Starting phenix.real_space_refine on Tue Aug 26 23:35:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.map" model { file = "/net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qpa_18546/08_2025/8qpa_18546.cif" } 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= 0.000 sd= 0.005 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 211 5.49 5 S 162 5.16 5 C 26821 2.51 5 N 7654 2.21 5 O 8607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43455 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 158 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "G" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1077 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2874 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "F" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 488 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "N" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3095 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 23, 'TRANS': 433} Chain breaks: 4 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 798 Unresolved non-hydrogen dihedrals: 542 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 7, 'ASP:plan': 8, 'ARG:plan': 15, 'GLU:plan': 16, 'ASN:plan1': 6, 'TRP:plan': 7, 'PHE:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 16383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1971, 16383 Classifications: {'peptide': 1971} Link IDs: {'PCIS': 1, 'PTRANS': 106, 'TRANS': 1863} Chain breaks: 2 Chain: "U" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3749 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain: "S" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6592 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 48, 'TRANS': 787} Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 962 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "D" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1170 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "5" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1660 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 26, 'rna3p_pyr': 40} Link IDs: {'rna2p': 13, 'rna3p': 65} Chain: "z" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 15} Chain: "7" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 650 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "4" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1322 Classifications: {'RNA': 62} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 25, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 47} Chain: "6" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1010 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 15} Link IDs: {'rna2p': 4, 'rna3p': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.46, per 1000 atoms: 0.19 Number of scatterers: 43455 At special positions: 0 Unit cell: (197.2, 205.32, 174, 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 162 16.00 P 211 15.00 O 8607 8.00 N 7654 7.00 C 26821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9290 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 35 sheets defined 50.8% alpha, 8.9% beta 52 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'G' and resid 242 through 255 Processing helix chain 'G' and resid 277 through 281 removed outlier: 3.714A pdb=" N GLU G 280 " --> pdb=" O ASP G 277 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G 281 " --> pdb=" O ALA G 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 277 through 281' Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 297 through 301 removed outlier: 3.517A pdb=" N ARG G 301 " --> pdb=" O LEU G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 316 Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 332 Processing helix chain 'G' and resid 333 through 354 removed outlier: 3.643A pdb=" N GLN G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 360 removed outlier: 3.518A pdb=" N GLN G 359 " --> pdb=" O HIS G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 376 Processing helix chain 'J' and resid 441 through 467 Processing helix chain 'J' and resid 480 through 485 Processing helix chain 'J' and resid 485 through 490 Processing helix chain 'J' and resid 492 through 519 Processing helix chain 'L' and resid 53 through 79 removed outlier: 4.331A pdb=" N PHE L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 119 removed outlier: 3.815A pdb=" N VAL L 92 " --> pdb=" O PRO L 88 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE L 109 " --> pdb=" O ASN L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 131 through 143 removed outlier: 3.559A pdb=" N GLY L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 157 removed outlier: 3.677A pdb=" N GLN L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 173 Processing helix chain 'L' and resid 180 through 216 removed outlier: 3.603A pdb=" N ARG L 186 " --> pdb=" O GLU L 182 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU L 188 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR L 207 " --> pdb=" O ARG L 203 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N PHE L 214 " --> pdb=" O SER L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 223 removed outlier: 3.834A pdb=" N ILE L 222 " --> pdb=" O ASN L 218 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE L 223 " --> pdb=" O LEU L 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 218 through 223' Processing helix chain 'L' and resid 224 through 235 removed outlier: 3.730A pdb=" N VAL L 234 " --> pdb=" O LYS L 230 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA L 235 " --> pdb=" O ILE L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 243 Processing helix chain 'L' and resid 245 through 251 removed outlier: 3.844A pdb=" N LEU L 251 " --> pdb=" O CYS L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 276 Processing helix chain 'L' and resid 277 through 282 Processing helix chain 'L' and resid 287 through 308 removed outlier: 3.505A pdb=" N VAL L 305 " --> pdb=" O LEU L 301 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE L 308 " --> pdb=" O ARG L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 332 Processing helix chain 'L' and resid 356 through 367 Processing helix chain 'L' and resid 369 through 377 removed outlier: 3.725A pdb=" N ARG L 377 " --> pdb=" O LYS L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 432 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 104 through 116 Processing helix chain 'F' and resid 125 through 138 Processing helix chain 'N' and resid 97 through 113 Processing helix chain 'N' and resid 116 through 135 removed outlier: 3.540A pdb=" N GLN N 122 " --> pdb=" O GLU N 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU N 129 " --> pdb=" O LYS N 125 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET N 133 " --> pdb=" O GLU N 129 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 142 through 149 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 153 through 159 removed outlier: 3.775A pdb=" N LEU N 158 " --> pdb=" O GLU N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 173 Processing helix chain 'N' and resid 184 through 194 removed outlier: 3.612A pdb=" N LEU N 191 " --> pdb=" O PHE N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 305 removed outlier: 3.978A pdb=" N LEU N 296 " --> pdb=" O LYS N 292 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU N 303 " --> pdb=" O LYS N 299 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 322 removed outlier: 3.911A pdb=" N TRP N 312 " --> pdb=" O HIS N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 336 Processing helix chain 'N' and resid 342 through 352 removed outlier: 3.607A pdb=" N TRP N 346 " --> pdb=" O SER N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 369 removed outlier: 3.634A pdb=" N ALA N 358 " --> pdb=" O PRO N 354 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS N 359 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN N 364 " --> pdb=" O ALA N 360 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL N 366 " --> pdb=" O VAL N 362 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG N 367 " --> pdb=" O ALA N 363 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 368 " --> pdb=" O GLN N 364 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 383 Processing helix chain 'N' and resid 385 through 399 Processing helix chain 'N' and resid 403 through 412 removed outlier: 3.606A pdb=" N GLU N 412 " --> pdb=" O LYS N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 793 through 806 Processing helix chain 'N' and resid 810 through 821 removed outlier: 3.972A pdb=" N ILE N 818 " --> pdb=" O TRP N 814 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE N 819 " --> pdb=" O SER N 815 " (cutoff:3.500A) Processing helix chain 'N' and resid 826 through 836 Processing helix chain 'N' and resid 842 through 854 Processing helix chain 'N' and resid 856 through 868 Processing helix chain 'N' and resid 869 through 873 removed outlier: 3.641A pdb=" N ASP N 873 " --> pdb=" O ILE N 870 " (cutoff:3.500A) Processing helix chain 'N' and resid 874 through 887 removed outlier: 3.797A pdb=" N TRP N 878 " --> pdb=" O LEU N 874 " (cutoff:3.500A) Processing helix