Starting phenix.real_space_refine on Fri Dec 27 04:05:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.map" model { file = "/net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bw1_44944/12_2024/9bw1_44944.cif" } resolution = 3.65 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= 0.002 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 290 5.49 5 Mg 11 5.21 5 S 136 5.16 5 C 29151 2.51 5 N 8356 2.21 5 O 9337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 47283 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 692 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "4" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "5" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 690 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 304 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "H" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1065 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "I" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1790 Classifications: {'DNA': 87} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 86} Chain: "J" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3707 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain: "M" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6349 Classifications: {'peptide': 779} Link IDs: {'PTRANS': 32, 'TRANS': 746} Chain breaks: 1 Chain: "N" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6349 Classifications: {'peptide': 779} Link IDs: {'PTRANS': 32, 'TRANS': 746} Chain breaks: 1 Chain: "O" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2788 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain: "P" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2788 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain: "Q" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2440 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Chain: "R" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "S" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "T" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "U" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "V" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "W" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2756 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "a" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "b" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "c" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 70 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "x" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 119 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "y" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 119 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 2, 'TRANS': 12} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6698 SG CYS J 139 113.771 100.177 204.450 1.00 87.21 S ATOM 6719 SG CYS J 142 116.816 98.286 203.136 1.00 75.34 S ATOM 6933 SG CYS J 167 117.042 100.463 206.324 1.00 99.09 S ATOM 7022 SG CYS J 178 98.953 96.902 203.975 1.00112.08 S ATOM 7045 SG CYS J 181 95.339 95.995 204.276 1.00114.07 S ATOM 7180 SG CYS J 197 98.077 93.216 204.247 1.00 94.44 S ATOM 7201 SG CYS J 200 97.286 95.137 201.095 1.00102.55 S Time building chain proxies: 21.07, per 1000 atoms: 0.45 Number of scatterers: 47283 At special positions: 0 Unit cell: (152.892, 163.578, 278.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 136 16.00 P 290 15.00 Mg 11 11.99 O 9337 8.00 N 8356 7.00 C 29151 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: 9.43 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" ND1 HIS J 170 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 139 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 167 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 142 " pdb=" ZN J 602 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 178 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 200 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 197 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 181 " Number of angles added : 9 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9708 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 36 sheets defined 55.4% alpha, 8.5% beta 113 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 13.03 Creating SS restraints... Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 55 through 63 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 81 through 87 removed outlier: 3.592A pdb=" N PHE J 85 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 139 through 149 Processing helix chain 'J' and resid 157 through 161 Processing helix chain 'J' and resid 219 through 244 removed outlier: 4.125A pdb=" N GLN J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N CYS J 243 " --> pdb=" O LEU J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 262 removed outlier: 3.568A pdb=" N ILE J 253 " --> pdb=" O SER J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 277 Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 308 through 314 Processing helix chain 'J' and resid 314 through 320 removed outlier: 3.888A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR J 320 " --> pdb=" O LYS J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 328 Processing helix chain 'J' and resid 345 through 359 Processing helix chain 'J' and resid 366 through 375 Processing helix chain 'J' and resid 377 through 383 removed outlier: 3.688A pdb=" N ILE J 381 " --> pdb=" O HIS J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 426 removed outlier: 3.544A pdb=" N CYS J 389 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 437 removed outlier: 3.640A pdb=" N LEU J 437 " --> pdb=" O ARG J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 446 removed outlier: 3.520A pdb=" N ARG J 445 " --> pdb=" O GLY J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 461 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 15 through 28 Processing helix chain 'M' and resid 62 through 72 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'M' and resid 147 through 155 Processing helix chain 'M' and resid 169 through 184 removed outlier: 5.113A pdb=" N ASP M 181 " --> pdb=" O GLN M 177 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR M 182 " --> pdb=" O PHE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 205 Processing helix chain 'M' and resid 209 through 215 Processing helix chain 'M' and resid 221 through 231 removed outlier: 3.551A pdb=" N ILE M 225 " --> pdb=" O LYS M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 Processing helix chain 'M' and resid 343 through 352 removed outlier: 3.800A pdb=" N ALA M 352 " --> pdb=" O ARG M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 368 Processing helix chain 'M' and resid 382 through 400 Processing helix chain 'M' and resid 402 through 408 removed outlier: 3.763A pdb=" N ILE M 405 " --> pdb=" O CYS M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 414 Processing helix chain 'M' and resid 422 through 437 Processing helix chain 'M' and resid 444 through 460 Processing helix chain 'M' and resid 465 through 474 Processing helix chain 'M' and resid 478 through 486 Processing helix chain 'M' and resid 487 through 492 Processing helix chain 'M' and resid 493 through 495 No H-bonds generated for 'chain 'M' and resid 493 through 495' Processing helix chain 'M' and resid 563 through 578 Processing helix chain 'M' and resid 595 through 605 removed outlier: 3.960A pdb=" N GLU M 599 " --> pdb=" O SER M 595 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE M 605 " --> pdb=" O LEU M 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 616 through 619 removed outlier: 3.760A pdb=" N PHE M 619 " --> pdb=" O LYS M 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 616 through 619' Processing helix chain 'M' and resid 620 through 634 removed outlier: 3.701A pdb=" N ARG M 625 " --> pdb=" O SER M 621 " (cutoff:3.500A) Processing helix chain 'M' and resid 643 through 651 removed outlier: 3.831A pdb=" N VAL M 648 " --> pdb=" O THR M 645 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG M 649 " --> pdb=" O ARG M 646 " (cutoff:3.500A) Processing helix chain 'M' and resid 656 through 661 removed outlier: 3.622A pdb=" N ALA M 661 " --> pdb=" O LYS M 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 664 through 683 removed outlier: 4.430A pdb=" N TYR M 680 " --> pdb=" O ALA M 676 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP M 681 " --> pdb=" O TYR M 677 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 703 Processing helix chain 'M' and resid 706 through 710 Processing helix chain 'M' and resid 714 through 722 Processing helix chain 'M' and resid 747 through 752 removed outlier: 3.536A pdb=" N ASP M 752 " --> pdb=" O SER M 749 " (cutoff:3.500A) Processing helix chain 'M' and resid 795 through 812 Processing helix chain 'M' and resid 820 through 831 Processing helix chain 'M' and resid 834 through 856 removed outlier: 3.530A pdb=" N GLY M 856 " --> pdb=" O ARG M 852 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 61 through 72 removed outlier: 4.025A pdb=" N ILE N 65 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 131 Processing helix chain 'N' and resid 146 through 155 Processing helix chain 'N' and resid 169 through 185 removed outlier: 5.115A pdb=" N ASP N 181 " --> pdb=" O GLN N 177 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR N 182 " --> pdb=" O PHE N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 205 removed outlier: 3.512A pdb=" N GLN N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'N' and resid 221 through 231 Processing helix chain 'N' and resid 254 through 263 Processing helix chain 'N' and resid 343 through 351 Processing helix chain 'N' and resid 353 through 368 Processing helix chain 'N' and resid 369 through 372 Processing helix chain 'N' and resid 382 through 400 Processing helix chain 'N' and resid 403 through 408 removed outlier: 3.987A pdb=" N LEU N 408 " --> pdb=" O ILE N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 410 through 414 removed outlier: 3.681A pdb=" N VAL N 413 " --> pdb=" O HIS N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 437 removed outlier: 3.682A pdb=" N TYR N 437 " --> pdb=" O ILE N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 460 Processing helix chain 'N' and resid 465 through 474 Processing helix chain 'N' and resid 479 through 486 Processing helix chain 'N' and resid 489 through 493 removed outlier: 3.527A pdb=" N TYR N 492 " --> pdb=" O ARG N 489 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN N 493 " --> pdb=" O ALA N 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 489 through 493' Processing helix chain 'N' and resid 564 through 578 Processing helix chain 'N' and resid 595 through 606 removed outlier: 3.963A pdb=" N GLU N 599 " --> pdb=" O SER N 595 " (cutoff:3.500A) Processing helix chain 'N' and resid 617 through 619 No H-bonds generated for 'chain 'N' and resid 617 through 619' Processing helix chain 'N' and resid 620 through 634 removed outlier: 3.804A pdb=" N LEU N 626 " --> pdb=" O VAL N 622 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE N 627 " --> pdb=" O CYS N 623 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY N 628 " --> pdb=" O GLU N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 643 through 647 removed outlier: 3.543A pdb=" N ASN N 647 " --> pdb=" O ILE N 644 " (cutoff:3.500A) Processing helix chain 'N' and resid 656 through 661 removed outlier: 3.544A pdb=" N LEU N 660 " --> pdb=" O ASN N 656 " (cutoff:3.500A) Processing