue 61 MET Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 237 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 157 optimal weight: 0.4980 chunk 266 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 91 optimal weight: 0.0870 chunk 86 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 276 GLN ** 2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.178591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.144475 restraints weight = 44434.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144653 restraints weight = 55616.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.146105 restraints weight = 45237.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146771 restraints weight = 29379.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.147323 restraints weight = 27757.122| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22933 Z= 0.105 Angle : 0.545 10.917 31290 Z= 0.271 Chirality : 0.038 0.265 3635 Planarity : 0.004 0.059 3880 Dihedral : 9.812 124.337 3659 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.74 % Allowed : 24.79 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2711 helix: 1.43 (0.14), residues: 1505 sheet: -0.03 (0.36), residues: 207 loop : -1.74 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 556 TYR 0.013 0.001 TYR 3 100 PHE 0.028 0.001 PHE 6 492 TRP 0.016 0.001 TRP 2 443 HIS 0.006 0.001 HIS 41013 Details of bonding type rmsd covalent geometry : bond 0.00236 (22932) covalent geometry : angle 0.54484 (31290) hydrogen bonds : bond 0.03054 ( 1055) hydrogen bonds : angle 3.89192 ( 3048) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 408 ARG cc_start: 0.7732 (ptm160) cc_final: 0.7406 (ptm160) REVERT: 1 419 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8505 (pp20) REVERT: 2 257 GLN cc_start: 0.6617 (tp40) cc_final: 0.6328 (tp-100) REVERT: 3 128 MET cc_start: 0.8300 (ttm) cc_final: 0.8090 (ttm) REVERT: 3 170 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7045 (mt) REVERT: 3 327 ILE cc_start: 0.8262 (mt) cc_final: 0.7949 (tp) REVERT: 4 564 MET cc_start: 0.7751 (tpp) cc_final: 0.7409 (tpp) REVERT: 4 778 ASP cc_start: 0.6544 (t70) cc_final: 0.6013 (t0) REVERT: 4 836 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6741 (m-70) REVERT: 5 103 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7564 (mmm-85) REVERT: 5 167 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: 5 265 TRP cc_start: 0.7678 (t-100) cc_final: 0.6603 (t-100) REVERT: 6 85 MET cc_start: 0.8362 (mmp) cc_final: 0.8072 (mmp) REVERT: 6 164 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6295 (tm-30) REVERT: 6 307 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.6743 (t80) outliers start: 87 outliers final: 59 residues processed: 314 average time/residue: 0.1383 time to fit residues: 71.1832 Evaluate side-chains 294 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 320 SER Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 122 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 5 residue 61 MET Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 170 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 116 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 276 GLN ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.176680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142190 restraints weight = 44054.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142286 restraints weight = 56251.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143922 restraints weight = 45167.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144336 restraints weight = 29320.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.144969 restraints weight = 28148.799| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22933 Z= 0.138 Angle : 0.587 15.593 31290 Z= 0.291 Chirality : 0.039 0.262 3635 Planarity : 0.004 0.060 3880 Dihedral : 9.797 124.912 3659 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.52 % Allowed : 25.39 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2711 helix: 1.32 (0.14), residues: 1508 sheet: -0.18 (0.35), residues: 207 loop : -1.81 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 4 556 TYR 0.018 0.001 TYR 5 184 PHE 0.028 0.001 PHE 6 492 TRP 0.019 0.001 TRP 2 443 HIS 0.010 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00325 (22932) covalent geometry : angle 0.58706 (31290) hydrogen bonds : bond 0.03469 ( 1055) hydrogen bonds : angle 3.96384 ( 3048) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 235 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 419 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8514 (pp20) REVERT: 2 291 MET cc_start: 0.7898 (ptt) cc_final: 0.6180 (ttt) REVERT: 3 128 MET cc_start: 0.8356 (ttm) cc_final: 0.8107 (ttm) REVERT: 3 170 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7225 (mt) REVERT: 3 183 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6350 (pp) REVERT: 3 327 ILE cc_start: 0.8312 (mt) cc_final: 0.7972 (tp) REVERT: 4 564 MET cc_start: 0.7687 (tpp) cc_final: 0.7390 (tpp) REVERT: 4 836 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6811 (m-70) REVERT: 5 103 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7604 (mmm-85) REVERT: 5 167 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: 