Starting phenix.real_space_refine on Fri Dec 27 13:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965.map" model { file = "/net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hra_34965/12_2024/8hra_34965_neut.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 63 5.49 5 S 220 5.16 5 C 30260 2.51 5 N 8313 2.21 5 O 9290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48146 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6754 Classifications: {'peptide': 847} Link IDs: {'PTRANS': 23, 'TRANS': 823} Chain breaks: 4 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "C" Number of atoms: 6784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6784 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 23, 'TRANS': 828} Chain breaks: 4 Chain: "D" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6757 Classifications: {'peptide': 848} Link IDs: {'PTRANS': 23, 'TRANS': 824} Chain breaks: 4 Chain: "E" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6654 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "G" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6665 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 6 Chain: "H" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "K" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "M" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 362 Classifications: {'RNA': 17} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9} Link IDs: {'rna3p': 16} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.25, per 1000 atoms: 0.44 Number of scatterers: 48146 At special positions: 0 Unit cell: (172.78, 177.02, 178.08, 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 220 16.00 P 63 15.00 O 9290 8.00 N 8313 7.00 C 30260 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: 9.21 Conformation dependent library (CDL) restraints added in 4.5 seconds 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11160 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 22 sheets defined 62.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.510A pdb=" N THR A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 28' Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.701A pdb=" N SER A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.912A pdb=" N SER A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 140 removed outlier: 3.804A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 168 removed outlier: 3.555A pdb=" N LYS A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.828A pdb=" N ASP A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 230 through 241 removed outlier: 3.777A pdb=" N SER A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.625A pdb=" N TYR A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.550A pdb=" N GLU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.598A pdb=" N VAL A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 removed outlier: 4.074A pdb=" N LYS A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 removed outlier: 3.756A pdb=" N SER A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.721A pdb=" N LYS A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 removed outlier: 4.013A pdb=" N TYR A 465 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 472 through 490 removed outlier: 4.103A pdb=" N SER A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 515 removed outlier: 3.983A pdb=" N PHE A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.765A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 621 through 633 removed outlier: 3.918A pdb=" N LEU A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.521A pdb=" N ASN A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 706 through 724 Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 752 Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.769A pdb=" N LEU A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.591A pdb=" N GLY A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.665A pdb=" N ILE A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 856' Processing helix chain 'A' and resid 864 through 883 removed outlier: 4.104A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 removed outlier: 3.674A pdb=" N ASP A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 896 " --> pdb=" O TRP A 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.189A pdb=" N THR B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.577A pdb=" N PHE B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 140 removed outlier: 3.527A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.139A pdb=" N GLN B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.693A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.985A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.659A pdb=" N TYR B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.751A pdb=" N ALA B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.925A pdb=" N TYR B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.903A pdb=" N THR B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 425 removed outlier: 3.613A pdb=" N LEU B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 442 through 458 removed outlier: 4.016A pdb=" N PHE B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.727A pdb=" N TYR B 465 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 466' Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.805A pdb=" N SER B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 4.267A pdb=" N CYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.682A pdb=" N GLU B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.771A pdb=" N ALA B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 4.136A pdb=" N ILE B 567 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 Processing helix chain 'B' and resid 622 through 633 removed outlier: 3.521A pdb=" N ILE B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 708 through 724 removed outlier: 3.666A pdb=" N LYS B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 732 through 749 Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.676A pdb=" N MET B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.760A pdb=" N LYS B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 Processing helix chain 'B' and resid 839 through 847 Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.770A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.774A pdb=" N LYS B 870 " --> pdb=" O LYS B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 916 through 920 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.598A pdb=" N THR C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 28 " --> pdb=" O GLY C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 28' Processing helix chain 'C' and resid 34 through 50 Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 117 through 140 removed outlier: 4.221A pdb=" N ILE C 121 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 164 removed outlier: 3.702A pdb=" N GLU C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 175 through 182 removed outlier: 4.140A pdb=" N ASP C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 212 Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.985A pdb=" N SER C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.873A pdb=" N TYR C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.859A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.601A pdb=" N ALA C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.751A pdb=" N ASP C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 393 removed outlier: 3.723A pdb=" N GLN C 381 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 3.686A pdb=" N