chain 'N' and resid 893 through 903 Processing helix chain 'N' and resid 907 through 919 Processing helix chain 'N' and resid 923 through 930 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.508A pdb=" N ILE A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.582A pdb=" N LYS A 93 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 removed outlier: 3.507A pdb=" N ARG A 152 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.361A pdb=" N ASP A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.539A pdb=" N LEU A 246 " --> pdb=" O ASN A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 396 through 406 removed outlier: 4.615A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.614A pdb=" N ASN A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.844A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 432' Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.991A pdb=" N SER A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.887A pdb=" N SER A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 595 through 596 No H-bonds generated for 'chain 'A' and resid 595 through 596' Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.131A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 656 removed outlier: 3.752A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.593A pdb=" N GLY A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 852 removed outlier: 3.998A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 933 removed outlier: 3.808A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.865A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1014 Processing helix chain 'A' and resid 1036 through 1062 removed outlier: 4.297A pdb=" N LEU A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A1051 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 3.726A pdb=" N GLU A1080 " --> pdb=" O ASP A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 3.601A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.595A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1272 removed outlier: 3.603A pdb=" N LEU A1270 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 3.925A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 4.244A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1400 removed outlier: 3.627A pdb=" N GLU A1395 " --> pdb=" O LEU A1391 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1396 " --> pdb=" O LYS A1392 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 Processing helix chain 'A' and resid 1410 through 1412 No H-bonds generated for 'chain 'A' and resid 1410 through 1412' Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1428 through 1433 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1486 Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1507 through 1516 removed outlier: 4.073A pdb=" N TRP A1515 " --> pdb=" O GLU A1511 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A1516 " --> pdb=" O SER A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1525 Processing helix chain 'A' and resid 1528 through 1538 removed outlier: 3.534A pdb=" N ARG A1532 " --> pdb=" O GLN A1528 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A1533 " --> pdb=" O ILE A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 removed outlier: 3.825A pdb=" N PHE A1597 " --> pdb=" O LEU A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1604 Processing helix chain 'A' and resid 1615 through 1620 removed outlier: 4.245A pdb=" N SER A1619 " --> pdb=" O PRO A1616 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A1620 " --> pdb=" O ARG A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1689 Processing helix chain 'A' and resid 1721 through 1736 removed outlier: 3.581A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1768 through 1772 Processing helix chain 'A' and resid 1823 through 1827 Processing helix chain 'A' and resid 1832 through 1852 removed outlier: 3.598A pdb=" N THR A1841 " --> pdb=" O ALA A1837 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A1842 " --> pdb=" O LYS A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1857 Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 removed outlier: 3.719A pdb=" N LEU A1872 " --> pdb=" O MET A1868 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1873 " --> pdb=" O LEU A1869 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A1874 " --> pdb=" O ASP A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1898 removed outlier: 3.897A pdb=" N LEU A1897 " --> pdb=" O GLN A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1908 removed outlier: 4.754A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A1906 " --> pdb=" O PHE A1902 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A1908 " --> pdb=" O ASP A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 Processing helix chain 'A' and resid 1928 through 1946 removed outlier: 3.708A pdb=" N SER A1934 " --> pdb=" O TYR A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1946 through 1955 removed outlier: 3.759A pdb=" N ALA A1950 " --> pdb=" O ASN A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1996 Processing helix chain 'A' and resid 1998 through 2002 Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 186 through 194 removed outlier: 3.814A pdb=" N THR U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL U 192 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU U 193 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS U 194 " --> pdb=" O THR U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 198 through 204 Processing helix chain 'U' and resid 233 through 244 Processing helix chain 'U' and resid 246 through 251 Processing helix chain 'U' and resid 255 through 259 removed outlier: 3.571A pdb=" N ASN U 258 " --> pdb=" O GLU U 255 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR U 259 " --> pdb=" O GLU U 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 255 through 259' Processing helix chain 'U' and resid 270 through 285 removed outlier: 3.809A pdb=" N VAL U 274 " --> pdb=" O MET U 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 296 through 307 removed outlier: 3.794A pdb=" N GLN U 301 " --> pdb=" O HIS U 297 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA U 302 " --> pdb=" O GLU U 298 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 334 removed outlier: 3.661A pdb=" N TRP U 325 " --> pdb=" O ASP U 321 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN U 328 " --> pdb=" O SER U 324 " (cutoff:3.500A) Processing helix chain 'U' and resid 345 through 350 Processing helix chain 'U' and resid 366 through 376 Processing helix chain 'U' and resid 415 through 420 Processing helix chain 'U' and resid 480 through 484 removed outlier: 3.603A pdb=" N LEU U 484 " --> pdb=" O ARG U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 485 through 490 Processing helix chain 'U' and resid 540 through 545 Processing helix chain 'S' and resid 157 through 185 removed outlier: 3.515A pdb=" N GLN S 182 " --> pdb=" O ARG S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 198 removed outlier: 4.236A pdb=" N ASP S 198 " --> pdb=" O PRO S 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 195 through 198' Processing helix chain 'S' and resid 199 through 217 removed outlier: 3.741A pdb=" N LYS S 214 " --> pdb=" O LEU S 210 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP S 215 " --> pdb=" O GLN S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 266 Processing helix chain 'S' and resid 291 through 309 Processing helix chain 'S' and resid 328 through 336 removed outlier: 4.259A pdb=" N LEU S 334 " --> pdb=" O PRO S 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 removed outlier: 3.716A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 220 removed outlier: 4.006A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.618A pdb=" N ARG C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 270 through 293 removed outlier: 4.330A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 391 through 398 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.687A pdb=" N GLN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.562A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.704A pdb=" N SER C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 613 removed outlier: 3.668A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 697 through 702 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.500A pdb=" N ARG C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 772 removed outlier: 4.037A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 removed outlier: 3.542A pdb=" N GLU C 776 " --> pdb=" O TRP C 772 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 777 " --> pdb=" O GLY C 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 772 through 777' Processing helix chain 'C' and resid 804 through 823 Proline residue: C 810 - end of helix Processing helix chain 'C' and resid 839 through 841 No H-bonds generated for 'chain 'C' and resid 839 through 841' Processing helix chain 'C' and resid 842 through 853 removed outlier: 3.786A pdb=" N VAL C 849 " --> pdb=" O ALA C 845 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 889 removed outlier: 3.901A pdb=" N