helix chain 'N' and resid 664 through 679 Processing helix chain 'N' and resid 691 through 703 Processing helix chain 'N' and resid 706 through 710 Processing helix chain 'N' and resid 714 through 722 removed outlier: 3.566A pdb=" N LEU N 722 " --> pdb=" O GLN N 718 " (cutoff:3.500A) Processing helix chain 'N' and resid 747 through 756 Proline residue: N 753 - end of helix Processing helix chain 'N' and resid 787 through 792 Processing helix chain 'N' and resid 795 through 812 Processing helix chain 'N' and resid 820 through 831 removed outlier: 3.717A pdb=" N LEU N 824 " --> pdb=" O SER N 820 " (cutoff:3.500A) Processing helix chain 'N' and resid 834 through 855 removed outlier: 3.755A pdb=" N GLU N 849 " --> pdb=" O ALA N 845 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL N 850 " --> pdb=" O GLU N 846 " (cutoff:3.500A) Processing helix chain 'O' and resid 564 through 579 removed outlier: 3.614A pdb=" N MET O 569 " --> pdb=" O ARG O 565 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL O 570 " --> pdb=" O SER O 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 605 Processing helix chain 'O' and resid 620 through 634 removed outlier: 3.699A pdb=" N GLU O 624 " --> pdb=" O GLY O 620 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG O 625 " --> pdb=" O SER O 621 " (cutoff:3.500A) Processing helix chain 'O' and resid 635 through 638 Processing helix chain 'O' and resid 643 through 651 removed outlier: 3.599A pdb=" N ARG O 646 " --> pdb=" O GLN O 643 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL O 648 " --> pdb=" O THR O 645 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG O 649 " --> pdb=" O ARG O 646 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 660 Processing helix chain 'O' and resid 664 through 678 Processing helix chain 'O' and resid 691 through 704 Processing helix chain 'O' and resid 706 through 710 Processing helix chain 'O' and resid 714 through 721 Processing helix chain 'O' and resid 747 through 756 Proline residue: O 753 - end of helix removed outlier: 3.673A pdb=" N GLU O 756 " --> pdb=" O PRO O 753 " (cutoff:3.500A) Processing helix chain 'O' and resid 788 through 792 Processing helix chain 'O' and resid 795 through 816 removed outlier: 3.965A pdb=" N LYS O 800 " --> pdb=" O GLU O 796 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU O 801 " --> pdb=" O LYS O 797 " (cutoff:3.500A) Processing helix chain 'O' and resid 816 through 842 Processing helix chain 'P' and resid 564 through 569 removed outlier: 3.639A pdb=" N MET P 569 " --> pdb=" O ARG P 565 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 579 Processing helix chain 'P' and resid 596 through 605 removed outlier: 3.560A pdb=" N PHE P 605 " --> pdb=" O LEU P 601 " (cutoff:3.500A) Processing helix chain 'P' and resid 617 through 619 No H-bonds generated for 'chain 'P' and resid 617 through 619' Processing helix chain 'P' and resid 620 through 634 removed outlier: 3.827A pdb=" N LEU P 626 " --> pdb=" O VAL P 622 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE P 634 " --> pdb=" O SER P 630 " (cutoff:3.500A) Processing helix chain 'P' and resid 643 through 651 removed outlier: 3.573A pdb=" N ARG P 646 " --> pdb=" O GLN P 643 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL P 648 " --> pdb=" O THR P 645 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG P 649 " --> pdb=" O ARG P 646 " (cutoff:3.500A) Processing helix chain 'P' and resid 652 through 656 removed outlier: 3.711A pdb=" N ASN P 656 " --> pdb=" O LYS P 653 " (cutoff:3.500A) Processing helix chain 'P' and resid 664 through 678 Processing helix chain 'P' and resid 691 through 703 Processing helix chain 'P' and resid 706 through 710 Processing helix chain 'P' and resid 714 through 721 Processing helix chain 'P' and resid 747 through 752 removed outlier: 3.517A pdb=" N ASP P 752 " --> pdb=" O SER P 749 " (cutoff:3.500A) Processing helix chain 'P' and resid 788 through 792 Processing helix chain 'P' and resid 796 through 816 removed outlier: 3.949A pdb=" N LYS P 800 " --> pdb=" O GLU P 796 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU P 801 " --> pdb=" O LYS P 797 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR P 814 " --> pdb=" O TYR P 810 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN P 816 " --> pdb=" O ASN P 812 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 842 Processing helix chain 'Q' and resid 15 through 26 removed outlier: 3.585A pdb=" N ARG Q 19 " --> pdb=" O PRO Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 79 Processing helix chain 'Q' and resid 80 through 82 No H-bonds generated for 'chain 'Q' and resid 80 through 82' Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'Q' and resid 149 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 4.110A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 196 Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.574A pdb=" N PHE Q 214 " --> pdb=" O LEU Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 removed outlier: 3.521A pdb=" N VAL Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.641A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 296 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.650A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 331 removed outlier: 3.756A pdb=" N CYS Q 315 " --> pdb=" O SER Q 311 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 331 " --> pdb=" O ARG Q 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 13 removed outlier: 3.505A pdb=" N LEU R 11 " --> pdb=" O PRO R 8 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR R 13 " --> pdb=" O GLU R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 3.700A pdb=" N ARG R 19 " --> pdb=" O PRO R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 46 removed outlier: 3.741A pdb=" N GLU R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 85 Proline residue: R 80 - end of helix Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 148 through 163 Processing helix chain 'R' and resid 172 through 178 Processing helix chain 'R' and resid 189 through 200 Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 218 through 224 Processing helix chain 'R' and resid 237 through 254 removed outlier: 3.594A pdb=" N VAL R 241 " --> pdb=" O SER R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 273 removed outlier: 3.617A pdb=" N ARG R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 295 removed outlier: 3.581A pdb=" N LEU R 281 " --> pdb=" O CYS R 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG R 295 " --> pdb=" O ASP R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 308 removed outlier: 3.521A pdb=" N ARG R 308 " --> pdb=" O ASP R 304 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 329 removed outlier: 4.319A pdb=" N GLN R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 343 removed outlier: 3.741A pdb=" N VAL R 336 " --> pdb=" O THR R 332 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU R 339 " --> pdb=" O ASP R 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 13 removed outlier: 3.646A pdb=" N THR S 13 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 Processing helix chain 'S' and resid 30 through 46 removed outlier: 3.972A pdb=" N GLU S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 82 Proline residue: S 80 - end of helix Processing helix chain 'S' and resid 105 through 118 Processing helix chain 'S' and resid 148 through 164 Processing helix chain 'S' and resid 172 through 178 removed outlier: 3.508A pdb=" N HIS S 175 " --> pdb=" O GLU S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 200 removed outlier: 3.742A pdb=" N GLN S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU S 192 " --> pdb=" O GLN S 188 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU S 195 " --> pdb=" O CYS S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 removed outlier: 3.766A pdb=" N THR S 213 " --> pdb=" O GLU S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 224 removed outlier: 3.974A pdb=" N ARG S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 254 removed outlier: 3.513A pdb=" N VAL S 241 " --> pdb=" O SER S 237 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS S 254 " --> pdb=" O THR S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 273 Processing helix chain 'S' and resid 277 through 296 removed outlier: 3.608A pdb=" N LEU S 281 " --> pdb=" O CYS S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 308 removed outlier: 4.559A pdb=" N ARG S 308 " --> pdb=" O ASP S 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 329 Processing helix chain 'S' and resid 332 through 344 removed outlier: 3.540A pdb=" N VAL S 336 " --> pdb=" O THR S 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 13 Processing helix chain 'T' and resid 15 through 25 Processing helix chain 'T' and resid 30 through 46 Processing helix chain 'T' and resid 62 through 75 Processing helix chain 'T' and resid 78 through 83 Processing helix chain 'T' and resid 105 through 118 Processing helix chain 'T' and resid 148 through 164 Processing helix chain 'T' and resid 173 through 178 Processing helix chain 'T' and resid 184 through 200 removed outlier: 3.586A pdb=" N GLN T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 215 Processing helix chain 'T' and resid 218 through 224 Processing helix chain 'T' and resid 237 through 254 Processing helix chain 'T' and resid 266 through 275 Processing helix chain 'T' and resid 277 through 296 Processing helix chain 'T' and resid 301 through 307 Processing helix chain 'T' and resid 311 through 327 Processing helix chain 'T' and resid 332 through 344 Processing helix chain 'U' and resid 9 through 14 removed outlier: 3.991A pdb=" N THR U 13 " --> pdb=" O LEU U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 25 Processing helix chain 'U' and resid 30 through 46 Processing helix chain 'U' and resid 62 through 83 removed outlier: 3.528A pdb=" N GLN U 72 " --> pdb=" O LEU U 68 " (cutoff:3.500A) Proline residue: U 80 - end of helix Processing helix chain 'U' and resid 105 through 118 removed outlier: 3.503A pdb=" N TYR U 109 " --> pdb=" O ASN U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 164 Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 186 through 200 removed outlier: 3.886A pdb=" N MET U 198 " --> pdb=" O SER U 194 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY U 200 " --> pdb=" O ALA U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 214 Processing helix chain 'U' and resid 218 through 224 Processing helix chain 'U' and resid 237 through 255 Processing helix chain 'U' and resid 266 through 275 Processing helix chain 'U' and resid 277 through 296 Processing helix chain 'U' and resid 301 through 307 Processing helix chain 'U' and resid 311 through 329 removed outlier: 3.810A pdb=" N GLN U 328 " --> pdb=" O GLU U 324 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU U 329 " --> pdb=" O GLY U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 343 Processing helix chain 'V' and resid 8 through 13 Processing helix chain 'V' and resid 15 through 25 removed outlier: 3.645A pdb=" N ARG V 19 " --> pdb=" O PRO V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 46 removed outlier: 3.517A pdb=" N GLU V 46 " --> pdb=" O ARG V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 77 Processing helix chain 'V' and resid 78 through 85 Processing helix chain 'V' and resid 105 through 118 Processing helix chain 'V' and resid 148 through 164 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.560A pdb=" N LYS V 178 " --> pdb=" O