GLY C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.596A pdb=" N GLY C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 458 removed outlier: 3.869A pdb=" N CYS C 447 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.681A pdb=" N TYR C 465 " --> pdb=" O THR C 462 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 472 through 490 removed outlier: 3.993A pdb=" N ILE C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 514 removed outlier: 3.972A pdb=" N CYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.170A pdb=" N SER C 561 " --> pdb=" O VAL C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 596 Processing helix chain 'C' and resid 597 through 607 removed outlier: 3.658A pdb=" N ALA C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 634 removed outlier: 3.931A pdb=" N ALA C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.532A pdb=" N ILE C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 671 removed outlier: 3.530A pdb=" N GLY C 671 " --> pdb=" O ALA C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 724 Processing helix chain 'C' and resid 730 through 752 removed outlier: 3.718A pdb=" N GLY C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 793 removed outlier: 3.525A pdb=" N PHE C 782 " --> pdb=" O ASN C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 832 removed outlier: 3.693A pdb=" N LYS C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 839 Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.673A pdb=" N ILE C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 856' Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 916 through 920 Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.747A pdb=" N ILE D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 117 through 140 removed outlier: 3.834A pdb=" N ILE D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 138 " --> pdb=" O SER D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 removed outlier: 3.781A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 173 through 181 removed outlier: 4.121A pdb=" N PHE D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.794A pdb=" N ASP D 188 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR D 189 " --> pdb=" O GLN D 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 185 through 189' Processing helix chain 'D' and resid 195 through 211 removed outlier: 3.968A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.566A pdb=" N PHE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.793A pdb=" N TYR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 281 through 302 removed outlier: 3.635A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 317 removed outlier: 3.515A pdb=" N LEU D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.570A pdb=" N ALA D 341 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'D' and resid 375 through 394 removed outlier: 4.196A pdb=" N LYS D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.636A pdb=" N GLY D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.980A pdb=" N ILE D 429 " --> pdb=" O MET D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 458 removed outlier: 4.048A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 451 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.580A pdb=" N TYR D 465 " --> pdb=" O THR D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 490 removed outlier: 4.042A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 515 removed outlier: 4.076A pdb=" N CYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 507 " --> pdb=" O VAL D 503 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 519 removed outlier: 3.533A pdb=" N ALA D 519 " --> pdb=" O THR D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 519' Processing helix chain 'D' and resid 526 through 540 Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.759A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 608 Processing helix chain 'D' and resid 622 through 633 Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.751A pdb=" N ILE D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 671 removed outlier: 3.851A pdb=" N MET D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 670 " --> pdb=" O ARG D 666 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 671 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 Processing helix chain 'D' and resid 706 through 724 removed outlier: 3.686A pdb=" N ASN D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 730 through 753 Processing helix chain 'D' and resid 770 through 793 removed outlier: 3.591A pdb=" N PHE D 782 " --> pdb=" O ASN D 778 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 786 " --> pdb=" O PHE D 782 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 831 Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 839 through 847 Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 851 through 856 removed outlier: 3.777A pdb=" N ILE D 855 " --> pdb=" O LEU D 851 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 851 through 856' Processing helix chain 'D' and resid 864 through 883 removed outlier: 4.056A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP D 879 " --> pdb=" O ASN D 875 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 880 " --> pdb=" O LYS D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 896 Processing helix chain 'D' and resid 916 through 920 removed outlier: 3.717A pdb=" N SER D 919 " --> pdb=" O SER D 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 removed outlier: 4.086A pdb=" N THR E 27 " --> pdb=" O PRO E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 51 removed outlier: 3.900A pdb=" N ILE E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.935A pdb=" N SER E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 139 Processing helix chain 'E' and resid 145 through 164 removed outlier: 3.697A pdb=" N HIS E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 195 through 212 Processing helix chain 'E' and resid 229 through 240 removed outlier: 3.542A pdb=" N VAL E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.560A pdb=" N TYR E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 279 through 300 removed outlier: 3.550A pdb=" N GLN E 296 " --> pdb=" O HIS E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.601A pdb=" N LEU E 316 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 317 " --> pdb=" O MET E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.634A pdb=" N ALA E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.751A pdb=" N TYR E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 395 removed outlier: 3.957A pdb=" N TYR E 391 " --> pdb=" O TYR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 425 removed outlier: 3.573A pdb=" N LEU E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 437 through 441 removed outlier: 4.154A pdb=" N PHE E 441 " --> pdb=" O GLN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 458 removed outlier: 3.693A pdb=" N PHE E 451 " --> pdb=" O CYS E 447 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.669A pdb=" N TYR E 465 " --> pdb=" O THR E 462 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 466 " --> pdb=" O GLY E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 472 through 490 removed outlier: 3.546A pdb=" N ARG E 476 " --> pdb=" O SER E 472 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 504 Processing helix chain 'E' and resid 505 through 515 removed outlier: 3.585A pdb=" N SER E 509 " --> pdb=" O CYS E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 540 removed outlier: 4.190A pdb=" N GLU E 529 " --> pdb=" O ARG E 525 