ARG C 888 " --> pdb=" O GLU C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 942 removed outlier: 4.334A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG C 931 " --> pdb=" O PRO C 927 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 32 removed outlier: 4.330A pdb=" N LYS M 21 " --> pdb=" O HIS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 48 Processing helix chain 'M' and resid 62 through 66 Processing helix chain 'M' and resid 67 through 77 removed outlier: 4.144A pdb=" N LEU M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 removed outlier: 3.510A pdb=" N LEU M 89 " --> pdb=" O SER M 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY M 94 " --> pdb=" O GLY M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 125 Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.773A pdb=" N VAL D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 42 removed outlier: 3.568A pdb=" N MET D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.837A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 126 " --> pdb=" O GLY D 122 " (cutoff:3.500A) Processing helix chain '7' and resid 424 through 433 removed outlier: 4.027A pdb=" N LEU 7 433 " --> pdb=" O MET 7 429 " (cutoff:3.500A) Processing helix chain '7' and resid 437 through 452 removed outlier: 3.899A pdb=" N GLN 7 441 " --> pdb=" O ARG 7 437 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER 7 445 " --> pdb=" O GLN 7 441 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE 7 446 " --> pdb=" O ARG 7 442 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG 7 447 " --> pdb=" O ASP 7 443 " (cutoff:3.500A) Processing helix chain '7' and resid 458 through 473 removed outlier: 3.587A pdb=" N ARG 7 472 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 180 through 181 removed outlier: 3.506A pdb=" N THR N 180 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.605A pdb=" N ARG A 419 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA7, first strand: chain 'A' and resid 905 through 910 Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 4.132A pdb=" N THR A1167 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1090 Processing sheet with id=AB1, first strand: chain 'A' and resid 1185 through 1188 Processing sheet with id=AB2, first strand: chain 'A' and resid 1342 through 1345 Processing sheet with id=AB3, first strand: chain 'A' and resid 1501 through 1503 removed outlier: 3.599A pdb=" N TYR A1754 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AB5, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 7.529A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A1629 " --> pdb=" O ILE A1662 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1808 through 1810 removed outlier: 3.554A pdb=" N PHE A1810 " --> pdb=" O PHE A1779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1799 through 1803 removed outlier: 4.495A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR S 258 " --> pdb=" O LEU S 289 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 142 through 143 removed outlier: 4.015A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 226 through 227 removed outlier: 6.035A pdb=" N GLY U 226 " --> pdb=" O VAL U 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 386 through 388 Processing sheet with id=AC2, first strand: chain 'U' and resid 391 through 393 removed outlier: 3.609A pdb=" N ILE U 549 " --> pdb=" O ILE U 503 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA U 501 " --> pdb=" O ILE U 551 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP U 526 " --> pdb=" O ILE U 537 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 412 through 414 removed outlier: 6.443A pdb=" N VAL U 413 " --> pdb=" O ASN U 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'U' and resid 457 through 459 Processing sheet with id=AC5, first strand: chain 'C' and resid 185 through 191 removed outlier: 8.614A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N CYS C 308 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 255 " --> pdb=" O CYS C 308 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER C 310 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE C 257 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 348 through 349 Processing sheet with id=AC7, first strand: chain 'C' and resid 523 through 526 removed outlier: 6.671A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN C 548 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP C 531 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AC9, first strand: chain 'C' and resid 620 through 621 removed outlier: 4.099A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 620 through 621 removed outlier: 4.099A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 783 through 784 removed outlier: 5.978A pdb=" N THR C 870 " --> pdb=" O ASP C 860 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP C 860 " --> pdb=" O THR C 870 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS C 872 " --> pdb=" O THR C 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.715A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 675 through 677 removed outlier: 6.460A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 35 through 37 removed outlier: 3.645A pdb=" N PHE M 53 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL M 81 " --> pdb=" O ILE M 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.483A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL D 25 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR D 59 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL D 27 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D 61 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG D 29 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AD8, first strand: chain '7' and resid 410 through 412 1764 hydrogen bonds defined for protein. 5052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 125 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 11.20 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11495 1.33 - 1.45: 9021 1.45 - 1.57: 23626 1.57 - 1.69: 413 1.69 - 1.81: 269 Bond restraints: 44824 Sorted by residual: bond pdb=" N GLY L 272 " pdb=" CA GLY L 272 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.10e-03 1.21e+04 1.27e+01 bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.609 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.607 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.609 0.060 2.00e-02 2.50e+03 9.09e+00 ... (remaining 44819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 60835 2.20 - 4.41: 739 4.41 - 6.61: 85 6.61 - 8.82: 19 8.82 - 11.02: 1 Bond angle restraints: 61679 Sorted by residual: angle pdb=" C SER A1756 " pdb=" CA SER A1756 " pdb=" CB SER A1756 " ideal model delta sigma weight residual 116.54 110.52 6.02 1.15e+00 7.56e-01 2.74e+01 angle pdb=" N ARG A 510 " pdb=" CA ARG A 510 " pdb=" C ARG A 510 " ideal model delta sigma weight residual 113.12 107.16 5.96 1.25e+00 6.40e-01 2.27e+01 angle pdb=" N VAL 7 479 " pdb=" CA VAL 7 479 " pdb=" C VAL 7 479 " ideal model delta sigma weight residual 113.71 109.25 4.46 9.50e-01 1.11e+00 2.20e+01 angle pdb=" C LYS A1838 " pdb=" N TRP A1839 " pdb=" CA TRP A1839 " ideal model delta sigma weight residual 122.06 114.22 7.84 1.86e+00 2.89e-01 1.78e+01 angle pdb=" N ILE L 223 " pdb=" CA ILE L 223 " pdb=" C ILE L 223 " ideal model delta sigma weight residual 113.53 109.53 4.00 9.80e-01 1.04e+00 1.67e+01 ... (remaining 61674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 26556 35.95 - 71.91: 830 71.91 - 107.86: 92 107.86 - 143.82: 8 143.82 - 179.77: 9 Dihedral angle restraints: 27495 sinusoidal: 13182 harmonic: 14313 Sorted by residual: dihedral pdb=" O4' U z 6 " pdb=" C1' U z 6 " pdb=" N1 U z 6 " pdb=" C2 U z 6 " ideal model delta sinusoidal sigma weight residual 200.00 39.51 160.49 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' C 5 68 " pdb=" C1' C 5 68 " pdb=" N1 C 5 68 " pdb=" C2 C 5 68 " ideal model delta sinusoidal sigma weight residual 200.00 52.70 147.30 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" O4' U 5 80 " pdb=" C1' U 5 80 " pdb=" N1 U 5 80 " pdb=" C2 U 5 80 " ideal model delta sinusoidal sigma weight residual 232.00 52.23 179.77 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 27492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 6984 1.000 - 2.001: 0 2.001 - 3.001: 0 3.001 - 4.002: 0 4.002 - 5.002: 4 Chirality restraints: 6988 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.48 -5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.51 -4.93 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C3 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" O13 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.34 2.44 -4.77 2.00e-01 2.50e+01 5.70e+02 ... (remaining 6985 not shown) Planarity restraints: 7182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1839 " -0.027 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP A1839 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A1839 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A1839 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A1839 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A1839 