Starting phenix.real_space_refine on Mon Jan 13 13:07:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bw1_44944/01_2025/9bw1_44944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bw1_44944/01_2025/9bw1_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_44944/01_2025/9bw1_44944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bw1_44944/01_2025/9bw1_44944.map" model { file = "/net/cci-nas-00/data/ceres_data/9bw1_44944/01_2025/9bw1_44944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bw1_44944/01_2025/9bw1_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 19.33, per 1000 atoms: 0.41 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: 8.50 Conformation dependent library (CDL) restraints added in 3.9 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: 13.30 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: 19.51 Time building geometry restraints manager: 10.07 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 94.940 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.740 ------------------------------------------------------------------------------- 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 : 3.497 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: 0.5177 time to fit residues: 747.8286 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 : 3.459 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137123 restraints weight = 80158.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140460 restraints weight = 43900.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142641 restraints weight = 29201.170| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 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 : 3.629 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: 0.7868 (p90) cc_final: 0.7569 (p90) REVERT: M 67 TYR cc_start: 0.7426 (m-80) cc_final: 0.7009 (m-80) REVERT: M 121 GLU cc_start: 0.7295 (tp30) cc_final: 0.6839 (tp30) REVERT: M 363 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5755 (mtt-85) REVERT: M 683 ASP cc_start: 0.6636 (t0) cc_final: 0.6416 (t70) REVERT: N 70 GLU cc_start: 0.7020 (tp30) cc_final: 0.6390 (tp30) REVERT: N 404 TYR cc_start: 0.7105 (t80) cc_final: 0.6773 (t80) REVERT: N 553 LEU cc_start: 0.7311 (mt) cc_final: 0.7096 (mt) REVERT: N 564 TYR cc_start: 0.7126 (p90) cc_final: 0.6855 (p90) REVERT: N 796 GLU cc_start: 0.6939 (tm-30) cc_final: 0.5581 (tm-30) REVERT: N 800 LYS cc_start: 0.7723 (pttt) cc_final: 0.6565 (pttt) REVERT: O 563 SER cc_start: 0.8812 (p) cc_final: 0.8338 (p) REVERT: P 545 VAL cc_start: 0.7029 (t) cc_final: 0.6685 (m) REVERT: P 779 GLN cc_start: 0.6664 (tp-100) cc_final: 0.6448 (tp-100) REVERT: Q 30 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.6074 (p-80) REVERT: S 119 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7183 (tm-30) REVERT: S 126 PHE cc_start: 0.6464 (t80) cc_final: 0.5948 (t80) REVERT: T 242 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7725 (tm-30) REVERT: U 253 GLN cc_start: 0.7375 (tt0) cc_final: 0.7123 (tt0) REVERT: V 27 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7274 (m) outliers start: 148 outliers final: 78 residues processed: 976 average time/residue: 0.5138 time to fit residues: 799.4837 Evaluate side-chains 933 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 852 time to evaluate : 3.420 ------------------------------------------------------------------------------- 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 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 172 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 321 optimal weight: 3.9990 chunk 438 optimal weight: 0.4980 chunk 421 optimal weight: 4.9990 chunk 507 optimal weight: 0.5980 chunk 374 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 494 optimal weight: 9.9990 chunk 273 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 378 ASN ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 169 ASN N 594 HIS N 718 GLN O 782 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** Q 242 GLN R 174 GLN R 314 GLN S 220 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.160735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135010 restraints weight = 80714.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138729 restraints weight = 48049.