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU E 531 " --> pdb=" O LYS E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 559 removed outlier: 3.823A pdb=" N ALA E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 removed outlier: 4.015A pdb=" N ILE E 567 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 606 Processing helix chain 'E' and resid 622 through 633 removed outlier: 3.669A pdb=" N ILE E 626 " --> pdb=" O VAL E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 647 removed outlier: 4.020A pdb=" N THR E 643 " --> pdb=" O ARG E 639 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN E 647 " --> pdb=" O THR E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 705 Processing helix chain 'E' and resid 706 through 724 removed outlier: 3.638A pdb=" N ASN E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 752 removed outlier: 3.798A pdb=" N ASN E 747 " --> pdb=" O PHE E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 756 removed outlier: 4.188A pdb=" N LEU E 756 " --> pdb=" O LYS E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 753 through 756' Processing helix chain 'E' and resid 770 through 794 removed outlier: 3.562A pdb=" N HIS E 794 " --> pdb=" O GLU E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 831 removed outlier: 4.008A pdb=" N LYS E 820 " --> pdb=" O GLU E 816 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 839 Processing helix chain 'E' and resid 839 through 847 Processing helix chain 'E' and resid 851 through 856 removed outlier: 4.148A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 857 through 861 removed outlier: 4.319A pdb=" N ILE E 861 " --> pdb=" O VAL E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 883 removed outlier: 3.919A pdb=" N LYS E 870 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 897 Processing helix chain 'G' and resid 35 through 51 Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.538A pdb=" N PHE G 85 " --> pdb=" O GLY G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 120 through 140 removed outlier: 3.558A pdb=" N TYR G 140 " --> pdb=" O LYS G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.588A pdb=" N GLU G 151 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.188A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 176 through 181 removed outlier: 3.542A pdb=" N ALA G 180 " --> pdb=" O TYR G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 212 Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.871A pdb=" N VAL G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.658A pdb=" N TYR G 257 " --> pdb=" O ASP G 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 263 " --> pdb=" O GLN G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 269 No H-bonds generated for 'chain 'G' and resid 267 through 269' Processing helix chain 'G' and resid 270 through 277 Processing helix chain 'G' and resid 279 through 302 removed outlier: 3.544A pdb=" N ARG G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR G 288 " --> pdb=" O ALA G 284 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N MET G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL G 290 " --> pdb=" O ARG G 286 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU G 291 " --> pdb=" O GLY G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 312 through 318 Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'G' and resid 363 through 373 removed outlier: 3.916A pdb=" N TYR G 367 " --> pdb=" O ASP G 363 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 368 " --> pdb=" O ALA G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 395 removed outlier: 3.878A pdb=" N TYR G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 425 Processing helix chain 'G' and resid 425 through 433 removed outlier: 3.866A pdb=" N ILE G 429 " --> pdb=" O MET G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 458 removed outlier: 3.760A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE G 451 " --> pdb=" O CYS G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.875A pdb=" N TYR G 465 " --> pdb=" O THR G 462 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU G 466 " --> pdb=" O GLY G 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 466' Processing helix chain 'G' and resid 472 through 490 removed outlier: 4.315A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR G 481 " --> pdb=" O ASN G 477 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 483 " --> pdb=" O SER G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 503 removed outlier: 3.842A pdb=" N MET G 500 " --> pdb=" O LYS G 496 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 501 " --> pdb=" O PHE G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 515 Processing helix chain 'G' and resid 525 through 540 Processing helix chain 'G' and resid 546 through 559 Processing helix chain 'G' and resid 563 through 567 removed outlier: 3.530A pdb=" N LYS G 566 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE G 567 " --> pdb=" O ASP G 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 563 through 567' Processing helix chain 'G' and resid 598 through 606 removed outlier: 3.538A pdb=" N ALA G 602 " --> pdb=" O GLY G 598 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 633 Processing helix chain 'G' and resid 639 through 647 removed outlier: 4.438A pdb=" N THR G 643 " --> pdb=" O ARG G 639 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN G 647 " --> pdb=" O THR G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 705 Processing helix chain 'G' and resid 706 through 724 removed outlier: 3.588A pdb=" N ASN G 719 " --> pdb=" O GLN G 715 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU G 722 " --> pdb=" O LYS G 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 727 No H-bonds generated for 'chain 'G' and resid 725 through 727' Processing helix chain 'G' and resid 730 through 752 removed outlier: 3.542A pdb=" N GLY G 735 " --> pdb=" O ALA G 731 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER G 739 " --> pdb=" O GLY G 735 " (cutoff:3.500A) Processing helix chain 'G' and resid 770 through 794 removed outlier: 3.594A pdb=" N SER G 791 " --> pdb=" O LEU G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 832 Processing helix chain 'G' and resid 834 through 839 removed outlier: 3.588A pdb=" N THR G 838 " --> pdb=" O THR G 834 " (cutoff:3.500A) Processing helix chain 'G' and resid 839 through 847 Processing helix chain 'G' and resid 851 through 856 removed outlier: 3.724A pdb=" N PHE G 856 " --> pdb=" O HIS G 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 857 through 861 removed outlier: 3.653A pdb=" N GLY G 860 " --> pdb=" O PRO G 857 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE G 861 " --> pdb=" O VAL G 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 857 through 861' Processing helix chain 'G' and resid 866 through 883 removed outlier: 3.638A pdb=" N LYS G 870 " --> pdb=" O LYS G 866 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'H' and resid 34 through 51 removed outlier: 3.547A pdb=" N ASP H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 95 Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.759A pdb=" N LEU H 115 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 141 removed outlier: 3.526A pdb=" N THR H 124 " --> pdb=" O PRO H 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP H 141 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 163 removed outlier: 3.627A pdb=" N LYS H 148 " --> pdb=" O ASN H 144 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 175 through 180 removed outlier: 3.808A pdb=" N ASP H 179 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 