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1839 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1839 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1839 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1839 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU U 538 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO U 539 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO U 539 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO U 539 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 624 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO A 625 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " -0.027 5.00e-02 4.00e+02 ... (remaining 7179 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3620 2.74 - 3.28: 45307 3.28 - 3.82: 76627 3.82 - 4.36: 91593 4.36 - 4.90: 146680 Nonbonded interactions: 363827 Sorted by model distance: nonbonded pdb=" O2' U 5 78 " pdb=" OP1 U 5 80 " model vdw 2.198 3.040 nonbonded pdb=" O PRO N 354 " pdb=" OG1 THR N 357 " model vdw 2.214 3.040 nonbonded pdb=" O THR C 632 " pdb=" OH TYR C 832 " model vdw 2.214 3.040 nonbonded pdb=" O CYS U 174 " pdb=" N ASN U 178 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU L 141 " pdb=" ND2 ASN L 152 " model vdw 2.220 3.120 ... (remaining 363822 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: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.068 44824 Z= 0.146 Angle : 0.601 11.022 61679 Z= 0.319 Chirality : 0.123 5.002 6988 Planarity : 0.004 0.050 7182 Dihedral : 16.937 179.771 18205 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.12), residues: 4830 helix: 0.47 (0.11), residues: 2140 sheet: -1.22 (0.24), residues: 466 loop : -1.12 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2023 TYR 0.024 0.001 TYR D 76 PHE 0.020 0.001 PHE U 164 TRP 0.072 0.002 TRP A1839 HIS 0.009 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00299 (44824) covalent geometry : angle 0.60051 (61679) hydrogen bonds : bond 0.18332 ( 1869) hydrogen bonds : angle 7.01329 ( 5274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 590 time to evaluate : 1.660 Fit side-chains revert: symmetry clash REVERT: G 311 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7103 (tm-30) REVERT: G 331 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7219 (tt0) REVERT: L 98 ASN cc_start: 0.7254 (m-40) cc_final: 0.7010 (t0) REVERT: N 253 MET cc_start: 0.8416 (tpp) cc_final: 0.8185 (tpp) REVERT: N 278 ASN cc_start: 0.6681 (p0) cc_final: 0.6232 (p0) REVERT: N 344 ASP cc_start: 0.7786 (t70) cc_final: 0.7501 (t70) REVERT: A 290 ASP cc_start: 0.7582 (m-30) cc_final: 0.7257 (m-30) REVERT: A 604 MET cc_start: 0.8207 (tpt) cc_final: 0.7924 (tpt) REVERT: A 848 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6231 (mm-30) REVERT: A 912 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7451 (tm-30) REVERT: A 1189 MET cc_start: 0.7746 (tpp) cc_final: 0.7135 (tpt) REVERT: A 1562 MET cc_start: 0.8607 (mmm) cc_final: 0.8349 (mmm) REVERT: A 1587 GLU cc_start: 0.7887 (tt0) cc_final: 0.6991 (tt0) REVERT: A 1600 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 1914 MET cc_start: 0.7734 (tmm) cc_final: 0.7502 (tmm) REVERT: A 1952 VAL cc_start: 0.8137 (t) cc_final: 0.7918 (t) REVERT: U 353 MET cc_start: 0.7253 (ttp) cc_final: 0.6923 (ttp) REVERT: S 265 SER cc_start: 0.8567 (m) cc_final: 0.8309 (m) REVERT: S 266 PHE cc_start: 0.8376 (m-10) cc_final: 0.8048 (m-10) REVERT: C 203 MET cc_start: 0.7636 (tpp) cc_final: 0.7339 (tpt) REVERT: C 465 MET cc_start: 0.7572 (mmp) cc_final: 0.7213 (mmp) REVERT: C 467 ASP cc_start: 0.7834 (m-30) cc_final: 0.7438 (p0) REVERT: C 837 GLN cc_start: 0.8189 (pp30) cc_final: 0.7442 (pp30) REVERT: M 28 GLN cc_start: 0.7018 (mt0) cc_final: 0.6327 (mm110) outliers start: 2 outliers final: 0 residues processed: 591 average time/residue: 0.2235 time to fit residues: 220.9143 Evaluate side-chains 448 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 248 ASN N 326 GLN A 97 HIS ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1013 ASN A1575 GLN ** A1580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1965 HIS ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN ** U 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 460 ASN S 291 ASN C 238 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 ASN M 115 GLN D 32 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085058 restraints weight = 114826.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086910 restraints weight = 65388.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087849 restraints weight = 40839.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088096 restraints weight = 35283.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088222 restraints weight = 32098.909| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 44824 Z= 0.164 Angle : 0.652 18.360 61679 Z= 0.319 Chirality : 0.045 0.955 6988 Planarity : 0.004 0.048 7182 Dihedral : 16.816 179.835 8538 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.75 % Allowed : 8.62 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 4830 helix: 0.46 (0.11), residues: 2239 sheet: -1.07 (0.25), residues: 463 loop : -1.17 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 302 TYR 0.020 0.001 TYR A1044 PHE 0.019 0.001 PHE A1174 TRP 0.039 0.001 TRP A1839 HIS 0.012 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00369 (44824) covalent geometry : angle 0.65177 (61679) hydrogen bonds : bond 0.04957 ( 1869) hydrogen bonds : angle 5.13335 ( 5274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 492 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: G 311 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7703 (tm-30) REVERT: G 331 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7226 (tt0) REVERT: G 337 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7336 (mm-30) REVERT: F 107 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7162 (mm-30) REVERT: N 179 LEU cc_start: 0.8735 (tp) cc_final: 0.8375 (tp) REVERT: N 253 MET cc_start: 0.8405 (tpp) cc_final: 0.8094 (tpp) REVERT: N 278 ASN cc_start: 0.6637 (p0) cc_final: 0.6164 (p0) REVERT: N 344 ASP cc_start: 0.7795 (t70) cc_final: 0.7430 (t70) REVERT: A 923 ASP cc_start: 0.8621 (t0) cc_final: 0.8239 (t0) REVERT: A 1562 MET cc_start: 0.8654 (mmm) cc_final: 0.8371 (mmm) REVERT: A 1734 MET cc_start: 0.7913 (mmm) cc_final: 0.7677 (mmm) REVERT: A 2008 ARG cc_start: 0.7875 (tmm-80) cc_final: 0.7651 (tmm-80) REVERT: U 353 MET cc_start: 0.7247 (ttp) cc_final: 0.6930 (ttp) REVERT: S 260 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7462 (tm-30) REVERT: S 265 SER cc_start: 0.8494 (m) cc_final: 0.8201 (m) REVERT: C 123 MET cc_start: 0.6465 (tpt) cc_final: 0.5992 (tpt) REVERT: C 203 MET cc_start: 0.7817 (tpp) cc_final: 0.7075 (tpt) REVERT: C 467 ASP cc_start: 0.7959 (m-30) cc_final: 0.7360 (p0) REVERT: C 837 GLN cc_start: 0.8191 (pp30) cc_final: 0.7332 (pp30) REVERT: M 28 GLN cc_start: 0.7056 (mt0) cc_final: 0.6331 (tp40) REVERT: 7 475 ASP cc_start: 0.8421 (p0) cc_final: 0.8057 (p0) outliers start: 31 outliers final: 19 residues processed: 511 average time/residue: 0.2335 time to fit residues: 199.4271 Evaluate side-chains 443 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 424 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1649 LYS Chi-restraints excluded: chain A residue 1951 LYS Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 532 LEU Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 483 optimal weight: 10.0000 chunk 383 optimal weight: 2.9990 chunk 476 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 431 optimal weight: 3.9990 chunk 460 optimal weight: 5.9990 chunk 421 optimal weight: 0.0060 chunk 320 optimal weight: 9.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN L 309 HIS L 332 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1075 GLN A1227 GLN A1522 GLN A1580 HIS A1583 GLN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2065 GLN U 144 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 460 ASN C 238 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN D 32 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.104309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083489 restraints weight = 115253.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085117 restraints weight = 64341.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086590 restraints weight = 42429.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086613 restraints weight = 34886.