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139875 restraints weight = 30085.618| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 48869 Z= 0.326 Angle : 0.602 11.212 67389 Z= 0.325 Chirality : 0.043 0.165 7436 Planarity : 0.005 0.113 7681 Dihedral : 20.344 172.834 9005 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 4.33 % Allowed : 26.36 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.12), residues: 5088 helix: 0.38 (0.10), residues: 2691 sheet: -1.01 (0.23), residues: 510 loop : -0.77 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 540 HIS 0.009 0.001 HIS T 30 PHE 0.018 0.002 PHE T 7 TYR 0.027 0.002 TYR O 742 ARG 0.010 0.001 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 1058 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 865 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 TRP cc_start: 0.7867 (p90) cc_final: 0.7632 (p90) REVERT: J 199 LYS cc_start: 0.7565 (ttmm) cc_final: 0.7273 (ttmm) REVERT: J 383 ARG cc_start: 0.6378 (ptp-170) cc_final: 0.6119 (ptp-170) REVERT: J 417 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: M 121 GLU cc_start: 0.7414 (tp30) cc_final: 0.6959 (tp30) REVERT: N 122 GLN cc_start: 0.7627 (mt0) cc_final: 0.7257 (mt0) REVERT: N 169 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7372 (t0) REVERT: N 404 TYR cc_start: 0.7268 (t80) cc_final: 0.6788 (t80) REVERT: N 796 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6193 (tp30) REVERT: N 800 LYS cc_start: 0.7683 (pttt) cc_final: 0.6775 (pttt) REVERT: O 563 SER cc_start: 0.8795 (p) cc_final: 0.8348 (p) REVERT: P 557 LEU cc_start: 0.7699 (tp) cc_final: 0.7355 (tt) REVERT: P 786 GLN cc_start: 0.6041 (OUTLIER) cc_final: 0.5811 (pm20) REVERT: Q 30 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6378 (p-80) REVERT: Q 257 LEU cc_start: 0.4265 (OUTLIER) cc_final: 0.3594 (mm) REVERT: S 126 PHE cc_start: 0.6553 (t80) cc_final: 0.6180 (t80) REVERT: S 190 ASP cc_start: 0.7022 (m-30) cc_final: 0.6797 (m-30) REVERT: S 217 LEU cc_start: 0.8099 (mt) cc_final: 0.7803 (mp) REVERT: S 270 PHE cc_start: 0.7785 (m-80) cc_final: 0.7455 (m-80) REVERT: T 242 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7668 (tm-30) REVERT: T 324 GLU cc_start: 0.6744 (mp0) cc_final: 0.6273 (mp0) REVERT: U 253 GLN cc_start: 0.7387 (tt0) cc_final: 0.7134 (tt0) REVERT: V 46 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.5712 (tm-30) outliers start: 193 outliers final: 120 residues processed: 991 average time/residue: 0.5211 time to fit residues: 822.6686 Evaluate side-chains 957 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 831 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 253 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 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 107 VAL 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 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 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 525 VAL Chi-restraints excluded: chain O residue 560 ASP Chi-restraints excluded: chain O residue 566 SER 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 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 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 123 ASP Chi-restraints excluded: chain Q residue 167 VAL 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 174 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 66 LEU 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 164 HIS Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 336 VAL 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 296 GLU Chi-restraints excluded: chain T residue 301 THR Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain U residue 20 LEU 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 V residue 20 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 170 VAL Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 225 SER 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 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 W residue 263 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 95 optimal weight: 0.0270 chunk 312 optimal weight: 0.0970 chunk 438 optimal weight: 0.0050 chunk 200 optimal weight: 0.9990 chunk 510 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 468 optimal weight: 0.6980 chunk 492 optimal weight: 1.9990 chunk 488 optimal weight: 0.0670 overall best weight: 0.1588 ------------------------------------------------------------------------------- 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 ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 594 HIS ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** 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** 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** W 72 GLN W 124 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138484 restraints weight = 80390.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141558 restraints weight = 47054.