removed outlier: 4.134A pdb=" N TYR H 189 " --> pdb=" O GLN H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 212 removed outlier: 3.814A pdb=" N ILE H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 239 removed outlier: 3.833A pdb=" N VAL H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 267 removed outlier: 4.441A pdb=" N GLN H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU H 267 " --> pdb=" O GLY H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 279 through 302 removed outlier: 3.513A pdb=" N MET H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL H 290 " --> pdb=" O ARG H 286 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 312 through 318 Processing helix chain 'H' and resid 344 through 354 Processing helix chain 'H' and resid 361 through 373 removed outlier: 3.793A pdb=" N TYR H 367 " --> pdb=" O ASP H 363 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 368 " --> pdb=" O ALA H 364 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 395 Processing helix chain 'H' and resid 412 through 425 removed outlier: 3.624A pdb=" N LEU H 416 " --> pdb=" O SER H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 433 removed outlier: 3.800A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 458 Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 472 through 490 removed outlier: 3.702A pdb=" N ILE H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR H 481 " --> pdb=" O ASN H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 504 removed outlier: 3.654A pdb=" N PHE H 497 " --> pdb=" O SER H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 515 Processing helix chain 'H' and resid 526 through 540 Processing helix chain 'H' and resid 546 through 560 removed outlier: 3.673A pdb=" N ASN H 552 " --> pdb=" O SER H 548 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG H 553 " --> pdb=" O HIS H 549 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 560 " --> pdb=" O ALA H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 567 removed outlier: 3.873A pdb=" N ILE H 567 " --> pdb=" O ASP H 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 596 removed outlier: 3.671A pdb=" N THR H 595 " --> pdb=" O ASN H 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 596 " --> pdb=" O ILE H 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 592 through 596' Processing helix chain 'H' and resid 600 through 606 Processing helix chain 'H' and resid 621 through 636 removed outlier: 4.301A pdb=" N LEU H 625 " --> pdb=" O SER H 621 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE H 626 " --> pdb=" O VAL H 622 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS H 635 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 640 through 646 removed outlier: 4.259A pdb=" N PHE H 646 " --> pdb=" O ILE H 642 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 724 removed outlier: 3.962A pdb=" N SER H 707 " --> pdb=" O ALA H 703 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP H 708 " --> pdb=" O THR H 704 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 709 " --> pdb=" O GLU H 705 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU H 722 " --> pdb=" O LYS H 718 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 723 " --> pdb=" O ASN H 719 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 727 No H-bonds generated for 'chain 'H' and resid 725 through 727' Processing helix chain 'H' and resid 730 through 752 Processing helix chain 'H' and resid 770 through 794 removed outlier: 3.710A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 786 " --> pdb=" O PHE H 782 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 787 " --> pdb=" O LEU H 783 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU H 789 " --> pdb=" O ALA H 785 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER H 791 " --> pdb=" O LEU H 787 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU H 792 " --> pdb=" O VAL H 788 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS H 794 " --> pdb=" O GLU H 790 " (cutoff:3.500A) Processing helix chain 'H' and resid 814 through 831 removed outlier: 3.541A pdb=" N ASP H 831 " --> pdb=" O LYS H 827 " (cutoff:3.500A) Processing helix chain 'H' and resid 839 through 847 removed outlier: 3.567A pdb=" N SER H 847 " --> pdb=" O PHE H 843 " (cutoff:3.500A) Processing helix chain 'H' and resid 851 through 856 removed outlier: 4.125A pdb=" N PHE H 856 " --> pdb=" O HIS H 852 " (cutoff:3.500A) Processing helix chain 'H' and resid 866 through 883 removed outlier: 3.929A pdb=" N LYS H 870 " --> pdb=" O LYS H 866 " (cutoff:3.500A) Processing helix chain 'H' and resid 888 through 898 removed outlier: 3.840A pdb=" N ASN H 898 " --> pdb=" O TYR H 894 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 6.240A pdb=" N ILE A 14 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS A 331 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 16 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 219 removed outlier: 3.863A pdb=" N GLY A 252 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 575 through 576 removed outlier: 4.452A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 655 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.867A pdb=" N ILE B 342 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 106 removed outlier: 7.064A pdb=" N LYS B 105 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N THR B 219 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE B 216 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 249 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 218 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 251 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 252 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 573 through 575 removed outlier: 3.507A pdb=" N VAL B 574 " --> pdb=" O CYS B 620 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 609 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N CYS B 655 " --> pdb=" O THR B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.367A pdb=" N ILE C 14 " --> pdb=" O LYS C 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 216 through 220 removed outlier: 6.154A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 252 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 308 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE C 73 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 573 through 574 removed outlier: 9.496A pdb=" N CYS C 655 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR C 610 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.100A pdb=" N ILE D 14 " --> pdb=" O LYS D 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.936A pdb=" N LYS D 101 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR D 219 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE D 72 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY D 252 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL D 74 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 575 through 576 removed outlier: 4.583A pdb=" N ASP D 618 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D 610 " --> pdb=" O CYS D 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 17 removed outlier: 3.503A pdb=" N ILE E 342 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.729A pdb=" N LYS E 105 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR E 219 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL E 74 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 569 through 570 removed outlier: 4.401A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 14 through 17 removed outlier: 3.804A