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086630 restraints weight = 30856.069| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 44824 Z= 0.212 Angle : 0.647 15.409 61679 Z= 0.322 Chirality : 0.044 0.647 6988 Planarity : 0.005 0.049 7182 Dihedral : 16.760 179.675 8538 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.54 % Allowed : 12.32 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.12), residues: 4830 helix: 0.45 (0.11), residues: 2252 sheet: -1.08 (0.26), residues: 449 loop : -1.24 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 91 TYR 0.016 0.002 TYR A2062 PHE 0.018 0.002 PHE A1442 TRP 0.046 0.002 TRP A1839 HIS 0.009 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00480 (44824) covalent geometry : angle 0.64660 (61679) hydrogen bonds : bond 0.04463 ( 1869) hydrogen bonds : angle 4.93550 ( 5274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 467 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 311 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7715 (tm-30) REVERT: G 331 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7218 (tt0) REVERT: N 179 LEU cc_start: 0.8765 (tp) cc_final: 0.8417 (tp) REVERT: N 253 MET cc_start: 0.8385 (tpp) cc_final: 0.8133 (tpp) REVERT: N 278 ASN cc_start: 0.6631 (p0) cc_final: 0.6193 (p0) REVERT: N 344 ASP cc_start: 0.7952 (t70) cc_final: 0.7541 (t70) REVERT: A 923 ASP cc_start: 0.8661 (t0) cc_final: 0.8302 (t0) REVERT: A 1177 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8926 (t) REVERT: A 1562 MET cc_start: 0.8650 (mmm) cc_final: 0.8342 (mmm) REVERT: U 144 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6328 (pt0) REVERT: U 202 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7198 (mp) REVERT: U 353 MET cc_start: 0.7157 (ttp) cc_final: 0.6851 (ttp) REVERT: S 260 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7466 (tm-30) REVERT: S 287 ASP cc_start: 0.7960 (p0) cc_final: 0.7558 (p0) REVERT: C 465 MET cc_start: 0.7688 (mmp) cc_final: 0.7426 (mmm) REVERT: C 467 ASP cc_start: 0.8070 (m-30) cc_final: 0.7436 (p0) REVERT: C 583 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7440 (t0) REVERT: C 837 GLN cc_start: 0.8269 (pp30) cc_final: 0.7401 (pp30) REVERT: 7 476 ILE cc_start: 0.8963 (mm) cc_final: 0.8735 (mm) outliers start: 64 outliers final: 45 residues processed: 513 average time/residue: 0.2202 time to fit residues: 190.2463 Evaluate side-chains 466 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 417 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1649 LYS Chi-restraints excluded: chain A residue 1657 THR Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1931 THR Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 1951 LYS Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 202 ILE Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 475 ILE Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 532 LEU Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 415 ILE Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 371 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 338 optimal weight: 0.0270 chunk 359 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 484 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 473 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 287 ASN ** J 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 332 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1227 GLN A1296 GLN ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2022 GLN U 144 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN D 32 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.106826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085983 restraints weight = 114154.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088335 restraints weight = 62919.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089030 restraints weight = 38984.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089307 restraints weight = 32578.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089315 restraints weight = 30966.929| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44824 Z= 0.114 Angle : 0.569 16.260 61679 Z= 0.283 Chirality : 0.040 0.485 6988 Planarity : 0.004 0.049 7182 Dihedral : 16.650 179.606 8538 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.83 % Allowed : 13.91 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.12), residues: 4830 helix: 0.71 (0.11), residues: 2244 sheet: -1.00 (0.25), residues: 467 loop : -1.13 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 309 TYR 0.020 0.001 TYR D 76 PHE 0.024 0.001 PHE F 90 TRP 0.027 0.001 TRP A1839 HIS 0.006 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00252 (44824) covalent geometry : angle 0.56939 (61679) hydrogen bonds : bond 0.03832 ( 1869) hydrogen bonds : angle 4.62574 ( 5274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 511 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 311 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7626 (tm-30) REVERT: G 331 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7169 (tt0) REVERT: G 337 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7455 (mm-30) REVERT: J 464 VAL cc_start: 0.8843 (t) cc_final: 0.8555 (m) REVERT: J 468 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6325 (tt) REVERT: J 492 ASP cc_start: 0.8099 (p0) cc_final: 0.7880 (p0) REVERT: N 179 LEU cc_start: 0.8618 (tp) cc_final: 0.8257 (tp) REVERT: N 253 MET cc_start: 0.8386 (tpp) cc_final: 0.8049 (tpp) REVERT: A 234 MET cc_start: 0.8371 (mtm) cc_final: 0.7972 (mtp) REVERT: A 422 LEU cc_start: 0.8932 (mt) cc_final: 0.8730 (mt) REVERT: A 923 ASP cc_start: 0.8652 (t0) cc_final: 0.8290 (t0) REVERT: A 1022 MET cc_start: 0.8243 (ptp) cc_final: 0.7964 (ptt) REVERT: A 1425 LYS cc_start: 0.7411 (ttmm) cc_final: 0.7196 (tttp) REVERT: A 1562 MET cc_start: 0.8578 (mmm) cc_final: 0.8308 (mmm) REVERT: A 1637 TRP cc_start: 0.7691 (m-10) cc_final: 0.6720 (m-90) REVERT: A 1702 LEU cc_start: 0.8245 (tp) cc_final: 0.7974 (tp) REVERT: A 1734 MET cc_start: 0.8111 (mmm) cc_final: 0.7807 (mmm) REVERT: A 1809 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 1890 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7642 (mm-40) REVERT: A 1914 MET cc_start: 0.8305 (tpp) cc_final: 0.8092 (tpp) REVERT: A 1960 THR cc_start: 0.5331 (m) cc_final: 0.5078 (p) REVERT: A 2008 ARG cc_start: 0.7893 (tmm-80) cc_final: 0.7660 (tmm-80) REVERT: U 144 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5767 (pt0) REVERT: U 299 MET cc_start: 0.6941 (mmm) cc_final: 0.6703 (tpt) REVERT: U 353 MET cc_start: 0.7164 (ttp) cc_final: 0.6791 (ttp) REVERT: S 163 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7809 (pt0) REVERT: S 260 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7381 (tm-30) REVERT: S 287 ASP cc_start: 0.7897 (p0) cc_final: 0.7504 (p0) REVERT: C 203 MET cc_start: 0.7855 (tpp) cc_final: 0.7116 (tpt) REVERT: C 465 MET cc_start: 0.7563 (mmp) cc_final: 0.7327 (mmp) REVERT: C 467 ASP cc_start: 0.7892 (m-30) cc_final: 0.7452 (p0) REVERT: C 837 GLN cc_start: 0.8223 (pp30) cc_final: 0.7457 (pp30) REVERT: M 28 GLN cc_start: 0.7053 (mt0) cc_final: 0.6375 (tp40) REVERT: 7 441 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (mm110) REVERT: 7 463 GLU cc_start: 0.6963 (tt0) cc_final: 0.6695 (mt-10) REVERT: 7 475 ASP cc_start: 0.8436 (p0) cc_final: 0.8071 (p0) outliers start: 76 outliers final: 33 residues processed: 568 average time/residue: 0.2709 time to fit residues: 257.7608 Evaluate side-chains 482 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 445 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1649 LYS Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 1951 LYS Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 532 LEU Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 441 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 303 optimal weight: 3.9990 chunk 348 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 479 optimal weight: 10.0000 chunk 291 optimal weight: 0.2980 chunk 443 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 332 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1227 GLN A1296 GLN A1575 GLN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2065 GLN U 144 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN D 32 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.104484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083558 restraints weight = 115109.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085345 restraints weight = 64641.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086240 restraints weight = 42709.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086601 restraints weight = 35011.