HIS V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 200 removed outlier: 3.639A pdb=" N GLN V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU V 192 " --> pdb=" O GLN V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 215 Processing helix chain 'V' and resid 219 through 224 Processing helix chain 'V' and resid 237 through 254 Processing helix chain 'V' and resid 263 through 265 No H-bonds generated for 'chain 'V' and resid 263 through 265' Processing helix chain 'V' and resid 266 through 274 Processing helix chain 'V' and resid 277 through 296 removed outlier: 4.000A pdb=" N LEU V 281 " --> pdb=" O CYS V 277 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 308 removed outlier: 3.577A pdb=" N LEU V 305 " --> pdb=" O THR V 301 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG V 308 " --> pdb=" O ASP V 304 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 329 removed outlier: 3.892A pdb=" N GLU V 324 " --> pdb=" O LYS V 320 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 343 removed outlier: 3.670A pdb=" N VAL V 336 " --> pdb=" O THR V 332 " (cutoff:3.500A) Processing helix chain 'W' and resid 15 through 24 Processing helix chain 'W' and resid 30 through 46 Processing helix chain 'W' and resid 64 through 79 Processing helix chain 'W' and resid 80 through 84 removed outlier: 3.804A pdb=" N GLU W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER W 84 " --> pdb=" O LYS W 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 80 through 84' Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 148 through 164 Processing helix chain 'W' and resid 172 through 178 removed outlier: 3.530A pdb=" N HIS W 175 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY W 177 " --> pdb=" O GLN W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 200 removed outlier: 3.769A pdb=" N GLN W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 214 Processing helix chain 'W' and resid 218 through 224 Processing helix chain 'W' and resid 237 through 254 Processing helix chain 'W' and resid 263 through 265 No H-bonds generated for 'chain 'W' and resid 263 through 265' Processing helix chain 'W' and resid 266 through 275 Processing helix chain 'W' and resid 277 through 295 Processing helix chain 'W' and resid 301 through 308 removed outlier: 3.504A pdb=" N ARG W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 330 Processing helix chain 'W' and resid 332 through 344 Processing sheet with id=AA1, first strand: chain 'J' and resid 166 through 167 removed outlier: 3.713A pdb=" N LYS J 172 " --> pdb=" O CYS J 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 52 through 56 removed outlier: 6.531A pdb=" N TRP M 540 " --> pdb=" O LEU M 557 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU M 557 " --> pdb=" O TRP M 540 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR M 542 " --> pdb=" O VAL M 555 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL M 555 " --> pdb=" O THR M 542 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU M 544 " --> pdb=" O LEU M 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 75 through 80 removed outlier: 6.851A pdb=" N ALA M 113 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ARG M 161 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TRP M 115 " --> pdb=" O ARG M 161 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N HIS M 163 " --> pdb=" O TRP M 115 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU M 117 " --> pdb=" O HIS M 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 85 through 90 Processing sheet with id=AA5, first strand: chain 'M' and resid 135 through 138 Processing sheet with id=AA6, first strand: chain 'M' and resid 235 through 236 Processing sheet with id=AA7, first strand: chain 'M' and resid 729 through 731 removed outlier: 4.850A pdb=" N GLN M 761 " --> pdb=" O PHE M 775 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP M 765 " --> pdb=" O ILE M 771 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE M 771 " --> pdb=" O ASP M 765 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY M 770 " --> pdb=" O SER M 785 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 52 through 56 removed outlier: 6.669A pdb=" N ASP N 546 " --> pdb=" O LEU N 552 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU N 552 " --> pdb=" O ASP N 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 75 through 80 removed outlier: 6.695A pdb=" N ILE N 108 " --> pdb=" O LEU N 76 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE N 78 " --> pdb=" O PHE N 106 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N PHE N 106 " --> pdb=" O PHE N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 85 through 90 Processing sheet with id=AB2, first strand: chain 'N' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'N' and resid 208 through 209 removed outlier: 3.522A pdb=" N ILE N 208 " --> pdb=" O ILE N 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 527 through 528 removed outlier: 6.219A pdb=" N LEU N 527 " --> pdb=" O LEU N 536 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 729 through 731 removed outlier: 4.329A pdb=" N GLN N 761 " --> pdb=" O PHE N 775 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 551 through 558 removed outlier: 6.332A pdb=" N LEU O 552 " --> pdb=" O ASP O 546 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP O 546 " --> pdb=" O LEU O 552 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA O 554 " --> pdb=" O LEU O 544 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL O 586 " --> pdb=" O GLY O 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE O 518 " --> pdb=" O VAL O 586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS O 610 " --> pdb=" O VAL O 585 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 527 through 528 removed outlier: 6.644A pdb=" N LEU O 527 " --> pdb=" O LEU O 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 729 through 731 removed outlier: 4.644A pdb=" N GLN O 761 " --> pdb=" O PHE O 775 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 738 through 740 Processing sheet with id=AC1, first strand: chain 'P' and resid 552 through 558 removed outlier: 6.488A pdb=" N LEU P 552 " --> pdb=" O ASP P 546 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP P 546 " --> pdb=" O LEU P 552 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA P 554 " --> pdb=" O LEU P 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 527 through 528 Processing sheet with id=AC3, first strand: chain 'P' and resid 729 through 731 removed outlier: 4.667A pdb=" N GLN P 761 " --> pdb=" O PHE P 775 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP P 765 " --> pdb=" O ILE P 771 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE P 771 " --> pdb=" O ASP P 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 738 through 740 Processing sheet with id=AC5, first strand: chain 'Q' and resid 55 through 56 Processing sheet with id=AC6, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.436A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 91 through 95 removed outlier: 6.792A pdb=" N VAL R 92 " --> pdb=" O PHE R 169 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP R 171 " --> pdb=" O VAL R 92 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE R 94 " --> pdb=" O ASP R 171 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE R 168 " --> pdb=" O CYS R 204 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU R 206 " --> pdb=" O PHE R 168 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL R 170 " --> pdb=" O LEU R 206 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE R 53 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLY R 207 " --> pdb=" O ILE R 53 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 55 " --> pdb=" O GLY R 207 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE R 52 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE R 228 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE R 54 " --> pdb=" O ILE R 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'S' and resid 92 through 95 removed outlier: 6.756A pdb=" N VAL S 92 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP S 171 " --> pdb=" O VAL S 92 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE S 94 " --> pdb=" O ASP S 171 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N PHE S 52 " --> pdb=" O VAL S 226 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE S 228 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE S 54 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 133 through 134 Processing sheet with id=AD1, first strand: chain 'T' and resid 92 through 95 removed outlier: 6.873A pdb=" N VAL T 92 " --> pdb=" O PHE T 169 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASP T 171 " --> pdb=" O VAL T 92 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE T 94 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE T 228 " --> pdb=" O PHE T 52 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE T 54 " --> pdb=" O ILE T 228 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE T 230 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR T 56 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 133 through 135 Processing sheet with id=AD3, first strand: chain 'U' and resid 92 through 95 removed outlier: 6.708A pdb=" N VAL U 92 " --> pdb=" O PHE U 169 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASP U 171 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE U 94 " --> pdb=" O ASP U 171 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE U 168 " --> pdb=" O CYS U 204 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU U 206 " --> pdb=" O PHE U 168 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL U 170 " --> pdb=" O LEU U 206 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY U 207 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY U 57 " --> pdb=" O GLY U 207 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE U 52 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE U 228 " --> pdb=" O PHE U 52 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE U 54 " --> pdb=" O ILE U 228 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE U 230 " --> pdb=" O PHE U 54 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR U 56 " --> pdb=" O PHE U 230 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 133 through 135 Processing sheet with id=AD5, first strand: chain 'V' and resid 91 through 95 removed outlier: 6.229A pdb=" N ILE V 53 " --> pdb=" O LEU V 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 133 through 134 removed outlier: 3.777A pdb=" N SER V 134 " --> pdb=" O ASN V 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 203 through 206 removed outlier: 6.893A pdb=" N PHE W 52 " --> pdb=" O VAL W 226 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE W 228 " --> pdb=" O PHE W 52 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE W 54 " --> pdb=" O ILE W 228 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE W 230 " --> pdb=" O PHE W 54 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR W 56 " --> pdb=" O PHE W 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 93 through 94 Processing sheet with id=AD9, first strand: chain 'W' and resid 134 through 135 2037 hydrogen bonds defined for protein. 