pdb=" N ILE G 342 " --> pdb=" O VAL G 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 104 through 106 removed outlier: 6.999A pdb=" N LYS G 105 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR G 219 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE G 220 " --> pdb=" O THR G 251 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA G 250 " --> pdb=" O PHE G 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY G 252 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 575 through 576 removed outlier: 4.476A pdb=" N ASP G 618 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE G 619 " --> pdb=" O SER G 609 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 609 " --> pdb=" O PHE G 619 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 14 through 17 removed outlier: 5.907A pdb=" N ILE H 14 " --> pdb=" O LYS H 329 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS H 331 " --> pdb=" O ILE H 14 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE H 16 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 342 " --> pdb=" O VAL H 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 104 through 106 removed outlier: 6.674A pdb=" N LYS H 105 " --> pdb=" O LEU H 217 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR H 219 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY H 252 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 569 through 570 Processing sheet with id=AC4, first strand: chain 'H' and resid 609 through 611 removed outlier: 3.523A pdb=" N SER H 609 " --> pdb=" O PHE H 619 " (cutoff:3.500A) 2298 hydrogen bonds defined for protein. 6735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.79 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15489 1.34 - 1.46: 6878 1.46 - 1.58: 26257 1.58 - 1.70: 116 1.70 - 1.82: 335 Bond restraints: 49075 Sorted by residual: bond pdb=" N LEU D 599 " pdb=" CA LEU D 599 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.23e-02 6.61e+03 1.20e+01 bond pdb=" N ILE D 593 " pdb=" CA ILE D 593 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.44e+00 bond pdb=" N GLU G 279 " pdb=" CA GLU G 279 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.27e-02 6.20e+03 8.43e+00 bond pdb=" N ASN D 597 " pdb=" CA ASN D 597 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.97e+00 bond pdb=" N GLU D 596 " pdb=" CA GLU D 596 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.66e+00 ... (remaining 49070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 65353 1.67 - 3.33: 952 3.33 - 5.00: 124 5.00 - 6.67: 13 6.67 - 8.33: 9 Bond angle restraints: 66451 Sorted by residual: angle pdb=" N ALA D 600 " pdb=" CA ALA D 600 " pdb=" C ALA D 600 " ideal model delta sigma weight residual 113.55 106.29 7.26 1.26e+00 6.30e-01 3.32e+01 angle pdb=" N VAL E 622 " pdb=" CA VAL E 622 " pdb=" C VAL E 622 " ideal model delta sigma weight residual 113.53 108.20 5.33 9.80e-01 1.04e+00 2.95e+01 angle pdb=" N LYS A 136 " pdb=" CA LYS A 136 " pdb=" C LYS A 136 " ideal model delta sigma weight residual 111.14 105.46 5.68 1.08e+00 8.57e-01 2.77e+01 angle pdb=" N VAL E 814 " pdb=" CA VAL E 814 " pdb=" C VAL E 814 " ideal model delta sigma weight residual 113.20 108.75 4.45 9.60e-01 1.09e+00 2.15e+01 angle pdb=" CA GLY D 598 " pdb=" C GLY D 598 " pdb=" O GLY D 598 " ideal model delta sigma weight residual 121.41 117.69 3.72 8.80e-01 1.29e+00 1.79e+01 ... (remaining 66446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 26512 17.98 - 35.96: 2848 35.96 - 53.94: 480 53.94 - 71.92: 141 71.92 - 89.89: 63 Dihedral angle restraints: 30044 sinusoidal: 12842 harmonic: 17202 Sorted by residual: dihedral pdb=" CA ILE E 223 " pdb=" C ILE E 223 " pdb=" N ASP E 224 " pdb=" CA ASP E 224 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLU H 789 " pdb=" C GLU H 789 " pdb=" N GLU H 790 " pdb=" CA GLU H 790 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU B 187 " pdb=" C LEU B 187 " pdb=" N ASP B 188 " pdb=" CA ASP B 188 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 30041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 5977 0.046 - 0.091: 1249 0.091 - 0.137: 254 0.137 - 0.182: 19 0.182 - 0.228: 6 Chirality restraints: 7505 Sorted by residual: chirality pdb=" CA LYS A 136 " pdb=" N LYS A 136 " pdb=" C LYS A 136 " pdb=" CB LYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LEU A 137 " pdb=" N LEU A 137 " pdb=" C LEU A 137 " pdb=" CB LEU A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP D 594 " pdb=" N ASP D 594 " pdb=" C ASP D 594 " pdb=" CB ASP D 594 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 7502 not shown) Planarity restraints: 8334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 374 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO A 375 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 119 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 120 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 120 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 120 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 140 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C TYR A 140 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR A 140 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP A 141 " 0.010 2.00e-02 2.50e+03 ... (remaining 8331 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5496 2.75 - 3.28: 48325 3.28 - 3.82: 73554 3.82 - 4.36: 88445 4.36 - 4.90: 151535 Nonbonded interactions: 367355 Sorted by model distance: nonbonded pdb=" OE2 GLU B 816 " pdb=" O2' A M 5 " model vdw 2.207 3.040 nonbonded pdb=" O MET A 132 " pdb=" CG LYS A 136 " model vdw 2.208 3.440 nonbonded pdb=" OH TYR B 189 " pdb=" OE1 GLU B 202 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU H 816 " pdb=" O2' A L 5 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN B 513 " pdb=" OH TYR B 742 " model vdw 2.222 3.040 ... (remaining 367350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 95 or resid 102 through 517 or resid 524 throug \ h 663 or resid 667 or resid 704 through 897 or resid 907 through 934)) selection = (chain 'B' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'C' and (resid 13 through 49 or resid 70 through 95 or resid 102 through \ 517 or resid 524 through 663 or resid 667 or resid 704 through 934)) selection = (chain 'D' and (resid 13 through 95 or resid 102 through 517 or resid 524 throug \ h 663 or resid 667 or resid 704 through 934)) selection = (chain 'E' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'G' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 517 or resid 524 through 663 or resid 703 through 897 or resid 907 through 934) \ ) selection = (chain 'H' and (resid 13 through 49 or resid 70 through 395 or resid 413 through \ 663 or resid 703 through 897 or resid 907 through 934)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 1.370 Check model and map are aligned: 0.280 Set scattering table: 0.330 Process input model: 77.830 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.043 49075 Z= 0.208 Angle : 0.499 8.332 66451 Z= 0.287 Chirality : 0.039 0.228 7505 Planarity : 0.003 0.048 8334 Dihedral : 15.369 89.894 18884 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5799 helix: 0.56 (0.09), residues: 3105 sheet: 0.60 (0.36), residues: 259 loop : -1.04 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 738 HIS 0.010 0.001 HIS D 118 PHE 0.013 0.001 PHE C 227 TYR 0.017 0.001 TYR D 146 ARG 0.008 0.000 ARG B 525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 4.189 Fit side-chains revert: symmetry clash REVERT: B 313 MET cc_start: 0.8996 (tpp) cc_final: 0.8752 (tpp) REVERT: B 525 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7755 (tpp-160) REVERT: C 132 MET cc_start: 0.8214 (tmm) cc_final: 0.7953 (tpp) REVERT: C 436 TYR cc_start: 0.8320 (p90) cc_final: 0.7132 (p90) REVERT: G 273 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8854 (tp) REVERT: G 789 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7654 (mm-30) REVERT: G 861 ILE cc_start: 0.7867 (mm) cc_final: 0.7638 (mm) REVERT: H 425 MET cc_start: 0.8617 (mtt) cc_final: 0.8403 (mtt) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.5082 time to fit residues: 439.5920 Evaluate side-chains 402 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 4.