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086682 restraints weight = 32835.855| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 44824 Z= 0.199 Angle : 0.621 14.699 61679 Z= 0.310 Chirality : 0.042 0.338 6988 Planarity : 0.004 0.049 7182 Dihedral : 16.620 179.471 8538 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.36 % Allowed : 14.99 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.12), residues: 4830 helix: 0.66 (0.11), residues: 2248 sheet: -0.99 (0.26), residues: 450 loop : -1.22 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1298 TYR 0.021 0.002 TYR L 207 PHE 0.032 0.002 PHE A1719 TRP 0.028 0.002 TRP A1839 HIS 0.006 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00454 (44824) covalent geometry : angle 0.62102 (61679) hydrogen bonds : bond 0.04010 ( 1869) hydrogen bonds : angle 4.68809 ( 5274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 449 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5443 (tt) cc_final: 0.5227 (tt) REVERT: G 311 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7582 (tm-30) REVERT: G 331 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7190 (tt0) REVERT: J 464 VAL cc_start: 0.8881 (t) cc_final: 0.8599 (m) REVERT: J 468 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6476 (tt) REVERT: N 179 LEU cc_start: 0.8725 (tp) cc_final: 0.8354 (tp) REVERT: N 253 MET cc_start: 0.8356 (tpp) cc_final: 0.8101 (tpp) REVERT: N 344 ASP cc_start: 0.7931 (t0) cc_final: 0.7627 (t70) REVERT: A 165 ARG cc_start: 0.7343 (mmm160) cc_final: 0.6869 (ttt90) REVERT: A 923 ASP cc_start: 0.8689 (t0) cc_final: 0.8293 (t0) REVERT: A 1177 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8974 (p) REVERT: A 1421 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8678 (t) REVERT: A 1562 MET cc_start: 0.8579 (mmm) cc_final: 0.8257 (mmm) REVERT: A 1734 MET cc_start: 0.8153 (mmm) cc_final: 0.7864 (mmm) REVERT: A 1960 THR cc_start: 0.5341 (m) cc_final: 0.5045 (p) REVERT: A 2008 ARG cc_start: 0.7946 (tmm-80) cc_final: 0.7730 (tmm-80) REVERT: U 175 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7849 (mm) REVERT: U 353 MET cc_start: 0.7031 (ttp) cc_final: 0.6729 (ttp) REVERT: S 163 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7758 (pt0) REVERT: S 260 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7402 (tm-30) REVERT: S 287 ASP cc_start: 0.7994 (p0) cc_final: 0.7592 (p0) REVERT: C 465 MET cc_start: 0.7598 (mmp) cc_final: 0.7285 (mmp) REVERT: C 467 ASP cc_start: 0.8050 (m-30) cc_final: 0.7400 (p0) REVERT: C 583 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7386 (t0) REVERT: C 837 GLN cc_start: 0.8106 (pp30) cc_final: 0.7342 (pp30) REVERT: 7 441 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7834 (mm-40) REVERT: 7 475 ASP cc_start: 0.8511 (p0) cc_final: 0.7970 (p0) REVERT: 7 476 ILE cc_start: 0.8980 (mm) cc_final: 0.8241 (mm) outliers start: 98 outliers final: 65 residues processed: 530 average time/residue: 0.2667 time to fit residues: 238.4636 Evaluate side-chains 487 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 416 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 468 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1649 LYS Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 1951 LYS Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 532 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 416 THR Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 441 GLN Chi-restraints excluded: chain 7 residue 480 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 164 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 478 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 122 optimal weight: 0.0670 chunk 243 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 325 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 464 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 332 GLN ** L 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A 963 GLN A1227 GLN A1261 ASN A1296 GLN ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2022 GLN U 144 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085937 restraints weight = 114336.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088129 restraints weight = 64439.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088998 restraints weight = 40969.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089267 restraints weight = 33315.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089496 restraints weight = 32278.196| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 44824 Z= 0.113 Angle : 0.568 15.903 61679 Z= 0.282 Chirality : 0.040 0.271 6988 Planarity : 0.004 0.057 7182 Dihedral : 16.571 178.751 8538 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.19 % Allowed : 16.03 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.12), residues: 4830 helix: 0.82 (0.11), residues: 2245 sheet: -0.95 (0.25), residues: 458 loop : -1.09 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 437 TYR 0.019 0.001 TYR D 76 PHE 0.030 0.001 PHE A1719 TRP 0.021 0.001 TRP A1839 HIS 0.004 0.001 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00251 (44824) covalent geometry : angle 0.56774 (61679) hydrogen bonds : bond 0.03594 ( 1869) hydrogen bonds : angle 4.49782 ( 5274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 483 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5315 (tt) cc_final: 0.5092 (tt) REVERT: G 311 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7528 (tm-30) REVERT: G 331 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7072 (tt0) REVERT: G 337 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7449 (mm-30) REVERT: N 179 LEU cc_start: 0.8636 (tp) cc_final: 0.8282 (tp) REVERT: A 151 MET cc_start: 0.7772 (mtt) cc_final: 0.7565 (mtt) REVERT: A 923 ASP cc_start: 0.8544 (t0) cc_final: 0.8165 (t0) REVERT: A 1143 MET cc_start: 0.8064 (mmm) cc_final: 0.7622 (mmp) REVERT: A 1216 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (mm) REVERT: A 1264 ASN cc_start: 0.8530 (m-40) cc_final: 0.8293 (m110) REVERT: A 1421 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8645 (t) REVERT: A 1562 MET cc_start: 0.8434 (mmm) cc_final: 0.8154 (mmm) REVERT: A 1809 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 1890 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7692 (mm-40) REVERT: A 1960 THR cc_start: 0.5393 (m) cc_final: 0.5137 (p) REVERT: A 2008 ARG cc_start: 0.7832 (tmm-80) cc_final: 0.7591 (tmm-80) REVERT: U 175 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7872 (mm) REVERT: U 353 MET cc_start: 0.6986 (ttp) cc_final: 0.6762 (ttp) REVERT: S 163 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7802 (pt0) REVERT: S 260 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7223 (tm-30) REVERT: S 287 ASP cc_start: 0.7964 (p0) cc_final: 0.7580 (p0) REVERT: C 123 MET cc_start: 0.6512 (tpp) cc_final: 0.6092 (tpt) REVERT: C 174 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: C 203 MET cc_start: 0.7816 (tpp) cc_final: 0.7052 (tpt) REVERT: C 465 MET cc_start: 0.7657 (mmp) cc_final: 0.7301 (mmp) REVERT: C 467 ASP cc_start: 0.7952 (m-30) cc_final: 0.7260 (p0) REVERT: C 837 GLN cc_start: 0.8059 (pp30) cc_final: 0.7372 (pp30) REVERT: M 28 GLN cc_start: 0.7003 (mt0) cc_final: 0.6381 (tp40) REVERT: 7 441 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: 7 475 ASP cc_start: 0.8376 (p0) cc_final: 0.8011 (p0) outliers start: 91 outliers final: 56 residues processed: 556 average time/residue: 0.2668 time to fit residues: 248.9927 Evaluate side-chains 503 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 441 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 513 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1809 ILE Chi-restraints excluded: chain A residue 1872 LEU Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain A residue 2016 ILE Chi-restraints excluded: chain A residue 2022 GLN Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain S residue 347 HIS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 441 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 428 optimal weight: 3.9990 chunk 248 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 chunk 402 optimal weight: 7.9990 chunk 438 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 483 optimal weight: 0.7980 chunk 385 optimal weight: 7.9990 chunk 342 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS L 332 GLN ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN U 275 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 924 GLN D 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.105833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084685 restraints weight = 113754.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087400 restraints weight = 64400.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.088018 restraints weight = 37956.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088402 restraints weight = 32691.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088445 restraints weight = 31117.172| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44824 Z= 0.149 Angle : 0.590 13.051 61679 Z= 0.293 Chirality : 0.041 0.286 6988 Planarity : 0.004 0.054 7182 Dihedral : 16.532 178.516 8538 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.24 % Allowed : 16.46 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.12), residues: 4830 helix: 0.85 (0.11), residues: 2240 sheet: -0.93 (0.25), residues: 466 loop : -1.08 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 437 TYR 0.027 0.001 TYR A1044 PHE 0.030 0.001 PHE A1719 TRP 0.022 0.001 TRP A1839 HIS 0.004 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00341 (44824) covalent geometry : angle 0.59007 (61679) hydrogen bonds : bond 0.03671 ( 1869) hydrogen bonds : angle 4.51066 ( 5274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 460 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5410 (tt) cc_final: 0.5197 (tt) REVERT: G 311 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7510 (tm-30) REVERT: G 331 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7074 (tt0) REVERT: N 179 LEU cc_start: 0.8709 (tp) cc_final: 0.8360 (tp) REVERT: N 319 GLU cc_start: 0.7995 (tt0) cc_final: 0.7795 (tt0) REVERT: A 448 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.6894 (mt0) REVERT: A 923 ASP cc_start: 0.8567 (t0) cc_final: 0.8217 (t0) REVERT: A 1048 