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142707 restraints weight = 30204.931| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 48869 Z= 0.154 Angle : 0.536 10.891 67389 Z= 0.289 Chirality : 0.039 0.158 7436 Planarity : 0.005 0.100 7681 Dihedral : 20.206 174.857 9003 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 3.74 % Allowed : 27.10 % Favored : 69.16 % 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: 0.71 (0.10), residues: 2680 sheet: -0.87 (0.23), residues: 512 loop : -0.62 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 8 HIS 0.007 0.001 HIS S 162 PHE 0.021 0.001 PHE T 7 TYR 0.019 0.001 TYR Q 269 ARG 0.010 0.000 ARG S 19 *********************** 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 1017 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 850 time to evaluate : 3.481 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 120 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5955 (tp) REVERT: J 199 LYS cc_start: 0.7585 (ttmm) cc_final: 0.7278 (ttmm) REVERT: J 383 ARG cc_start: 0.6384 (ptp-170) cc_final: 0.6034 (ptp-170) REVERT: M 67 TYR cc_start: 0.7338 (m-80) cc_final: 0.6847 (m-80) REVERT: M 121 GLU cc_start: 0.7369 (tp30) cc_final: 0.6903 (tp30) REVERT: M 388 HIS cc_start: 0.8220 (t70) cc_final: 0.8015 (t-170) REVERT: M 588 ASP cc_start: 0.7406 (t0) cc_final: 0.7203 (t0) REVERT: M 612 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.8125 (mtm110) REVERT: N 119 LYS cc_start: 0.6968 (mtpp) cc_final: 0.6735 (mtmm) REVERT: N 122 GLN cc_start: 0.7481 (mt0) cc_final: 0.7230 (mt0) REVERT: N 126 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7871 (mmtp) REVERT: N 404 TYR cc_start: 0.7291 (t80) cc_final: 0.6784 (t80) REVERT: N 744 TYR cc_start: 0.7125 (m-80) cc_final: 0.6896 (m-80) REVERT: N 796 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6037 (tp30) REVERT: N 800 LYS cc_start: 0.7685 (pttt) cc_final: 0.6683 (pttt) REVERT: O 563 SER cc_start: 0.8823 (p) cc_final: 0.8332 (p) REVERT: O 583 GLN cc_start: 0.7563 (pm20) cc_final: 0.7323 (mp10) REVERT: O 754 GLN cc_start: 0.6498 (pm20) cc_final: 0.6239 (pm20) REVERT: O 815 GLN cc_start: 0.5859 (OUTLIER) cc_final: 0.5405 (mp10) REVERT: O 834 GLN cc_start: 0.7978 (tp40) cc_final: 0.7538 (tp-100) REVERT: P 713 TYR cc_start: 0.6988 (t80) cc_final: 0.6673 (t80) REVERT: Q 30 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6037 (p-80) REVERT: Q 257 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3645 (mm) REVERT: T 242 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7559 (tm-30) REVERT: T 267 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6612 (p-90) REVERT: T 319 PHE cc_start: 0.7766 (t80) cc_final: 0.7496 (t80) REVERT: T 320 LYS cc_start: 0.6891 (ttmt) cc_final: 0.6182 (ttmt) REVERT: T 324 GLU cc_start: 0.6648 (mp0) cc_final: 0.6203 (mp0) REVERT: U 253 GLN cc_start: 0.7308 (tt0) cc_final: 0.7094 (tt0) REVERT: U 318 MET cc_start: 0.6860 (mtm) cc_final: 0.6646 (mpp) REVERT: V 27 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7280 (m) REVERT: W 71 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5379 (mt-10) outliers start: 167 outliers final: 98 residues processed: 956 average time/residue: 0.5195 time to fit residues: 792.3338 Evaluate side-chains 930 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 826 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 141 ILE 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 307 ILE Chi-restraints excluded: chain J residue 405 LEU 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 225 ILE 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 N residue 1 MET Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 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 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 581 LEU 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 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 601 LEU Chi-restraints excluded: chain P residue 608 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 710 MET 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 147 VAL Chi-restraints excluded: chain Q residue 160 LEU 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 266 HIS Chi-restraints excluded: chain Q residue 275 LEU Chi-restraints excluded: chain Q residue 296 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 218 SER Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 27 THR 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 164 HIS Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 268 GLU Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 152 LEU Chi-restraints excluded: chain T residue 255 LEU Chi-restraints excluded: chain T residue 267 TRP Chi-restraints excluded: chain T residue 303 LYS Chi-restraints excluded: chain T residue 336 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 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 194 SER Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 210 GLU Chi-restraints excluded: chain V residue 302 LEU 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 46 GLU Chi-restraints excluded: chain W residue 56 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 451 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 294 optimal weight: 0.0010 chunk 493 optimal weight: 0.0870 chunk 300 optimal weight: 2.9990 chunk 521 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 chunk 315 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 30.0000 overall best weight: 0.5564 ------------------------------------------------------------------------------- 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** N 155 GLN N 594 HIS N 637 ASN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 812 ASN ** Q 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** S 323 GLN ** 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** V 142 ASN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137405 restraints weight = 79894.