5 265 TRP cc_start: 0.7697 (t-100) cc_final: 0.6760 (t-100) REVERT: 6 85 MET cc_start: 0.8467 (mmp) cc_final: 0.8199 (mmp) REVERT: 6 164 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6378 (tm-30) REVERT: 6 307 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.6840 (t80) outliers start: 82 outliers final: 61 residues processed: 308 average time/residue: 0.1376 time to fit residues: 69.3216 Evaluate side-chains 294 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 225 PHE Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 175 SER Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 366 ILE Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 1062 LEU Chi-restraints excluded: chain 5 residue 103 ARG Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 170 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 86 LEU Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 38 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 271 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 321 HIS ** 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 = 0.4411 r_free = 0.4411 target = 0.178276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.145367 restraints weight = 44737.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.147112 restraints weight = 58720.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147986 restraints weight = 43340.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.148325 restraints weight = 29395.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.148951 restraints weight = 27864.287| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22933 Z= 0.111 Angle : 0.583 11.041 31290 Z= 0.290 Chirality : 0.039 0.266 3635 Planarity : 0.004 0.059 3880 Dihedral : 9.718 123.566 3659 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.05 % Allowed : 26.12 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2711 helix: 1.34 (0.14), residues: 1506 sheet: -0.12 (0.36), residues: 207 loop : -1.80 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 4 556 TYR 0.016 0.001 TYR 6 507 PHE 0.022 0.001 PHE 6 302 TRP 0.019 0.001 TRP 2 443 HIS 0.032 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00252 (22932) covalent geometry : angle 0.58266 (31290) hydrogen bonds : bond 0.03193 ( 1055) hydrogen bonds : angle 3.91051 ( 3048) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 237 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 419 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8506 (pp20) REVERT: 2 291 MET cc_start: 0.7851 (ptt) cc_final: 0.6322 (ttt) REVERT: 3 128 MET cc_start: 0.8285 (ttm) cc_final: 0.8073 (ttm) REVERT: 3 170 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7650 (mt) REVERT: 3 183 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6417 (pp) REVERT: 3 327 ILE cc_start: 0.8199 (mt) cc_final: 0.7902 (tp) REVERT: 4 564 MET cc_start: 0.7665 (tpp) cc_final: 0.7416 (tpp) REVERT: 4 836 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6821 (m-70) REVERT: 5 167 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6164 (m-80) REVERT: 5 265 TRP cc_start: 0.7604 (t-100) cc_final: 0.6656 (t-100) REVERT: 6 85 MET cc_start: 0.8431 (mmp) cc_final: 0.8132 (mmp) REVERT: 6 164 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6302 (tm-30) REVERT: 6 307 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6774 (t80) outliers start: 71 outliers final: 56 residues processed: 298 average time/residue: 0.1312 time to fit residues: 64.8237 Evaluate side-chains 286 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 224 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 170 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 308 PHE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 216 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 240 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 321 HIS ** 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 = 0.4405 r_free = 0.4405 target = 0.177448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.143332 restraints weight = 44469.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144407 restraints weight = 57128.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145761 restraints weight = 42561.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.146290 restraints weight = 28149.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.146878 restraints weight = 26904.577| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22933 Z= 0.121 Angle : 0.608 16.386 31290 Z= 0.298 Chirality : 0.039 0.269 3635 Planarity : 0.004 0.060 3880 Dihedral : 9.673 124.223 3659 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.05 % Allowed : 26.37 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2711 helix: 1.30 (0.14), residues: 1508 sheet: -0.13 (0.36), residues: 207 loop : -1.81 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 4 556 TYR 0.016 0.001 TYR 3 393 PHE 0.022 0.001 PHE 4 473 TRP 0.022 0.001 TRP 4 700 HIS 0.032 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00279 (22932) covalent geometry : angle 0.60848 (31290) hydrogen bonds : bond 0.03279 ( 1055) hydrogen bonds : angle 3.88882 ( 3048) Misc. bond : bond 0.00037 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 230 