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7300 (mtm) REVERT: A 1177 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (p) REVERT: A 1421 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 1562 MET cc_start: 0.8488 (mmm) cc_final: 0.8218 (mmm) REVERT: A 1960 THR cc_start: 0.5287 (m) cc_final: 0.4999 (p) REVERT: U 175 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7916 (mm) REVERT: U 353 MET cc_start: 0.6842 (ttp) cc_final: 0.6598 (ttp) REVERT: S 163 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7793 (pt0) REVERT: S 260 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7344 (tm-30) REVERT: S 272 MET cc_start: 0.6756 (tpt) cc_final: 0.6408 (tpp) REVERT: C 174 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: C 203 MET cc_start: 0.7852 (tpp) cc_final: 0.7212 (tpt) REVERT: C 433 MET cc_start: 0.8494 (tmm) cc_final: 0.8143 (tmm) REVERT: C 465 MET cc_start: 0.7650 (mmp) cc_final: 0.7299 (mmp) REVERT: C 467 ASP cc_start: 0.8009 (m-30) cc_final: 0.7344 (p0) REVERT: C 837 GLN cc_start: 0.8084 (pp30) cc_final: 0.7401 (pp30) REVERT: M 28 GLN cc_start: 0.6979 (mt0) cc_final: 0.6338 (tp40) REVERT: 7 441 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7933 (mm110) REVERT: 7 475 ASP cc_start: 0.8518 (p0) cc_final: 0.8231 (p0) outliers start: 93 outliers final: 65 residues processed: 532 average time/residue: 0.2638 time to fit residues: 237.2353 Evaluate side-chains 520 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 448 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 466 LEU Chi-restraints excluded: chain J residue 513 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1369 TYR Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 532 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 416 THR Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 441 GLN Chi-restraints excluded: chain 7 residue 480 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 373 optimal weight: 0.8980 chunk 453 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 341 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 309 HIS ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1563 HIS ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085966 restraints weight = 114998.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088410 restraints weight = 64686.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088985 restraints weight = 39226.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090756 restraints weight = 34068.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.090612 restraints weight = 28671.236| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44824 Z= 0.114 Angle : 0.578 16.622 61679 Z= 0.285 Chirality : 0.040 0.259 6988 Planarity : 0.004 0.053 7182 Dihedral : 16.502 178.177 8538 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.09 % Allowed : 16.87 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.12), residues: 4830 helix: 0.92 (0.11), residues: 2240 sheet: -0.80 (0.25), residues: 472 loop : -1.03 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1744 TYR 0.023 0.001 TYR A1044 PHE 0.028 0.001 PHE A1719 TRP 0.021 0.001 TRP A1839 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00257 (44824) covalent geometry : angle 0.57794 (61679) hydrogen bonds : bond 0.03516 ( 1869) hydrogen bonds : angle 4.44593 ( 5274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 486 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5362 (tt) cc_final: 0.5144 (tt) REVERT: G 311 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7524 (tm-30) REVERT: G 331 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7046 (tt0) REVERT: N 319 GLU cc_start: 0.7661 (tt0) cc_final: 0.7391 (tt0) REVERT: A 309 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6699 (mtp85) REVERT: A 686 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7777 (ttp-170) REVERT: A 923 ASP cc_start: 0.8497 (t0) cc_final: 0.8236 (t0) REVERT: A 978 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6533 (mm-30) REVERT: A 1048 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6943 (mpp) REVERT: A 1143 MET cc_start: 0.8037 (mmm) cc_final: 0.7689 (mmp) REVERT: A 1177 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8802 (t) REVERT: A 1189 MET cc_start: 0.7435 (tpp) cc_final: 0.6154 (tpt) REVERT: A 1562 MET cc_start: 0.8480 (mmm) cc_final: 0.8250 (mmm) REVERT: A 1890 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7802 (mm110) REVERT: A 1953 ILE cc_start: 0.8306 (mt) cc_final: 0.8019 (mt) REVERT: A 1960 THR cc_start: 0.5338 (m) cc_final: 0.5023 (p) REVERT: A 2014 MET cc_start: 0.5792 (mmm) cc_final: 0.5394 (mmm) REVERT: U 175 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7829 (mm) REVERT: U 353 MET cc_start: 0.6889 (ttp) cc_final: 0.6667 (ttp) REVERT: S 163 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7778 (pt0) REVERT: S 260 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7204 (tm-30) REVERT: S 272 MET cc_start: 0.6606 (tpt) cc_final: 0.6215 (tpp) REVERT: S 287 ASP cc_start: 0.7772 (p0) cc_final: 0.7436 (p0) REVERT: S 296 ASP cc_start: 0.7828 (t70) cc_final: 0.7608 (t0) REVERT: C 123 MET cc_start: 0.6517 (tpp) cc_final: 0.6152 (tpt) REVERT: C 174 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: C 203 MET cc_start: 0.7839 (tpp) cc_final: 0.7188 (tpt) REVERT: C 433 MET cc_start: 0.8416 (tmm) cc_final: 0.8048 (tmm) REVERT: C 465 MET cc_start: 0.7644 (mmp) cc_final: 0.7291 (mmp) REVERT: C 467 ASP cc_start: 0.7858 (m-30) cc_final: 0.7264 (p0) REVERT: C 837 GLN cc_start: 0.8050 (pp30) cc_final: 0.7384 (pp30) REVERT: M 28 GLN cc_start: 0.7051 (mt0) cc_final: 0.6434 (tp40) REVERT: 7 441 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8172 (mm110) REVERT: 7 475 ASP cc_start: 0.8475 (p0) cc_final: 0.8195 (p0) outliers start: 87 outliers final: 59 residues processed: 555 average time/residue: 0.2676 time to fit residues: 248.7620 Evaluate side-chains 517 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 452 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 513 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain S residue 347 HIS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 441 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 477 optimal weight: 7.9990 chunk 126 optimal weight: 0.0770 chunk 435 optimal weight: 3.9990 chunk 123 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 354 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 434 optimal weight: 2.9990 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 309 HIS A 270 ASN ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1013 ASN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085878 restraints weight = 114027.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088591 restraints weight = 64123.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088889 restraints weight = 37711.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089305 restraints weight = 35523.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089355 restraints weight = 32133.324| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 44824 Z= 0.117 Angle : 0.578 12.135 61679 Z= 0.285 Chirality : 0.040 0.259 6988 Planarity : 0.004 0.051 7182 Dihedral : 16.463 177.920 8538 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.90 % Allowed : 17.28 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.12), residues: 4830 helix: 0.98 (0.11), residues: 2232 sheet: -0.75 (0.25), residues: 470 loop : -1.00 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 93 TYR 0.022 0.001 TYR A1044 PHE 0.027 0.001 PHE A1719 TRP 0.022 0.001 TRP A1839 HIS 0.005 0.001 HIS A1096 Details of bonding type rmsd covalent geometry : bond 0.00266 (44824) covalent geometry : angle 0.57767 (61679) hydrogen bonds : bond 0.03466 ( 1869) hydrogen bonds : angle 4.40933 ( 5274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 476 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5333 (tt) cc_final: 0.5100 (tt) REVERT: G 311 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7457 (tm-30) REVERT: G 331 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7045 (tt0) REVERT: A 422 LEU cc_start: 0.8531 (mp) cc_final: 0.8231 (mt) REVERT: A 686 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7780 (ttp-170) REVERT: A 923 ASP cc_start: 0.8476 (t0) cc_final: 0.8260 (t0) REVERT: A 976 MET cc_start: 0.7791 (tpp) cc_final: 0.7590 (tpp) REVERT: A 1048 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7027 (mpp) REVERT: A 1143 MET cc_start: 0.8104 (mmm) cc_final: 0.7794 (mmp) REVERT: A 1177 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8824 (t) REVERT: A 1189 MET cc_start: 0.7672 (tpp) cc_final: 0.6617 (tpt) REVERT: A 1562 MET cc_start: 0.8478 (mmm) cc_final: 0.8246 (mmm) REVERT: A 1652 MET cc_start: 0.6824 (tpp) cc_final: 0.6018 (tpp) REVERT: A 1890 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7793 (mm110) REVERT: A 1953 ILE cc_start: 0.8422 (mt) cc_final: 0.7683 (mt) REVERT: A 1960 THR cc_start: 0.5708 (m) cc_final: 0.5382 (p) REVERT: A 2014 MET cc_start: 0.5828 (mmm) cc_final: 0.5457 (mmm) REVERT: U 175 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7862 (mm) REVERT: U 271 PHE cc_start: 0.6320 (t80) cc_final: 