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 8.9990 chunk 445 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 chunk 178 optimal weight: 0.0040 chunk 280 optimal weight: 0.3980 chunk 343 optimal weight: 2.9990 chunk 533 optimal weight: 6.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 512 ASN B 721 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 721 ASN D 292 HIS D 597 ASN D 624 ASN E 118 HIS ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 614 ASN G 624 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS H 624 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49075 Z= 0.184 Angle : 0.535 10.106 66451 Z= 0.290 Chirality : 0.039 0.177 7505 Planarity : 0.004 0.061 8334 Dihedral : 9.635 89.931 7287 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.62 % Allowed : 6.97 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5799 helix: 1.41 (0.09), residues: 3213 sheet: 0.86 (0.38), residues: 212 loop : -1.02 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 738 HIS 0.006 0.001 HIS D 118 PHE 0.013 0.001 PHE C 817 TYR 0.026 0.001 TYR D 146 ARG 0.014 0.000 ARG G 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 461 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7753 (mtp85) REVERT: A 513 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: A 928 ASP cc_start: 0.6499 (m-30) cc_final: 0.6245 (m-30) REVERT: B 525 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7878 (tpp-160) REVERT: B 775 MET cc_start: 0.8398 (mmm) cc_final: 0.8023 (tpt) REVERT: C 132 MET cc_start: 0.8686 (tmm) cc_final: 0.8208 (tpp) REVERT: C 431 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7528 (ttt180) REVERT: C 443 MET cc_start: 0.8773 (mmm) cc_final: 0.8391 (mmm) REVERT: H 75 ASP cc_start: 0.8406 (t0) cc_final: 0.8183 (t0) REVERT: H 425 MET cc_start: 0.8324 (mtt) cc_final: 0.8099 (mtt) outliers start: 32 outliers final: 20 residues processed: 482 average time/residue: 0.4930 time to fit residues: 390.8245 Evaluate side-chains 417 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 396 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain H residue 613 SER Chi-restraints excluded: chain H residue 841 LEU Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 444 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 534 optimal weight: 10.0000 chunk 577 optimal weight: 0.0870 chunk 476 optimal weight: 5.9990 chunk 530 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 429 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 491 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN D 744 ASN E 296 GLN E 530 GLN G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 752 HIS H 392 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 49075 Z= 0.284 Angle : 0.527 7.994 66451 Z= 0.282 Chirality : 0.040 0.166 7505 Planarity : 0.004 0.061 8334 Dihedral : 9.506 87.635 7285 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 1.08 % Allowed : 10.11 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5799 helix: 1.50 (0.09), residues: 3223 sheet: 0.46 (0.36), residues: 236 loop : -1.11 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 738 HIS 0.007 0.001 HIS D 156 PHE 0.017 0.001 PHE C 227 TYR 0.023 0.001 TYR D 146 ARG 0.008 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8925 (tt0) REVERT: B 525 ARG cc_start: 0.8089 (tpp-160) cc_final: 0.7843 (tpp-160) REVERT: B 775 MET cc_start: 0.8492 (mmm) cc_final: 0.8127 (tpt) REVERT: C 132 MET cc_start: 0.8691 (tmm) cc_final: 0.8220 (tpp) REVERT: C 431 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7534 (ttt180) REVERT: C 443 MET cc_start: 0.8660 (mmm) cc_final: 0.8413 (mmm) REVERT: D 105 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7596 (mtmt) REVERT: H 75 ASP cc_start: 0.8411 (t0) cc_final: 0.8105 (t0) REVERT: H 530 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7560 (tm-30) outliers start: 56 outliers final: 38 residues processed: 443 average time/residue: 0.5068 time to fit residues: 370.9303 Evaluate side-chains 422 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 382 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 613 SER Chi-restraints excluded: chain H residue 845 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 2.9990 chunk 402 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 255 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 536 optimal weight: 1.9990 chunk 568 optimal weight: 0.0770 chunk 280 optimal weight: 2.9990 chunk 508 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 ASN D 292 HIS E 759 ASN G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 49075 Z= 0.169 Angle : 0.468 10.111 66451 Z= 0.252 Chirality : 0.038 0.157 7505 Planarity : 0.003 0.059 8334 Dihedral : 9.343 87.310 7285 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 1.27 % Allowed : 11.90 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.11), residues: 5799 helix: 1.68 (0.09), residues: 3234 sheet: 0.58 (0.36), residues: 236 loop : -1.06 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 738 HIS 0.014 0.001 HIS H 392 PHE 0.013 0.001 PHE C 227 TYR 0.018 0.001 TYR D 146 ARG 0.004 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 433 time to evaluate : 4.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 443 MET cc_start: 0.8241 (mmm) cc_final: 0.7979 (mmt) REVERT: A 513 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: B 525 ARG cc_start: 0.8088 (tpp-160) cc_final: 0.7870 (tpp-160) REVERT: B 529 GLU cc_start: 0.7160 (pm20) cc_final: 0.6882 (mp0) REVERT: B 775 MET cc_start: 0.8449 (mmm) cc_final: 0.8108 (tpt) REVERT: C 132 MET cc_start: 0.8690 (tmm) cc_final: 0.8262 (tpp) REVERT: C 431 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7485 (ttt180) REVERT: C 443 MET cc_start: 0.8628 (mmm) cc_final: 0.8365 (mmm) REVERT: D 565 GLU cc_start: 0.7896 (mp0) cc_final: 0.7662 (mp0) REVERT: E 140 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.4318 (m-10) REVERT: E 744 ASN cc_start: 0.8849 (t0) cc_final: 0.8477 (t0) REVERT: G 291 GLU cc_start: 0.8458 (pt0) cc_final: 0.8241 (pt0) REVERT: H 75 ASP cc_start: 0.8399 (t0) cc_final: 0.8071 (t0) REVERT: H 282 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8211 (mmm-85) REVERT: H 530 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: H 917 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7625 (tt) outliers start: 66 outliers final: 31 residues processed: 478 average time/residue: 0.4917 time to fit residues: 387.4448 Evaluate side-chains 439 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 403 time to evaluate : 4.