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: 1 419 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: 2 291 MET cc_start: 0.8081 (ptt) cc_final: 0.7632 (ptt) REVERT: 3 128 MET cc_start: 0.8315 (ttm) cc_final: 0.8087 (ttm) REVERT: 3 170 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7600 (mt) REVERT: 3 327 ILE cc_start: 0.8313 (mt) cc_final: 0.7986 (tp) REVERT: 4 564 MET cc_start: 0.7759 (tpp) cc_final: 0.7433 (tpp) REVERT: 4 836 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6800 (m-70) REVERT: 5 167 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: 5 265 TRP cc_start: 0.7698 (t-100) cc_final: 0.6783 (t-100) REVERT: 6 85 MET cc_start: 0.8429 (mmp) cc_final: 0.8155 (mmp) REVERT: 6 164 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6335 (tm-30) REVERT: 6 307 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6876 (t80) outliers start: 71 outliers final: 62 residues processed: 292 average time/residue: 0.1323 time to fit residues: 63.4113 Evaluate side-chains 291 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 LEU Chi-restraints excluded: chain 1 residue 261 TRP Chi-restraints excluded: chain 1 residue 388 THR Chi-restraints excluded: chain 1 residue 394 VAL Chi-restraints excluded: chain 1 residue 419 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 444 VAL Chi-restraints excluded: chain 1 residue 446 LEU Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 2 residue 111 VAL Chi-restraints excluded: chain 2 residue 182 THR Chi-restraints excluded: chain 2 residue 202 VAL Chi-restraints excluded: chain 2 residue 267 VAL Chi-restraints excluded: chain 2 residue 275 HIS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 368 ILE Chi-restraints excluded: chain 2 residue 399 CYS Chi-restraints excluded: chain 2 residue 416 THR Chi-restraints excluded: chain 2 residue 420 VAL Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 456 ILE Chi-restraints excluded: chain 3 residue 37 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 183 LEU Chi-restraints excluded: chain 3 residue 188 THR Chi-restraints excluded: chain 3 residue 256 THR Chi-restraints excluded: chain 3 residue 336 TYR Chi-restraints excluded: chain 3 residue 410 LEU Chi-restraints excluded: chain 4 residue 366 ILE Chi-restraints excluded: chain 4 residue 527 CYS Chi-restraints excluded: chain 4 residue 569 SER Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 625 VAL Chi-restraints excluded: chain 4 residue 636 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 737 VAL Chi-restraints excluded: chain 4 residue 761 LEU Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 836 HIS Chi-restraints excluded: chain 4 residue 889 ILE Chi-restraints excluded: chain 4 residue 895 VAL Chi-restraints excluded: chain 4 residue 944 VAL Chi-restraints excluded: chain 4 residue 955 THR Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 964 ILE Chi-restraints excluded: chain 4 residue 1009 THR Chi-restraints excluded: chain 5 residue 121 THR Chi-restraints excluded: chain 5 residue 126 CYS Chi-restraints excluded: chain 5 residue 167 PHE Chi-restraints excluded: chain 5 residue 170 PHE Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 222 LEU Chi-restraints excluded: chain 5 residue 235 ASP Chi-restraints excluded: chain 5 residue 246 TYR Chi-restraints excluded: chain 6 residue 109 VAL Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 193 SER Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 282 PHE Chi-restraints excluded: chain 6 residue 297 GLN Chi-restraints excluded: chain 6 residue 307 TYR Chi-restraints excluded: chain 6 residue 308 PHE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 449 LEU Chi-restraints excluded: chain 6 residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 92 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 145 optimal weight: 0.0770 chunk 103 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.177940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.143587 restraints weight = 44540.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143906 restraints weight = 55868.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.145459 restraints weight = 44725.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.146017 restraints weight = 29051.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.146591 restraints weight = 27689.280| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22933 Z= 0.115 Angle : 0.601 15.103 31290 Z= 0.296 Chirality : 0.040 0.329 3635 Planarity : 0.004 0.060 3880 Dihedral : 9.618 123.231 3659 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.22 % Allowed : 26.25 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2711 helix: 1.33 (0.14), residues: 1506 sheet: -0.08 (0.36), residues: 206 loop : -1.82 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 6 470 TYR 0.016 0.001 TYR 3 100 PHE 0.021 0.001 PHE 6 302 TRP 0.020 0.001 TRP 2 443 HIS 0.031 0.001 HIS 3 321 Details of bonding type rmsd covalent geometry : bond 0.00261 (22932) covalent geometry : angle 0.60100 (31290) hydrogen bonds : bond 0.03184 ( 1055) hydrogen bonds : angle 3.88037 ( 3048) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3303.17 seconds wall clock time: 58 minutes 2.46 seconds (3482.46 seconds total)