5655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 554 hydrogen bond angles 0 basepair planarities 113 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 17.74 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7954 1.32 - 1.45: 14189 1.45 - 1.57: 25971 1.57 - 1.69: 570 1.69 - 1.82: 185 Bond restraints: 48869 Sorted by residual: bond pdb=" CA TYR P 788 " pdb=" C TYR P 788 " ideal model delta sigma weight residual 1.524 1.435 0.089 7.00e-03 2.04e+04 1.62e+02 bond pdb=" CA ARG T 223 " pdb=" C ARG T 223 " ideal model delta sigma weight residual 1.524 1.421 0.102 1.26e-02 6.30e+03 6.61e+01 bond pdb=" CA SER P 811 " pdb=" C SER P 811 " ideal model delta sigma weight residual 1.526 1.441 0.085 1.07e-02 8.73e+03 6.31e+01 bond pdb=" CA THR U 65 " pdb=" C THR U 65 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.30e-02 5.92e+03 4.96e+01 bond pdb=" CA ARG N 580 " pdb=" C ARG N 580 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.34e-02 5.57e+03 4.89e+01 ... (remaining 48864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 66549 2.45 - 4.89: 704 4.89 - 7.34: 101 7.34 - 9.79: 31 9.79 - 12.23: 4 Bond angle restraints: 67389 Sorted by residual: angle pdb=" N ALA N 591 " pdb=" CA ALA N 591 " pdb=" C ALA N 591 " ideal model delta sigma weight residual 113.88 101.65 12.23 1.23e+00 6.61e-01 9.89e+01 angle pdb=" N ARG T 223 " pdb=" CA ARG T 223 " pdb=" C ARG T 223 " ideal model delta sigma weight residual 111.14 101.41 9.73 1.08e+00 8.57e-01 8.12e+01 angle pdb=" N GLY M 43 " pdb=" CA GLY M 43 " pdb=" C GLY M 43 " ideal model delta sigma weight residual 110.38 120.14 -9.76 1.28e+00 6.10e-01 5.81e+01 angle pdb=" N THR W 64 " pdb=" CA THR W 64 " pdb=" C THR W 64 " ideal model delta sigma weight residual 113.88 105.38 8.50 1.23e+00 6.61e-01 4.78e+01 angle pdb=" N LEU J 357 " pdb=" CA LEU J 357 " pdb=" C LEU J 357 " ideal model delta sigma weight residual 111.28 104.06 7.22 1.09e+00 8.42e-01 4.39e+01 ... (remaining 67384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 26421 34.34 - 68.69: 2289 68.69 - 103.03: 97 103.03 - 137.37: 1 137.37 - 171.71: 3 Dihedral angle restraints: 28811 sinusoidal: 13766 harmonic: 15045 Sorted by residual: dihedral pdb=" C TYR P 788 " pdb=" N TYR P 788 " pdb=" CA TYR P 788 " pdb=" CB TYR P 788 " ideal model delta harmonic sigma weight residual -122.60 -111.05 -11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C4' DA 4 -20 " pdb=" C3' DA 4 -20 " pdb=" O3' DA 4 -20 " pdb=" P DA 4 -19 " ideal model delta sinusoidal sigma weight residual 220.00 48.29 171.71 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA MET J 438 " pdb=" C MET J 438 " pdb=" N PRO J 439 " pdb=" CA PRO J 439 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 28808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6752 0.069 - 0.139: 646 0.139 - 0.208: 31 0.208 - 0.277: 6 0.277 - 0.347: 1 Chirality restraints: 7436 Sorted by residual: chirality pdb=" CG LEU V 221 " pdb=" CB LEU V 221 " pdb=" CD1 LEU V 221 " pdb=" CD2 LEU V 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA LEU S 114 " pdb=" N LEU S 114 " pdb=" C LEU S 114 " pdb=" CB LEU S 114 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR N 564 " pdb=" N TYR N 564 " pdb=" C TYR N 564 " pdb=" CB TYR N 564 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 7433 not shown) Planarity restraints: 7681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU S 119 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO S 120 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO S 120 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO S 120 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 46 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO Q 47 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO Q 47 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 47 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 362 " 0.070 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO J 363 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO J 363 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO J 363 " 0.057 5.00e-02 4.00e+02 ... (remaining 7678 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 365 2.51 - 3.11: 33791 3.11 - 3.71: 78298 3.71 - 4.30: 108678 4.30 - 4.90: 173769 Nonbonded interactions: 394901 Sorted by model distance: nonbonded pdb=" O3B ATP W 600 " pdb="MG MG W 601 " model vdw 1.917 2.170 nonbonded pdb=" OG1 THR U 64 " pdb="MG MG U 601 " model vdw 1.923 2.170 nonbonded pdb=" O1G ATP V 600 " pdb="MG MG V 601 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR R 64 " pdb="MG MG R 601 " model vdw 1.951 2.170 nonbonded pdb=" OD1 ASP M 104 " pdb="MG MG M 901 " model vdw 1.960 2.170 ... (remaining 394896 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 '2' and (resid -3 through 25 or resid 28 through 29)) selection = (chain '5' and (resid -3 through 25 or resid 28 through 29)) } ncs_group { reference = (chain 'M' and resid 1 through 857) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'S' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'T' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'U' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'V' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) selection = (chain 'W' and (resid 4 through 130 or resid 148 through 214 or resid 225 throug \ h 332 or resid 600 through 601)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'x' selection = chain 'y' } 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: 4.140 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: 0.050 Extract box with map and model: 1.570 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 101.450 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.004 0.102 48869 Z= 0.262 Angle : 0.649 12.235 67389 Z= 0.368 Chirality : 0.042 0.347 7436 Planarity : 0.005 0.133 7681 Dihedral : 21.267 171.714 19103 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.11 % Favored : 95.64 % Rotamer: Outliers : 1.28 % Allowed : 29.92 % Favored : 68.80 % Cbeta Deviations : 0.02 % 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: -0.53 (0.12), residues: 5088 helix: 0.30 (0.10), residues: 2589 sheet: -1.09 (0.22), residues: 538 loop : -0.86 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 284 HIS 0.015 0.001 HIS S 162 PHE 0.029 0.001 PHE W 23 TYR 0.022 0.001 TYR O 742 ARG 0.015 0.000 ARG M 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 882 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 144 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: M 67 TYR cc_start: 0.7341 (m-80) cc_final: 0.6541 (m-80) REVERT: M 143 GLN cc_start: 0.7486 (tp-100) cc_final: 0.7002 (tm-30) REVERT: M 479 TYR cc_start: 0.6710 (t80) cc_final: 0.6498 (t80) REVERT: N 70 GLU cc_start: 0.7208 (tp30) cc_final: 0.6813 (tp30) REVERT: P 786 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: Q 192 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7031 (mm) REVERT: S 124 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5096 (p-80) REVERT: U 41 MET cc_start: 0.6520 (mmt) cc_final: 0.6247 (tmm) REVERT: V 41 MET cc_start: 0.6970 (mmm) cc_final: 0.6629 (mmm) outliers start: 57 outliers final: 29 residues processed: 909 average time/residue: 0.5176 time to fit residues: 751.8626 Evaluate side-chains 905 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 872 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain M residue 388 HIS Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain N residue 165 ASP Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 568 LEU Chi-restraints excluded: chain N residue 573 ILE Chi-restraints excluded: chain N residue 576 LYS Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain P residue 809 HIS Chi-restraints excluded: chain P residue 811 SER Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain S residue 124 HIS Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 224 ARG Chi-restraints excluded: chain U residue 67 ARG Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 220 GLN Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain W residue 213 THR Chi-restraints excluded: chain W residue 215 ARG Chi-restraints excluded: chain W residue 249 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 446 optimal weight: 0.9980 chunk 400 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 414 optimal weight: 0.8980 chunk 160 optimal weight: 0.0870 chunk 252 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 480 optimal weight: 2.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN J 360 ASN J 378 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 840 GLN N 169 ASN N 594 HIS P 741 ASN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 328 GLN ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 ASN ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 254 HIS ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 ASN V 220 GLN V 314 GLN V 338 ASN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 186 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 48869 Z= 0.226 Angle : 0.564 9.093 67389 Z= 0.305 Chirality : 0.041 0.169 7436 Planarity : 0.005 0.123 7681 Dihedral : 20.267 172.280 9058 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 3.32 % Allowed : 26.80 % Favored : 69.88 % 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: -0.26 (0.12), residues: 5088 helix: 0.46 (0.10), residues: 2664 sheet: -1.01 (0.23), residues: 508 loop : -0.67 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 8 HIS 0.007 0.001 HIS S 30 PHE 0.017 0.001 PHE V 230 TYR 0.017 0.001 TYR V 110 ARG 0.008 0.000 ARG N 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 883 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 TRP cc_start: 0.8056 (p90) cc_final: 0.7647 (p90) REVERT: J 417 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: M 67 TYR cc_start: 0.7621 (m-80) cc_final: 0.7213 (m-80) REVERT: M 121 GLU cc_start: 0.7598 (tp30) cc_final: 0.7070 (tp30) REVERT: M 363 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5883 (mtt-85) REVERT: M 683 ASP cc_start: 0.7113 (t0) cc_final: 0.6883 (t70) REVERT: N 70 GLU cc_start: 0.7282 (tp30) cc_final: 0.6688 (tp30) REVERT: N 404 TYR cc_start: 0.7332 (t80) cc_final: 0.7061 (t80) REVERT: N 564 TYR cc_start: 0.7368 (p90) cc_final: 0.7088 (p90) REVERT: N 796 GLU cc_start: 0.7047 (tm-30) cc_final: 0.5659 (tm-30) REVERT: N 800 LYS cc_start: 0.7722 (pttt) cc_final: 0.6651 (pttt) REVERT: O 563 SER cc_start: 0.8901 (p) cc_final: 0.8484 (p) REVERT: P 545 VAL cc_start: 0.7107 (t) cc_final: 0.6733 (m) REVERT: P 779 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6935 (tp-100) REVERT: Q 30 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.6153 (p-80) REVERT: S 119 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7247 (tm-30) REVERT: S 126 PHE cc_start: 0.6664 (t80) cc_final: 0.6131 (t80) REVERT: T 242 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7730 (tm-30) REVERT: U 253 GLN cc_start: 0.7300 (tt0) cc_final: 0.7043 (tt0) REVERT: V 27 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7285 (m) REVERT: V 41 MET cc_start: 0.6973 (mmm) cc_final: 0.6751 (tpp) outliers start: 148 outliers final: 78 residues processed: 976 average time/residue: 0.5097 time to fit residues: 797.4355 Evaluate side-chains 934 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 852 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 285 MET Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain J residue 430 THR Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 363 ARG Chi-restraints excluded: chain M residue 408 LEU Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 568 LEU Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 230 PHE Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 248 LEU Chi-restraints excluded: chain W residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 