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 808 LEU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 613 SER Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 423 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 485 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 290 optimal weight: 0.0020 chunk 510 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 276 GLN A 439 HIS A 512 ASN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN B 721 ASN D 292 HIS E 530 GLN G 560 ASN ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS H 784 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 49075 Z= 0.429 Angle : 0.612 9.435 66451 Z= 0.323 Chirality : 0.043 0.171 7505 Planarity : 0.004 0.060 8334 Dihedral : 9.483 85.363 7285 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 1.91 % Allowed : 13.71 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.11), residues: 5799 helix: 1.39 (0.09), residues: 3219 sheet: 0.27 (0.36), residues: 243 loop : -1.28 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 738 HIS 0.010 0.001 HIS A 583 PHE 0.023 0.002 PHE C 227 TYR 0.022 0.002 TYR D 146 ARG 0.006 0.001 ARG H 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 400 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7815 (ttm) REVERT: B 775 MET cc_start: 0.8618 (mmm) cc_final: 0.8258 (tpt) REVERT: C 132 MET cc_start: 0.8694 (tmm) cc_final: 0.8229 (tpp) REVERT: C 431 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7498 (ttt180) REVERT: C 910 PHE cc_start: 0.7460 (m-80) cc_final: 0.7161 (m-80) REVERT: D 285 GLU cc_start: 0.7788 (tp30) cc_final: 0.7154 (tp30) REVERT: D 565 GLU cc_start: 0.7918 (mp0) cc_final: 0.7695 (mp0) REVERT: E 140 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.4392 (m-10) REVERT: H 75 ASP cc_start: 0.8486 (t0) cc_final: 0.8264 (t0) REVERT: H 530 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: H 917 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7694 (tt) outliers start: 99 outliers final: 64 residues processed: 469 average time/residue: 0.4745 time to fit residues: 371.9642 Evaluate side-chains 442 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 374 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 765 MET Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 656 ILE Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 642 ILE Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 2.9990 chunk 511 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 568 optimal weight: 9.9990 chunk 472 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS G 439 HIS G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 49075 Z= 0.237 Angle : 0.511 7.385 66451 Z= 0.273 Chirality : 0.039 0.154 7505 Planarity : 0.003 0.058 8334 Dihedral : 9.375 86.567 7285 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 1.50 % Allowed : 14.73 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5799 helix: 1.57 (0.09), residues: 3214 sheet: 0.25 (0.36), residues: 230 loop : -1.21 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 738 HIS 0.005 0.001 HIS A 165 PHE 0.017 0.001 PHE C 227 TYR 0.019 0.001 TYR D 146 ARG 0.007 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 407 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7602 (ttm) REVERT: B 775 MET cc_start: 0.8545 (mmm) cc_final: 0.8221 (tpt) REVERT: C 132 MET cc_start: 0.8714 (tmm) cc_final: 0.8272 (tpp) REVERT: C 431 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7471 (ttt180) REVERT: C 443 MET cc_start: 0.8600 (mmm) cc_final: 0.7750 (mmm) REVERT: D 105 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7631 (mtmt) REVERT: E 140 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.4493 (m-10) REVERT: E 744 ASN cc_start: 0.8923 (t0) cc_final: 0.8460 (t0) REVERT: H 530 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: H 917 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7657 (tt) outliers start: 78 outliers final: 54 residues processed: 459 average time/residue: 0.4799 time to fit residues: 365.8442 Evaluate side-chains 446 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 388 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 643 THR Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 415 optimal weight: 0.9980 chunk 321 optimal weight: 4.9990 chunk 478 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 chunk 566 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 345 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 49075 Z= 0.156 Angle : 0.474 10.150 66451 Z= 0.253 Chirality : 0.038 0.204 7505 Planarity : 0.003 0.058 8334 Dihedral : 9.196 84.738 7285 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 1.42 % Allowed : 15.54 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 5799 helix: 1.77 (0.09), residues: 3227 sheet: 0.68 (0.37), residues: 212 loop : -1.09 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 738 HIS 0.004 0.001 HIS B 784 PHE 0.013 0.001 PHE E 646 TYR 0.020 0.001 TYR H 140 ARG 0.006 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 423 time to evaluate : 4.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7590 (ttm) REVERT: A 147 ARG cc_start: 0.7381 (mmp80) cc_final: 0.7117 (mmp-170) REVERT: A 211 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8181 (pp) REVERT: B 525 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7756 (tpp-160) REVERT: C 132 MET cc_start: 0.8696 (tmm) cc_final: 0.8262 (tpp) REVERT: C 431 ARG cc_start: 0.7729 (ttt180) cc_final: 0.7435 (ttt180) REVERT: C 443 MET cc_start: 0.8575 (mmm) cc_final: 0.7721 (mmm) REVERT: D 105 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7615 (mtmt) REVERT: D 775 MET cc_start: 0.8314 (mmm) cc_final: 0.7862 (mmp) REVERT: E 140 TYR cc_start: 0.5055 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: E 744 ASN cc_start: 0.8910 (t0) cc_final: 0.8480 (t0) REVERT: G 560 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7559 (t0) REVERT: H 75 ASP cc_start: 0.8501 (t0) cc_final: 0.8237 (t0) REVERT: H 282 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.8232 (mmm-85) REVERT: H 530 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: H 917 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7542 (tt) outliers start: 74 outliers final: 45 residues processed: 476 average time/residue: 0.4747 time to fit residues: 377.9328 Evaluate side-chains 458 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 407 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 386 optimal weight: 8.9990 chunk 280 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 445 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 392 HIS A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B 614 ASN D 292 HIS E 530 GLN E 615 ASN ** G 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS ** H 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 49075 Z= 0.412 Angle : 0.609 9.867 66451 Z= 0.321 Chirality : 0.043 0.186 7505 Planarity : 0.004 0.060 8334 Dihedral : 9.373 85.618 7285 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 1.81 % Allowed : 16.12 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5799 helix: 1.47 (0.09), residues: 3220 sheet: 0.10 (0.35), residues: 244 loop : -1.31 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 738 HIS 0.011 0.001 HIS B 156 PHE 0.022 0.002 PHE C 227 TYR 0.025 0.002 TYR H 588 ARG 0.006 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 399 time to evaluate : 4.245 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: A 147 ARG cc_start: 0.7325 (mmp80) cc_final: 0.7029 (mmp-170) REVERT: B 171 GLU cc_start: 0.8157 (pm20) cc_final: 0.7769 (pm20) REVERT: B 525 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7741 (tpp-160) REVERT: B 529 GLU cc_start: 0.7460 (pm20) cc_final: 0.7108 (mp0) REVERT: C 132 MET cc_start: 0.8652 (tmm) cc_final: 0.8182 (tpp) REVERT: C 431 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7473 (ttt180) REVERT: C 443 MET cc_start: 0.8572 (mmm) cc_final: 0.7770 (mmm) REVERT: C 910 PHE cc_start: 0.7540 (m-80) cc_final: 0.7232 (m-80) REVERT: D 105 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7666 (mtmt) REVERT: D 146 