0.5867 (t80) REVERT: U 353 MET cc_start: 0.6827 (ttp) cc_final: 0.6615 (ttp) REVERT: S 163 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7788 (pt0) REVERT: S 260 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7178 (tm-30) REVERT: S 272 MET cc_start: 0.6658 (tpt) cc_final: 0.6252 (tpp) REVERT: S 287 ASP cc_start: 0.7777 (p0) cc_final: 0.7430 (p0) REVERT: S 296 ASP cc_start: 0.7811 (t70) cc_final: 0.7584 (t0) REVERT: C 174 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: C 203 MET cc_start: 0.7894 (tpp) cc_final: 0.7354 (tpt) REVERT: C 433 MET cc_start: 0.8406 (tmm) cc_final: 0.8048 (tmm) REVERT: C 465 MET cc_start: 0.7658 (mmp) cc_final: 0.7278 (mmp) REVERT: C 467 ASP cc_start: 0.7946 (m-30) cc_final: 0.7308 (p0) REVERT: C 837 GLN cc_start: 0.8037 (pp30) cc_final: 0.7361 (pp30) REVERT: M 28 GLN cc_start: 0.7053 (mt0) cc_final: 0.6445 (tp40) REVERT: D 106 MET cc_start: 0.7240 (ptp) cc_final: 0.6880 (ttp) REVERT: 7 475 ASP cc_start: 0.8464 (p0) cc_final: 0.8190 (p0) outliers start: 79 outliers final: 62 residues processed: 536 average time/residue: 0.2624 time to fit residues: 237.4197 Evaluate side-chains 511 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 444 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 513 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1369 TYR Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1945 VAL Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 144 GLN Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain S residue 347 HIS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 435 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 142 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 250 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 369 optimal weight: 0.8980 chunk 459 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 381 optimal weight: 0.4980 chunk 487 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 480 ASN L 309 HIS ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1013 ASN A1227 GLN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2065 GLN U 144 GLN ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS 7 441 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085784 restraints weight = 114206.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088155 restraints weight = 65082.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089001 restraints weight = 40116.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089192 restraints weight = 32751.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089343 restraints weight = 32141.271| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44824 Z= 0.127 Angle : 0.593 18.302 61679 Z= 0.291 Chirality : 0.041 0.277 6988 Planarity : 0.004 0.051 7182 Dihedral : 16.456 177.900 8538 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.83 % Allowed : 17.52 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.12), residues: 4830 helix: 0.97 (0.11), residues: 2232 sheet: -0.76 (0.25), residues: 470 loop : -1.00 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 93 TYR 0.021 0.001 TYR A1044 PHE 0.027 0.001 PHE A1719 TRP 0.023 0.001 TRP A1839 HIS 0.004 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00292 (44824) covalent geometry : angle 0.59293 (61679) hydrogen bonds : bond 0.03472 ( 1869) hydrogen bonds : angle 4.44511 ( 5274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9660 Ramachandran restraints generated. 4830 Oldfield, 0 Emsley, 4830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 452 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 309 LEU cc_start: 0.5346 (tt) cc_final: 0.5116 (tt) REVERT: G 311 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7466 (tm-30) REVERT: G 331 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7045 (tt0) REVERT: G 337 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7539 (mm-30) REVERT: N 124 GLU cc_start: 0.7882 (pt0) cc_final: 0.7585 (pt0) REVERT: A 422 LEU cc_start: 0.8604 (mp) cc_final: 0.8310 (mt) REVERT: A 686 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7780 (ttp-170) REVERT: A 923 ASP cc_start: 0.8475 (t0) cc_final: 0.8255 (t0) REVERT: A 976 MET cc_start: 0.7994 (tpp) cc_final: 0.7538 (tpp) REVERT: A 1048 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7026 (mpp) REVERT: A 1143 MET cc_start: 0.8070 (mmm) cc_final: 0.7721 (mmp) REVERT: A 1177 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8825 (t) REVERT: A 1189 MET cc_start: 0.7700 (tpp) cc_final: 0.6611 (tpt) REVERT: A 1562 MET cc_start: 0.8478 (mmm) cc_final: 0.8245 (mmm) REVERT: A 1652 MET cc_start: 0.6640 (tpp) cc_final: 0.5869 (tpp) REVERT: A 1890 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7797 (mm110) REVERT: A 1960 THR cc_start: 0.5466 (m) cc_final: 0.5178 (p) REVERT: A 2014 MET cc_start: 0.5830 (mmm) cc_final: 0.5455 (mmm) REVERT: U 175 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7975 (mm) REVERT: U 353 MET cc_start: 0.6807 (ttp) cc_final: 0.6591 (ttp) REVERT: S 163 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7793 (pt0) REVERT: S 260 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7306 (tm-30) REVERT: S 287 ASP cc_start: 0.7799 (p0) cc_final: 0.7455 (p0) REVERT: S 296 ASP cc_start: 0.7841 (t70) cc_final: 0.7622 (t0) REVERT: C 123 MET cc_start: 0.6594 (tpp) cc_final: 0.6197 (tpt) REVERT: C 174 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: C 203 MET cc_start: 0.7922 (tpp) cc_final: 0.7393 (tpt) REVERT: C 433 MET cc_start: 0.8404 (tmm) cc_final: 0.8037 (tmm) REVERT: C 465 MET cc_start: 0.7649 (mmp) cc_final: 0.7262 (mmp) REVERT: C 467 ASP cc_start: 0.7937 (m-30) cc_final: 0.7329 (p0) REVERT: C 837 GLN cc_start: 0.8035 (pp30) cc_final: 0.7355 (pp30) REVERT: M 28 GLN cc_start: 0.7058 (mt0) cc_final: 0.6442 (tp40) REVERT: D 106 MET cc_start: 0.7324 (ptp) cc_final: 0.6852 (ttp) REVERT: 7 475 ASP cc_start: 0.8488 (p0) cc_final: 0.8206 (p0) outliers start: 76 outliers final: 61 residues processed: 509 average time/residue: 0.2651 time to fit residues: 227.9700 Evaluate side-chains 504 residues out of total 4351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 438 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 480 ASN Chi-restraints excluded: chain J residue 513 GLU Chi-restraints excluded: chain L residue 133 LEU Chi-restraints excluded: chain L residue 396 LEU Chi-restraints excluded: chain L residue 424 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 278 ASN Chi-restraints excluded: chain N residue 318 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 766 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 974 ASN Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1110 ILE Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1369 TYR Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1541 THR Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain U residue 123 LEU Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 383 MET Chi-restraints excluded: chain U residue 384 VAL Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain U residue 444 THR Chi-restraints excluded: chain U residue 458 THR Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 273 ILE Chi-restraints excluded: chain S residue 347 HIS Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain 7 residue 425 MET Chi-restraints excluded: chain 7 residue 435 ASP Chi-restraints excluded: chain 7 residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 256 optimal weight: 0.0980 chunk 412 optimal weight: 4.9990 chunk 310 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 301 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 309 HIS ** A 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1013 ASN A1227 GLN ** A1737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1966 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 442 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.085137 restraints weight = 114795.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087250 restraints weight = 61877.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088609 restraints weight = 42009.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089439 restraints weight = 32981.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089987 restraints weight = 28426.457| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 44824 Z= 0.146 Angle : 0.666 59.082 61679 Z= 0.351 Chirality : 0.042 0.980 6988 Planarity : 0.004 0.051 7182 Dihedral : 16.457 177.899 8538 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.73 % Allowed : 17.67 % Favored : 80.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.12), residues: 4830 helix: 0.97 (0.11), residues: 2232 sheet: -0.77 (0.25), residues: 470 loop : -1.00 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 309 TYR 0.020 0.001 TYR D 76 PHE 0.026 0.001 PHE A1719 TRP 0.022 0.001 TRP A1839 HIS 0.004 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00330 (44824) covalent geometry : angle 0.66606 (61679) hydrogen bonds : bond 0.03488 ( 1869) hydrogen bonds : angle 4.44662 ( 5274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7711.92 seconds wall clock time: 134 minutes 37.35 seconds (8077.35 seconds total)