266 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 399 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 481 optimal weight: 0.9990 chunk 519 optimal weight: 1.9990 chunk 428 optimal weight: 0.4980 chunk 477 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 386 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN N 169 ASN N 594 HIS N 718 GLN P 741 ASN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 314 GLN ** S 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 ASN ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 48869 Z= 0.192 Angle : 0.539 10.471 67389 Z= 0.292 Chirality : 0.040 0.162 7436 Planarity : 0.005 0.111 7681 Dihedral : 20.186 173.064 9005 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.50 % Allowed : 26.87 % Favored : 69.63 % 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: -0.10 (0.12), residues: 5088 helix: 0.63 (0.10), residues: 2675 sheet: -0.92 (0.22), residues: 528 loop : -0.66 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 8 HIS 0.006 0.001 HIS R 266 PHE 0.019 0.001 PHE T 7 TYR 0.017 0.001 TYR O 742 ARG 0.011 0.000 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 874 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 TRP cc_start: 0.8019 (p90) cc_final: 0.7682 (p90) REVERT: J 144 GLN cc_start: 0.6421 (mp10) cc_final: 0.6182 (mp10) REVERT: J 199 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7316 (ttmm) REVERT: J 417 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: M 121 GLU cc_start: 0.7611 (tp30) cc_final: 0.7090 (tp30) REVERT: M 363 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5873 (mtt-85) REVERT: M 479 TYR cc_start: 0.6762 (t80) cc_final: 0.6540 (t80) REVERT: M 569 MET cc_start: 0.8458 (mmm) cc_final: 0.8242 (mmm) REVERT: N 70 GLU cc_start: 0.7265 (tp30) cc_final: 0.6611 (tp30) REVERT: N 122 GLN cc_start: 0.7758 (mt0) cc_final: 0.7354 (mt0) REVERT: N 126 LYS cc_start: 0.8318 (mttp) cc_final: 0.8096 (mmtp) REVERT: N 169 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7808 (t0) REVERT: N 404 TYR cc_start: 0.7428 (t80) cc_final: 0.6933 (t80) REVERT: N 564 TYR cc_start: 0.7417 (p90) cc_final: 0.7141 (p90) REVERT: N 796 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6361 (tp30) REVERT: N 800 LYS cc_start: 0.7744 (pttt) cc_final: 0.6927 (pttt) REVERT: O 563 SER cc_start: 0.8900 (p) cc_final: 0.8467 (p) REVERT: O 612 ARG cc_start: 0.6734 (mmt180) cc_final: 0.6517 (mmt180) REVERT: O 815 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: O 834 GLN cc_start: 0.8252 (tp40) cc_final: 0.7836 (tp-100) REVERT: P 557 LEU cc_start: 0.7785 (tp) cc_final: 0.7450 (tt) REVERT: P 569 MET cc_start: 0.6892 (mmm) cc_final: 0.6684 (mmt) REVERT: P 786 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6318 (pm20) REVERT: Q 30 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6085 (p-80) REVERT: Q 257 LEU cc_start: 0.4288 (OUTLIER) cc_final: 0.3658 (mm) REVERT: S 118 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: S 126 PHE cc_start: 0.6621 (t80) cc_final: 0.6205 (t80) REVERT: T 242 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7651 (tm-30) REVERT: T 320 LYS cc_start: 0.7316 (ttmt) cc_final: 0.6603 (ttmt) REVERT: T 324 GLU cc_start: 0.6877 (mp0) cc_final: 0.6415 (mp0) REVERT: U 253 GLN cc_start: 0.7283 (tt0) cc_final: 0.7035 (tt0) REVERT: U 318 MET cc_start: 0.7744 (mtm) cc_final: 0.7524 (mtm) REVERT: V 27 THR cc_start: 0.7663 (OUTLIER) cc_final: 0.7320 (m) REVERT: W 71 GLU cc_start: 0.5991 (mt-10) cc_final: 0.5777 (mt-10) REVERT: W 72 GLN cc_start: 0.7791 (pp30) cc_final: 0.7591 (pp30) REVERT: W 79 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5197 (mm) outliers start: 156 outliers final: 90 residues processed: 968 average time/residue: 0.5335 time to fit residues: 835.0517 Evaluate side-chains 948 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 848 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 285 MET Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 363 ARG Chi-restraints excluded: chain M residue 486 GLN Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 563 SER Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 230 PHE Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 296 GLU Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 303 LYS Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain V residue 308 ARG Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 248 LEU Chi-restraints excluded: chain W residue 249 LEU Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 475 optimal weight: 0.5980 chunk 361 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 482 optimal weight: 0.9990 chunk 511 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 457 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN J 423 ASN J 425 GLN M 388 HIS N 594 HIS O 782 GLN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 812 ASN ** P 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 242 GLN R 174 GLN S 220 GLN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 ASN ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 48869 Z= 0.263 Angle : 0.568 9.365 67389 Z= 0.306 Chirality : 0.041 0.151 7436 Planarity : 0.005 0.101 7681 Dihedral : 20.270 172.697 9003 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 4.73 % Allowed : 26.13 % Favored : 69.14 % 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: -0.12 (0.12), residues: 5088 helix: 0.61 (0.10), residues: 2676 sheet: -0.89 (0.22), residues: 530 loop : -0.68 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 284 HIS 0.008 0.001 HIS S 162 PHE 0.021 0.002 PHE T 7 TYR 0.031 0.002 TYR M 67 ARG 0.010 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 861 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 120 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6050 (tp) REVERT: J 138 TRP cc_start: 0.8029 (p90) cc_final: 0.7648 (p90) REVERT: J 144 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: J 199 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7379 (ttmm) REVERT: J 290 LYS cc_start: 0.7372 (ptmm) cc_final: 0.6882 (ptmm) REVERT: J 383 ARG cc_start: 0.6284 (ptp-170) cc_final: 0.5991 (ptp-170) REVERT: M 121 GLU cc_start: 0.7617 (tp30) cc_final: 0.7095 (tp30) REVERT: M 569 MET cc_start: 0.8413 (mmm) cc_final: 0.8203 (mmm) REVERT: M 612 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8333 (ptp-170) REVERT: M 804 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6965 (mt) REVERT: N 122 GLN cc_start: 0.7755 (mt0) cc_final: 0.7347 (mt0) REVERT: N 404 TYR cc_start: 0.7528 (t80) cc_final: 0.7004 (t80) REVERT: N 414 LYS cc_start: 0.6930 (mtpt) cc_final: 0.6678 (mtmt) REVERT: N 479 TYR cc_start: 0.8216 (t80) cc_final: 0.7953 (t80) REVERT: N 779 GLN cc_start: 0.7552 (tp40) cc_final: 0.6516 (mt0) REVERT: N 796 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6101 (tp30) REVERT: N 800 LYS cc_start: 0.7799 (pttt) cc_final: 0.6829 (pttt) REVERT: O 563 SER cc_start: 0.8875 (p) cc_final: 0.8465 (p) REVERT: O 815 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6262 (mp10) REVERT: O 834 GLN cc_start: 0.8218 (tp40) cc_final: 0.7795 (tp-100) REVERT: P 557 LEU cc_start: 0.7815 (tp) cc_final: 0.7452 (tt) REVERT: P 565 ARG cc_start: 0.8229 (mpt180) cc_final: 0.8013 (mpt180) REVERT: P 786 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: P 787 TYR cc_start: 0.7282 (m-80) cc_final: 0.6740 (m-80) REVERT: Q 30 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6333 (p-80) REVERT: Q 160 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7925 (mm) REVERT: Q 257 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.3633 (mm) REVERT: S 190 ASP cc_start: 0.7507 (m-30) cc_final: 0.7288 (m-30) REVERT: S 217 LEU cc_start: 0.8174 (mt) cc_final: 0.7874 (mp) REVERT: T 242 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7645 (tm-30) REVERT: T 267 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.7148 (p-90) REVERT: T 324 GLU cc_start: 0.6946 (mp0) cc_final: 0.6460 (mp0) REVERT: U 253 GLN cc_start: 0.7308 (tt0) cc_final: 0.7060 (tt0) REVERT: V 27 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7311 (m) REVERT: W 46 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6778 (pm20) outliers start: 211 outliers final: 133 residues processed: 1003 average time/residue: 0.5040 time to fit residues: 812.4653 Evaluate side-chains 978 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 834 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 285 MET Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 430 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 388 HIS Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 602 LEU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain M residue 804 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 525 VAL Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 568 LEU Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 160 LEU Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 230 PHE Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 174 GLN Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 296 GLU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 142 ASN Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 194 SER Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 248 LEU Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 425 optimal weight: 0.7980 chunk 290 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 436 optimal weight: 0.7980 chunk 353 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 458 optimal weight: 0.3980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS N 637 ASN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 812 ASN ** P 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 GLN R 254 HIS ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 ASN ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 142 ASN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 HIS W 252 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 48869 Z= 0.218 Angle : 0.556 8.261 67389 Z= 0.298 Chirality : 0.040 0.198 7436 Planarity : 0.005 0.094 7681 Dihedral : 20.253 173.669 8998 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 4.03 % Allowed : 27.10 % Favored : 68.87 % 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: -0.05 (0.12), residues: 5088 helix: 0.68 (0.10), residues: 2676 sheet: -0.90 (0.22), residues: 530 loop : -0.66 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 8 HIS 0.009 0.001 HIS M 388 PHE 0.022 0.001 PHE T 7 TYR 0.018 0.001 TYR O 810 ARG 0.011 0.000 ARG S 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 851 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 120 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.6048 (tp) REVERT: J 138 TRP cc_start: 0.7982 (p90) cc_final: 0.7655 (p90) REVERT: J 290 LYS cc_start: 0.7383 (ptmm) cc_final: 0.6876 (ptmm) REVERT: J 383 ARG cc_start: 0.6283 (ptp-170) cc_final: 0.5953 (ptp-170) REVERT: J 417 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: M 32 ARG cc_start: 0.7590 (ptm160) cc_final: 0.7387 (ptm160) REVERT: M 121 GLU cc_start: 0.7636 (tp30) cc_final: 0.7092 (tp30) REVERT: M 411 ARG cc_start: 0.7170 (ptp-110) cc_final: 0.6947 (ptm160) REVERT: M 804 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6957 (mt) REVERT: N 122 GLN cc_start: 0.7633 (mt0) cc_final: 0.7384 (mt0) REVERT: N 404 TYR cc_start: 0.7526 (t80) cc_final: 0.6987 (t80) REVERT: N 414 LYS cc_start: 0.6907 (mtpt) cc_final: 0.6597 (mtpt) REVERT: N 479 TYR cc_start: 0.8241 (t80) cc_final: 0.7898 (t80) REVERT: N 796 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6010 (tp30) REVERT: N 800 LYS cc_start: 0.7802 (pttt) cc_final: 0.6772 (pttt) REVERT: O 563 SER cc_start: 0.8881 (p) cc_final: 0.8473 (p) REVERT: O 700 MET cc_start: 0.5675 (tmm) cc_final: 0.5379 (tmm) REVERT: O 815 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.5998 (mp10) REVERT: O 834 GLN cc_start: 0.8208 (tp40) cc_final: 0.7792 (tp-100) REVERT: P 557 LEU cc_start: 0.7809 (tp) cc_final: 0.7444 (tt) REVERT: P 713 TYR cc_start: 0.7357 (t80) cc_final: 0.7033 (t80) REVERT: P 786 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6396 (pm20) REVERT: Q 30 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6272 (p-80) REVERT: Q 257 LEU cc_start: 0.4046 (OUTLIER) cc_final: 0.3370 (mm) REVERT: S 190 ASP cc_start: 0.7527 (m-30) cc_final: 0.7323 (m-30) REVERT: T 242 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7605 (tm-30) REVERT: T 267 TRP cc_start: 0.7413 (OUTLIER) cc_final: 0.7099 (p-90) REVERT: T 324 GLU cc_start: 0.6922 (mp0) cc_final: 0.6439 (mp0) REVERT: U 228 ILE cc_start: 0.7670 (mm) cc_final: 0.7447 (mm) REVERT: U 253 GLN cc_start: 0.7301 (tt0) cc_final: 0.7056 (tt0) REVERT: U 318 MET cc_start: 0.7729 (mtm) cc_final: 0.7343 (mtm) REVERT: V 27 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7283 (m) REVERT: W 39 ILE cc_start: 0.8178 (tp) cc_final: 0.7972 (mp) REVERT: W 71 GLU cc_start: 0.5792 (mt-10) cc_final: 0.5586 (mt-10) REVERT: W 249 LEU cc_start: 0.7804 (mp) cc_final: 0.7556 (mp) outliers start: 180 outliers final: 133 residues processed: 966 average time/residue: 0.5038 time to fit residues: 787.1705 Evaluate side-chains 980 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 838 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 285 MET Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 251 ILE Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 602 LEU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain M residue 795 SER Chi-restraints excluded: chain M residue 804 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 462 ILE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain P residue 796 GLU Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 230 PHE Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 128 TYR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 184 LYS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 296 GLU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 194 SER Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain V residue 302 LEU Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 172 optimal weight: 0.8980 chunk 460 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 300 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 511 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 236 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN J 29 GLN J 378 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 812 ASN ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 254 HIS ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 142 ASN ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 252 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 48869 Z= 0.191 Angle : 0.545 10.497 67389 Z= 0.293 Chirality : 0.040 0.187 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.224 174.238 8997 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 4.01 % Allowed : 27.05 % Favored : 68.94 % 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: 0.10 (0.12), residues: 5088 helix: 0.79 (0.10), residues: 2665 sheet: -0.91 (0.23), residues: 516 loop : -0.55 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 284 HIS 0.015 0.001 HIS M 388 PHE 0.022 0.001 PHE T 7 TYR 0.023 0.001 TYR W 271 ARG 0.010 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 841 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 THR cc_start: 0.7036 (m) cc_final: 0.6385 (p) REVERT: J 120 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.6001 (tp) REVERT: J 138 TRP cc_start: 0.7970 (p90) cc_final: 0.7615 (p90) REVERT: J 146 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7448 (mmm160) REVERT: J 202 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6705 (mt-10) REVERT: J 283 LEU cc_start: 0.6532 (mm) cc_final: 0.6315 (mm) REVERT: J 290 LYS cc_start: 0.7410 (ptmm) cc_final: 0.6920 (ptmm) REVERT: J 417 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: M 32 ARG cc_start: 0.7626 (ptm160) cc_final: 0.7412 (ptm160) REVERT: M 121 GLU cc_start: 0.7621 (tp30) cc_final: 0.7094 (tp30) REVERT: M 479 TYR cc_start: 0.6796 (t80) cc_final: 0.6537 (t80) REVERT: M 523 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7407 (mp) REVERT: M 804 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6945 (mt) REVERT: N 86 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6269 (tppt) REVERT: N 122 GLN cc_start: 0.7699 (mt0) cc_final: 0.7402 (mt0) REVERT: N 221 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7695 (mmtm) REVERT: N 404 TYR cc_start: 0.7582 (t80) cc_final: 0.7026 (t80) REVERT: N 414 LYS cc_start: 0.6896 (mtpt) cc_final: 0.6582 (mtpt) REVERT: N 479 TYR cc_start: 0.8228 (t80) cc_final: 0.7834 (t80) REVERT: N 796 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6515 (tp30) REVERT: O 563 SER cc_start: 0.8882 (p) cc_final: 0.8471 (p) REVERT: O 700 MET cc_start: 0.5693 (tmm) cc_final: 0.5267 (tmm) REVERT: O 815 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6021 (mp10) REVERT: O 834 GLN cc_start: 0.8186 (tp40) cc_final: 0.7784 (tp-100) REVERT: P 713 TYR cc_start: 0.7379 (t80) cc_final: 0.7093 (t80) REVERT: P 786 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: Q 30 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6092 (p-80) REVERT: Q 257 LEU cc_start: 0.4019 (OUTLIER) cc_final: 0.3377 (mm) REVERT: R 19 ARG cc_start: 0.7151 (mpp80) cc_final: 0.6896 (mpt-90) REVERT: R 24 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5571 (pp20) REVERT: T 242 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7587 (tm-30) REVERT: T 267 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.7112 (p-90) REVERT: T 320 LYS cc_start: 0.7325 (ttmt) cc_final: 0.6622 (ttmt) REVERT: T 324 GLU cc_start: 0.6918 (mp0) cc_final: 0.6409 (mp0) REVERT: T 326 GLU cc_start: 0.7936 (pt0) cc_final: 0.7215 (pt0) REVERT: U 253 GLN cc_start: 0.7281 (tt0) cc_final: 0.7055 (tt0) REVERT: V 19 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7122 (ptp90) REVERT: V 27 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7258 (m) REVERT: W 39 ILE cc_start: 0.8174 (tp) cc_final: 0.7971 (mp) REVERT: W 249 LEU cc_start: 0.7778 (mp) cc_final: 0.7556 (mp) outliers start: 179 outliers final: 128 residues processed: 959 average time/residue: 0.5157 time to fit residues: 800.3659 Evaluate side-chains 958 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 817 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 523 LEU Chi-restraints excluded: chain M residue 532 THR Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 602 LEU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain M residue 795 SER Chi-restraints excluded: chain M residue 804 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 462 ILE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 179 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 206 LEU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 296 GLU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 183 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain V residue 302 LEU Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 493 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 291 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 430 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 509 optimal weight: 0.6980 chunk 319 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN J 378 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 388 HIS ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN N 155 GLN N 594 HIS ** O 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 254 HIS S 220 GLN ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 48869 Z= 0.262 Angle : 0.577 9.980 67389 Z= 0.309 Chirality : 0.041 0.216 7436 Planarity : 0.005 0.094 7681 Dihedral : 20.281 173.925 8997 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 4.46 % Allowed : 26.87 % Favored : 68.67 % 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: -0.00 (0.12), residues: 5088 helix: 0.72 (0.10), residues: 2668 sheet: -1.00 (0.23), residues: 522 loop : -0.60 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 284 HIS 0.008 0.001 HIS S 162 PHE 0.022 0.002 PHE T 7 TYR 0.022 0.001 TYR N 159 ARG 0.010 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 850 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 TRP cc_start: 0.7980 (p90) cc_final: 0.7602 (p90) REVERT: J 144 GLN cc_start: 0.6702 (mp10) cc_final: 0.6483 (mp10) REVERT: J 268 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.4983 (t0) REVERT: J 290 LYS cc_start: 0.7425 (ptmm) cc_final: 0.6933 (ptmm) REVERT: J 383 ARG cc_start: 0.6338 (ptp-110) cc_final: 0.5951 (ptp-170) REVERT: J 411 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7101 (tp) REVERT: J 417 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7413 (pm20) REVERT: M 121 GLU cc_start: 0.7671 (tp30) cc_final: 0.7146 (tp30) REVERT: M 150 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7106 (tp30) REVERT: M 479 TYR cc_start: 0.6767 (t80) cc_final: 0.6543 (t80) REVERT: M 523 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7390 (mp) REVERT: M 804 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6971 (mt) REVERT: N 86 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6299 (tppt) REVERT: N 122 GLN cc_start: 0.7824 (mt0) cc_final: 0.7527 (mt0) REVERT: N 126 LYS cc_start: 0.8387 (mmtp) cc_final: 0.8138 (mmtp) REVERT: N 221 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7681 (mmtm) REVERT: N 404 TYR cc_start: 0.7628 (t80) cc_final: 0.7015 (t80) REVERT: N 414 LYS cc_start: 0.6900 (mtpt) cc_final: 0.6661 (mtpt) REVERT: N 756 GLU cc_start: 0.7211 (tt0) cc_final: 0.6937 (tt0) REVERT: N 796 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6491 (tp30) REVERT: O 563 SER cc_start: 0.8844 (p) cc_final: 0.8455 (p) REVERT: O 690 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.6128 (pm20) REVERT: O 700 MET cc_start: 0.5716 (tmm) cc_final: 0.5233 (tmm) REVERT: O 815 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.6054 (mp10) REVERT: O 834 GLN cc_start: 0.8180 (tp40) cc_final: 0.7766 (tp-100) REVERT: P 713 TYR cc_start: 0.7402 (t80) cc_final: 0.7136 (t80) REVERT: P 786 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: Q 11 LEU cc_start: 0.7333 (mt) cc_final: 0.6855 (tt) REVERT: Q 30 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.6111 (p-80) REVERT: Q 257 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3195 (mm) REVERT: R 24 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5619 (pp20) REVERT: T 242 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7614 (tm-30) REVERT: T 267 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.7078 (p-90) REVERT: T 324 GLU cc_start: 0.6974 (mp0) cc_final: 0.6449 (mp0) REVERT: T 326 GLU cc_start: 0.7970 (pt0) cc_final: 0.7303 (pt0) REVERT: U 38 GLU cc_start: 0.7071 (tp30) cc_final: 0.6473 (tp30) REVERT: U 253 GLN cc_start: 0.7287 (tt0) cc_final: 0.7031 (tt0) REVERT: U 286 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7470 (mttm) REVERT: V 19 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7060 (ptp90) REVERT: V 27 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7278 (m) REVERT: V 46 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: W 39 ILE cc_start: 0.8169 (tp) cc_final: 0.7926 (mp) REVERT: W 46 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: W 249 LEU cc_start: 0.7778 (mp) cc_final: 0.7539 (mp) outliers start: 199 outliers final: 146 residues processed: 981 average time/residue: 0.5028 time to fit residues: 796.0288 Evaluate side-chains 997 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 834 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 285 MET Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain J residue 430 THR Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 388 HIS Chi-restraints excluded: chain M residue 523 LEU Chi-restraints excluded: chain M residue 532 THR Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 602 LEU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 722 LEU Chi-restraints excluded: chain M residue 734 VAL Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain M residue 795 SER Chi-restraints excluded: chain M residue 804 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 445 MET Chi-restraints excluded: chain N residue 462 ILE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 650 GLN Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 690 GLN Chi-restraints excluded: chain O residue 752 ASP Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 600 THR Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 749 SER Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain P residue 796 GLU Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 190 ASP Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 179 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 206 LEU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 296 GLU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 128 TYR Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 147 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 56 TYR Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 264 VAL Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 315 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 304 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 324 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 252 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 400 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** J 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 388 HIS N 155 GLN N 594 HIS ** O 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 48869 Z= 0.194 Angle : 0.558 9.919 67389 Z= 0.299 Chirality : 0.040 0.221 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.238 174.891 8997 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 3.94 % Allowed : 27.61 % Favored : 68.44 % 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: 0.08 (0.12), residues: 5088 helix: 0.80 (0.10), residues: 2671 sheet: -1.03 (0.23), residues: 482 loop : -0.58 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 284 HIS 0.033 0.001 HIS M 388 PHE 0.021 0.001 PHE T 7 TYR 0.027 0.001 TYR N 479 ARG 0.012 0.000 ARG N 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 826 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 THR cc_start: 0.7050 (m) cc_final: 0.6302 (p) REVERT: J 138 TRP cc_start: 0.7963 (p90) cc_final: 0.7610 (p90) REVERT: J 202 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6675 (mt-10) REVERT: J 268 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.5000 (t0) REVERT: J 290 LYS cc_start: 0.7429 (ptmm) cc_final: 0.6924 (ptmm) REVERT: J 383 ARG cc_start: 0.6321 (ptp-170) cc_final: 0.5919 (ptp-170) REVERT: J 411 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7087 (tp) REVERT: M 121 GLU cc_start: 0.7673 (tp30) cc_final: 0.7135 (tp30) REVERT: M 150 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7095 (tp30) REVERT: M 479 TYR cc_start: 0.6764 (t80) cc_final: 0.6523 (t80) REVERT: M 523 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7408 (mp) REVERT: M 700 MET cc_start: 0.6629 (mmt) cc_final: 0.6427 (mmt) REVERT: M 727 GLU cc_start: 0.6676 (mp0) cc_final: 0.6399 (mp0) REVERT: M 804 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6978 (mt) REVERT: N 86 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6030 (tppt) REVERT: N 122 GLN cc_start: 0.7681 (mt0) cc_final: 0.7254 (mt0) REVERT: N 126 LYS cc_start: 0.8303 (mmtp) cc_final: 0.7992 (mmtp) REVERT: N 152 TYR cc_start: 0.6368 (m-10) cc_final: 0.6159 (m-10) REVERT: N 221 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7659 (mmtm) REVERT: N 404 TYR cc_start: 0.7627 (t80) cc_final: 0.7127 (t80) REVERT: N 414 LYS cc_start: 0.6882 (mtpt) cc_final: 0.6655 (mtpt) REVERT: N 472 GLU cc_start: 0.6069 (tt0) cc_final: 0.5694 (tp30) REVERT: N 756 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6874 (tt0) REVERT: N 796 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6588 (tp30) REVERT: O 690 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5965 (pm20) REVERT: O 700 MET cc_start: 0.5712 (tmm) cc_final: 0.5190 (tmm) REVERT: O 752 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5971 (t70) REVERT: O 815 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: O 834 GLN cc_start: 0.8161 (tp40) cc_final: 0.7751 (tp-100) REVERT: P 713 TYR cc_start: 0.7368 (t80) cc_final: 0.7144 (t80) REVERT: P 786 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6381 (pm20) REVERT: Q 11 LEU cc_start: 0.7327 (mt) cc_final: 0.6844 (tt) REVERT: Q 30 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.5986 (p-80) REVERT: Q 257 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.3202 (mm) REVERT: Q 272 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: R 19 ARG cc_start: 0.7124 (mpp80) cc_final: 0.6859 (mpt-90) REVERT: R 24 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5565 (pp20) REVERT: S 42 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7562 (mmm160) REVERT: S 118 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: S 270 PHE cc_start: 0.7934 (m-80) cc_final: 0.7566 (m-80) REVERT: T 242 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7596 (tm-30) REVERT: T 267 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.7071 (p-90) REVERT: T 324 GLU cc_start: 0.6941 (mp0) cc_final: 0.6441 (mp0) REVERT: T 326 GLU cc_start: 0.7933 (pt0) cc_final: 0.6990 (pt0) REVERT: U 38 GLU cc_start: 0.7011 (tp30) cc_final: 0.6497 (tp30) REVERT: U 253 GLN cc_start: 0.7270 (tt0) cc_final: 0.7040 (tt0) REVERT: V 19 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7083 (ptp90) REVERT: V 27 THR cc_start: 0.7610 (OUTLIER) cc_final: 0.7247 (m) REVERT: W 39 ILE cc_start: 0.8172 (tp) cc_final: 0.7940 (mp) REVERT: W 249 LEU cc_start: 0.7752 (mp) cc_final: 0.7525 (mp) outliers start: 176 outliers final: 133 residues processed: 944 average time/residue: 0.5402 time to fit residues: 828.9252 Evaluate side-chains 964 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 814 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 233 VAL Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 388 HIS Chi-restraints excluded: chain M residue 523 LEU Chi-restraints excluded: chain M residue 532 THR Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 602 LEU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 722 LEU Chi-restraints excluded: chain M residue 734 VAL Chi-restraints excluded: chain M residue 738 ILE Chi-restraints excluded: chain M residue 804 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 462 ILE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 650 GLN Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 738 ILE Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 574 CYS Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 690 GLN Chi-restraints excluded: chain O residue 752 ASP Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain S residue 311 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 206 LEU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 296 GLU Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 183 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 280 THR Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 264 VAL Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 463 optimal weight: 0.9990 chunk 488 optimal weight: 0.5980 chunk 445 optimal weight: 0.0000 chunk 475 optimal weight: 0.0010 chunk 285 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 373 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 429 optimal weight: 0.6980 chunk 449 optimal weight: 0.7980 chunk 473 optimal weight: 0.0970 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN J 378 ASN M 388 HIS N 155 GLN N 594 HIS ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 48869 Z= 0.165 Angle : 0.553 9.743 67389 Z= 0.296 Chirality : 0.039 0.224 7436 Planarity : 0.004 0.093 7681 Dihedral : 20.177 174.996 8997 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 3.09 % Allowed : 28.73 % Favored : 68.18 % 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: 0.19 (0.12), residues: 5088 helix: 0.89 (0.10), residues: 2676 sheet: -0.93 (0.23), residues: 496 loop : -0.54 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 389 HIS 0.032 0.001 HIS M 388 PHE 0.019 0.001 PHE M 851 TYR 0.039 0.001 TYR M 67 ARG 0.012 0.000 ARG N 384 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 828 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 THR cc_start: 0.6993 (m) cc_final: 0.6268 (p) REVERT: J 138 TRP cc_start: 0.7938 (p90) cc_final: 0.7707 (p90) REVERT: J 202 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6683 (mt-10) REVERT: J 268 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.4902 (t0) REVERT: J 290 LYS cc_start: 0.7425 (ptmm) cc_final: 0.6930 (ptmm) REVERT: J 383 ARG cc_start: 0.6326 (ptp-170) cc_final: 0.5919 (ptp-170) REVERT: J 411 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6995 (tp) REVERT: J 417 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: M 11 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7152 (ttp80) REVERT: M 121 GLU cc_start: 0.7637 (tp30) cc_final: 0.7103 (tp30) REVERT: M 150 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7071 (tp30) REVERT: M 235 TYR cc_start: 0.7150 (t80) cc_final: 0.6780 (t80) REVERT: M 479 TYR cc_start: 0.6795 (t80) cc_final: 0.6530 (t80) REVERT: M 727 GLU cc_start: 0.6663 (mp0) cc_final: 0.6375 (mp0) REVERT: N 86 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6257 (tppt) REVERT: N 122 GLN cc_start: 0.7660 (mt0) cc_final: 0.7253 (mt0) REVERT: N 126 LYS cc_start: 0.8360 (mmtp) cc_final: 0.8068 (mmtp) REVERT: N 221 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7648 (mmtm) REVERT: N 404 TYR cc_start: 0.7632 (t80) cc_final: 0.7191 (t80) REVERT: N 414 LYS cc_start: 0.6841 (mtpt) cc_final: 0.6524 (mtpt) REVERT: N 649 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6934 (mtp85) REVERT: N 756 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6788 (tt0) REVERT: N 796 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6576 (tp30) REVERT: O 563 SER cc_start: 0.8865 (p) cc_final: 0.8464 (p) REVERT: O 690 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.5946 (pm20) REVERT: O 700 MET cc_start: 0.5709 (tmm) cc_final: 0.5174 (tmm) REVERT: O 752 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5962 (t70) REVERT: O 815 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5983 (mp10) REVERT: O 834 GLN cc_start: 0.8120 (tp40) cc_final: 0.7755 (tp-100) REVERT: P 618 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4498 (mtt180) REVERT: P 713 TYR cc_start: 0.7345 (t80) cc_final: 0.7133 (t80) REVERT: P 786 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: P 805 GLU cc_start: 0.8238 (tp30) cc_final: 