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.5912 (t80) REVERT: E 140 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.4531 (m-10) REVERT: E 488 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8292 (tm-30) REVERT: E 744 ASN cc_start: 0.8998 (t0) cc_final: 0.8523 (t0) REVERT: H 530 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: H 917 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7740 (tt) outliers start: 94 outliers final: 65 residues processed: 466 average time/residue: 0.4887 time to fit residues: 379.7696 Evaluate side-chains 451 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 342 ILE Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 8.9990 chunk 542 optimal weight: 5.9990 chunk 495 optimal weight: 7.9990 chunk 528 optimal weight: 0.9980 chunk 317 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 414 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 477 optimal weight: 9.9990 chunk 499 optimal weight: 7.9990 chunk 526 optimal weight: 0.2980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 392 HIS A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 615 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 49075 Z= 0.214 Angle : 0.516 8.607 66451 Z= 0.276 Chirality : 0.039 0.192 7505 Planarity : 0.003 0.057 8334 Dihedral : 9.268 85.647 7285 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 1.42 % Allowed : 16.52 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 5799 helix: 1.62 (0.09), residues: 3221 sheet: 0.14 (0.36), residues: 232 loop : -1.20 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 738 HIS 0.033 0.001 HIS A 392 PHE 0.020 0.001 PHE H 528 TYR 0.031 0.001 TYR H 140 ARG 0.005 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 403 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7623 (ttm) REVERT: A 147 ARG cc_start: 0.7358 (mmp80) cc_final: 0.7060 (mmp-170) REVERT: B 171 GLU cc_start: 0.8144 (pm20) cc_final: 0.7775 (pm20) REVERT: B 385 ASP cc_start: 0.8648 (t0) cc_final: 0.8415 (t70) REVERT: B 529 GLU cc_start: 0.7366 (pm20) cc_final: 0.7083 (mp0) REVERT: C 132 MET cc_start: 0.8713 (tmm) cc_final: 0.8287 (tpp) REVERT: C 431 ARG cc_start: 0.7736 (ttt180) cc_final: 0.7432 (ttt180) REVERT: C 443 MET cc_start: 0.8542 (mmm) cc_final: 0.7891 (mmm) REVERT: D 105 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7625 (mtmt) REVERT: E 140 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4586 (m-10) REVERT: E 488 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 744 ASN cc_start: 0.8919 (t0) cc_final: 0.8444 (t0) REVERT: H 75 ASP cc_start: 0.8540 (t0) cc_final: 0.8248 (t0) REVERT: H 448 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8725 (mmmt) REVERT: H 530 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: H 917 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7544 (tt) outliers start: 74 outliers final: 59 residues processed: 453 average time/residue: 0.4817 time to fit residues: 362.4421 Evaluate side-chains 453 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 390 time to evaluate : 4.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 808 LEU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 8.9990 chunk 558 optimal weight: 0.8980 chunk 340 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 388 optimal weight: 9.9990 chunk 585 optimal weight: 10.0000 chunk 539 optimal weight: 6.9990 chunk 466 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 360 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 392 HIS A 512 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 49075 Z= 0.401 Angle : 0.610 11.940 66451 Z= 0.320 Chirality : 0.042 0.187 7505 Planarity : 0.004 0.059 8334 Dihedral : 9.374 89.816 7285 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.33 % Favored : 94.60 % Rotamer: Outliers : 1.66 % Allowed : 16.52 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5799 helix: 1.42 (0.09), residues: 3219 sheet: -0.08 (0.35), residues: 245 loop : -1.35 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 738 HIS 0.028 0.001 HIS A 392 PHE 0.020 0.002 PHE C 227 TYR 0.035 0.002 TYR H 588 ARG 0.005 0.000 ARG E 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11598 Ramachandran restraints generated. 5799 Oldfield, 0 Emsley, 5799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 388 time to evaluate : 4.312 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7625 (ttm) REVERT: A 147 ARG cc_start: 0.7394 (mmp80) cc_final: 0.7057 (mmp-170) REVERT: B 171 GLU cc_start: 0.8136 (pm20) cc_final: 0.7795 (pm20) REVERT: B 529 GLU cc_start: 0.7412 (pm20) cc_final: 0.7181 (mp0) REVERT: C 132 MET cc_start: 0.8621 (tmm) cc_final: 0.8153 (tpp) REVERT: C 431 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7463 (ttt180) REVERT: C 443 MET cc_start: 0.8594 (mmm) cc_final: 0.7927 (mmm) REVERT: D 775 MET cc_start: 0.8478 (mmm) cc_final: 0.8163 (mmp) REVERT: E 140 TYR cc_start: 0.5138 (OUTLIER) cc_final: 0.4558 (m-10) REVERT: E 488 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8186 (tm-30) REVERT: H 443 MET cc_start: 0.8037 (mmm) cc_final: 0.7795 (mmm) REVERT: H 530 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: H 917 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7722 (tt) outliers start: 86 outliers final: 68 residues processed: 451 average time/residue: 0.4858 time to fit residues: 365.9639 Evaluate side-chains 452 residues out of total 5193 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 GLU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 435 ASN Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 775 MET Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 884 ASP Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain G residue 454 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 560 ASN Chi-restraints excluded: chain G residue 642 ILE Chi-restraints excluded: chain G residue 662 GLU Chi-restraints excluded: chain G residue 811 VAL Chi-restraints excluded: chain G residue 914 ILE Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 344 VAL Chi-restraints excluded: chain H residue 392 HIS Chi-restraints excluded: chain H residue 421 LEU Chi-restraints excluded: chain H residue 530 GLN Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 788 VAL Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain H residue 917 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 0.9980 chunk 496 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 430 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 467 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 479 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN D 118 HIS D 292 HIS ** E 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086100 restraints weight = 98346.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088331 restraints weight = 62215.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089848 restraints weight = 46054.597| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 49075 Z= 0.353 Angle : 0.706 59.180 66451 Z= 0.392 Chirality : 0.044 1.290 7505 Planarity : 0.005 0.171 8334 Dihedral : 9.372 89.741 7285 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 1.46 % Allowed : 16.62 % Favored : 81.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.11), residues: 5799 helix: 1.43 (0.09), residues: 3219 sheet: -0.09 (0.35), residues: 245 loop : -1.35 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 738 HIS 0.228 0.004 HIS A 392 PHE 0.019 0.002 PHE C 227 TYR 0.030 0.002 TYR H 588 ARG 0.004 0.000 ARG E 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7432.47 seconds wall clock time: 132 minutes 57.49 seconds (7977.49 seconds total)