0.7981 (tp30) REVERT: Q 11 LEU cc_start: 0.7337 (mt) cc_final: 0.6827 (tt) REVERT: Q 30 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.5871 (p-80) REVERT: Q 69 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.6824 (tpt-90) REVERT: Q 257 LEU cc_start: 0.4141 (OUTLIER) cc_final: 0.3464 (mm) REVERT: R 19 ARG cc_start: 0.7101 (mpp80) cc_final: 0.6843 (mpt-90) REVERT: R 24 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5493 (pp20) REVERT: S 270 PHE cc_start: 0.7932 (m-80) cc_final: 0.7576 (m-80) REVERT: T 242 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7526 (tm-30) REVERT: T 267 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.7053 (p-90) REVERT: T 320 LYS cc_start: 0.7347 (ttmt) cc_final: 0.6640 (ttmt) REVERT: T 324 GLU cc_start: 0.6901 (mp0) cc_final: 0.6419 (mp0) REVERT: T 326 GLU cc_start: 0.7903 (pt0) cc_final: 0.6965 (pt0) REVERT: U 38 GLU cc_start: 0.6947 (tp30) cc_final: 0.6419 (tp30) REVERT: U 228 ILE cc_start: 0.7620 (mm) cc_final: 0.7395 (mm) REVERT: V 19 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7022 (ptp90) REVERT: V 27 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7277 (m) REVERT: W 245 LYS cc_start: 0.7732 (ptmt) cc_final: 0.7425 (ptmt) REVERT: W 249 LEU cc_start: 0.7716 (mp) cc_final: 0.7487 (mp) outliers start: 138 outliers final: 104 residues processed: 919 average time/residue: 0.5223 time to fit residues: 769.2829 Evaluate side-chains 936 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 816 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 532 THR Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 705 SER Chi-restraints excluded: chain M residue 722 LEU Chi-restraints excluded: chain M residue 734 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 552 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 690 GLN Chi-restraints excluded: chain O residue 752 ASP Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 618 ARG Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET Chi-restraints excluded: chain P residue 749 SER Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 143 VAL Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 264 VAL Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 312 optimal weight: 3.9990 chunk 502 optimal weight: 0.9980 chunk 306 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 527 optimal weight: 3.9990 chunk 485 optimal weight: 0.0980 chunk 419 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 324 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** J 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS ** O 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 GLN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 48869 Z= 0.204 Angle : 0.567 13.361 67389 Z= 0.304 Chirality : 0.040 0.229 7436 Planarity : 0.004 0.093 7681 Dihedral : 20.191 174.352 8994 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.32 % Allowed : 28.48 % Favored : 68.20 % 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: 0.17 (0.12), residues: 5088 helix: 0.86 (0.10), residues: 2673 sheet: -0.99 (0.23), residues: 502 loop : -0.51 (0.15), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 284 HIS 0.007 0.001 HIS V 30 PHE 0.019 0.001 PHE T 7 TYR 0.022 0.001 TYR N 479 ARG 0.012 0.000 ARG M 572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 820 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 THR cc_start: 0.7065 (m) cc_final: 0.6377 (p) REVERT: J 138 TRP cc_start: 0.7962 (p90) cc_final: 0.7648 (p90) REVERT: J 202 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6649 (mt-10) REVERT: J 268 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.4897 (t0) REVERT: J 290 LYS cc_start: 0.7422 (ptmm) cc_final: 0.6921 (ptmm) REVERT: J 383 ARG cc_start: 0.6316 (ptp-170) cc_final: 0.5971 (ptp-170) REVERT: J 411 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7010 (tp) REVERT: J 417 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: M 11 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7152 (ttp80) REVERT: M 121 GLU cc_start: 0.7611 (tp30) cc_final: 0.7079 (tp30) REVERT: M 150 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7081 (tp30) REVERT: M 235 TYR cc_start: 0.7158 (t80) cc_final: 0.6806 (t80) REVERT: M 479 TYR cc_start: 0.6779 (t80) cc_final: 0.6505 (t80) REVERT: M 597 TYR cc_start: 0.8097 (t80) cc_final: 0.7689 (t80) REVERT: M 727 GLU cc_start: 0.6665 (mp0) cc_final: 0.6379 (mp0) REVERT: N 86 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6266 (tppt) REVERT: N 122 GLN cc_start: 0.7719 (mt0) cc_final: 0.7337 (mt0) REVERT: N 126 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8113 (mmtp) REVERT: N 404 TYR cc_start: 0.7670 (t80) cc_final: 0.7155 (t80) REVERT: N 414 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6636 (mtpt) REVERT: N 756 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6806 (tt0) REVERT: N 796 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6542 (tp30) REVERT: O 563 SER cc_start: 0.8835 (p) cc_final: 0.8441 (p) REVERT: O 700 MET cc_start: 0.5704 (tmm) cc_final: 0.5161 (tmm) REVERT: O 752 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5995 (t70) REVERT: O 815 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.6010 (mp10) REVERT: P 618 ARG cc_start: 0.4804 (OUTLIER) cc_final: 0.4492 (mtt180) REVERT: P 713 TYR cc_start: 0.7348 (t80) cc_final: 0.7127 (t80) REVERT: P 786 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: Q 11 LEU cc_start: 0.7349 (mt) cc_final: 0.6867 (tt) REVERT: Q 30 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.5946 (p-80) REVERT: Q 69 ARG cc_start: 0.7365 (tpt-90) cc_final: 0.6838 (tpt-90) REVERT: Q 257 LEU cc_start: 0.3864 (OUTLIER) cc_final: 0.3171 (mm) REVERT: Q 272 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5923 (tm-30) REVERT: R 19 ARG cc_start: 0.7127 (mpp80) cc_final: 0.6875 (mpt-90) REVERT: R 24 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5506 (pp20) REVERT: S 270 PHE cc_start: 0.7917 (m-80) cc_final: 0.7547 (m-80) REVERT: T 242 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7523 (tm-30) REVERT: T 267 TRP cc_start: 0.7447 (OUTLIER) cc_final: 0.7069 (p-90) REVERT: T 324 GLU cc_start: 0.6943 (mp0) cc_final: 0.6448 (mp0) REVERT: T 326 GLU cc_start: 0.7926 (pt0) cc_final: 0.7040 (pt0) REVERT: U 38 GLU cc_start: 0.6949 (tp30) cc_final: 0.6389 (tp30) REVERT: U 108 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7118 (mt-10) REVERT: U 228 ILE cc_start: 0.7662 (mm) cc_final: 0.7428 (mm) REVERT: V 19 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7104 (ptp90) REVERT: V 27 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7236 (m) REVERT: W 245 LYS cc_start: 0.7742 (ptmt) cc_final: 0.7434 (ptmt) REVERT: W 249 LEU cc_start: 0.7725 (mp) cc_final: 0.7490 (mp) outliers start: 148 outliers final: 113 residues processed: 922 average time/residue: 0.5121 time to fit residues: 758.7568 Evaluate side-chains 946 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 817 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 264 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 417 GLU Chi-restraints excluded: chain J residue 431 GLU Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 532 THR Chi-restraints excluded: chain M residue 592 GLU Chi-restraints excluded: chain M residue 624 GLU Chi-restraints excluded: chain M residue 641 ASN Chi-restraints excluded: chain M residue 648 VAL Chi-restraints excluded: chain M residue 652 THR Chi-restraints excluded: chain M residue 656 ASN Chi-restraints excluded: chain M residue 670 GLU Chi-restraints excluded: chain M residue 722 LEU Chi-restraints excluded: chain M residue 734 VAL Chi-restraints excluded: chain M residue 795 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 349 PHE Chi-restraints excluded: chain N residue 534 ARG Chi-restraints excluded: chain N residue 552 LEU Chi-restraints excluded: chain N residue 581 LEU Chi-restraints excluded: chain N residue 650 GLN Chi-restraints excluded: chain N residue 710 MET Chi-restraints excluded: chain N residue 823 ASN Chi-restraints excluded: chain N residue 837 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 587 VAL Chi-restraints excluded: chain O residue 752 ASP Chi-restraints excluded: chain O residue 815 GLN Chi-restraints excluded: chain O residue 831 VAL Chi-restraints excluded: chain O residue 839 GLU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 618 ARG Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 749 SER Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain P residue 786 GLN Chi-restraints excluded: chain Q residue 30 HIS Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 205 LEU Chi-restraints excluded: chain Q residue 212 LEU Chi-restraints excluded: chain Q residue 246 SER Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 257 LEU Chi-restraints excluded: chain Q residue 266 HIS Chi-restraints excluded: chain Q residue 272 GLU Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 300 ILE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 130 VAL Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 239 GLU Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain R residue 295 ARG Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 179 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 251 PHE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 237 SER Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 185 LEU Chi-restraints excluded: chain U residue 230 PHE Chi-restraints excluded: chain U residue 311 SER Chi-restraints excluded: chain U residue 327 ARG Chi-restraints excluded: chain V residue 19 ARG Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 337 GLN Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 143 VAL Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 194 SER Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 218 SER Chi-restraints excluded: chain W residue 231 ARG Chi-restraints excluded: chain W residue 264 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain d residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 333 optimal weight: 0.9990 chunk 447 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 386 optimal weight: 2.9990 chunk 61 optimal weight: 0.0370 chunk 116 optimal weight: 0.4980 chunk 420 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 431 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN ** J 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** M 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN ** U 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 GLN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137236 restraints weight = 80233.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140554 restraints weight = 43792.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142750 restraints weight = 29115.643| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 48869 Z= 0.198 Angle : 0.573 13.555 67389 Z= 0.305 Chirality : 0.040 0.218 7436 Planarity : 0.005 0.093 7681 Dihedral : 20.191 174.563 8994 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 3.25 % Allowed : 28.64 % Favored : 68.11 % 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: 0.17 (0.12), residues: 5088 helix: 0.88 (0.10), residues: 2660 sheet: -0.99 (0.23), residues: 502 loop : -0.53 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 284 HIS 0.007 0.001 HIS V 30 PHE 0.025 0.001 PHE M 851 TYR 0.024 0.001 TYR Q 209 ARG 0.012 0.000 ARG M 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12211.53 seconds wall clock time: 213 minutes 22.78 seconds (12802.78 seconds total)