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140726 restraints weight = 43661.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.142898 restraints weight = 29022.014| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 48869 Z= 0.185 Angle : 0.539 8.781 67389 Z= 0.289 Chirality : 0.039 0.150 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.201 174.190 8997 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 3.45 % Allowed : 27.75 % Favored : 68.80 % 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: 0.78 (0.10), residues: 2683 sheet: -0.89 (0.23), residues: 518 loop : -0.54 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 138 HIS 0.006 0.001 HIS P 813 PHE 0.021 0.001 PHE T 7 TYR 0.020 0.001 TYR Q 209 ARG 0.009 0.000 ARG Q 69 *********************** 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 984 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 830 time to evaluate : 3.446 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 290 LYS cc_start: 0.7334 (ptmm) cc_final: 0.6831 (ptmm) REVERT: J 383 ARG cc_start: 0.6322 (ptp-170) cc_final: 0.6003 (ptp-170) REVERT: M 121 GLU cc_start: 0.7313 (tp30) cc_final: 0.6851 (tp30) REVERT: M 588 ASP cc_start: 0.7356 (t0) cc_final: 0.7128 (t0) REVERT: M 612 ARG cc_start: 0.8421 (ptp-170) cc_final: 0.8123 (mtm110) REVERT: M 660 LEU cc_start: 0.7982 (mt) cc_final: 0.7758 (mp) REVERT: M 800 LYS cc_start: 0.7667 (tptp) cc_final: 0.7438 (tptp) REVERT: N 122 GLN cc_start: 0.7428 (mt0) cc_final: 0.7087 (mt0) REVERT: N 126 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7770 (mmtp) REVERT: N 404 TYR cc_start: 0.7320 (t80) cc_final: 0.6801 (t80) REVERT: N 569 MET cc_start: 0.7594 (mmm) cc_final: 0.7312 (mmm) REVERT: N 700 MET cc_start: 0.6589 (mmm) cc_final: 0.6375 (mmm) REVERT: N 744 TYR cc_start: 0.7194 (m-80) cc_final: 0.6976 (m-80) REVERT: N 779 GLN cc_start: 0.7232 (tp40) cc_final: 0.6441 (mt0) REVERT: N 796 GLU cc_start: 0.7021 (tm-30) cc_final: 0.5942 (tp30) REVERT: N 800 LYS cc_start: 0.7782 (pttt) cc_final: 0.6695 (pttt) REVERT: O 563 SER cc_start: 0.8786 (p) cc_final: 0.8311 (p) REVERT: O 583 GLN cc_start: 0.7557 (pm20) cc_final: 0.7307 (mp10) REVERT: O 700 MET cc_start: 0.5537 (tmm) cc_final: 0.5244 (tmm) REVERT: O 815 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.5430 (mp10) REVERT: O 834 GLN cc_start: 0.7967 (tp40) cc_final: 0.7538 (tp-100) REVERT: P 713 TYR cc_start: 0.6971 (t80) cc_final: 0.6680 (t80) REVERT: Q 30 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.6017 (p-80) REVERT: Q 257 LEU cc_start: 0.4372 (OUTLIER) cc_final: 0.3727 (mm) REVERT: R 19 ARG cc_start: 0.6823 (mpp80) cc_final: 0.6599 (mpt-90) REVERT: S 190 ASP cc_start: 0.6906 (m-30) cc_final: 0.6677 (m-30) REVERT: T 242 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7532 (tm-30) REVERT: T 267 TRP cc_start: 0.6951 (OUTLIER) cc_final: 0.6718 (p-90) REVERT: T 319 PHE cc_start: 0.7786 (t80) cc_final: 0.7482 (t80) REVERT: T 324 GLU cc_start: 0.6669 (mp0) cc_final: 0.6254 (mp0) REVERT: U 253 GLN cc_start: 0.7462 (tt0) cc_final: 0.7241 (tt0) REVERT: V 27 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7306 (m) REVERT: W 71 GLU cc_start: 0.5582 (mt-10) cc_final: 0.5291 (mt-10) outliers start: 154 outliers final: 104 residues processed: 925 average time/residue: 0.5442 time to fit residues: 812.8428 Evaluate side-chains 921 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 812 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 141 ILE 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 314 THR Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 251 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 632 THR 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 172 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 552 LEU Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 660 LEU 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 573 ILE 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 799 LEU Chi-restraints excluded: chain O residue 815 GLN 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 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 160 LEU 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 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 166 ASP Chi-restraints excluded: chain R residue 218 SER Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 28 VAL 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 143 VAL 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 152 LEU Chi-restraints excluded: chain T residue 197 ASN Chi-restraints excluded: chain T residue 228 ILE 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 V residue 20 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 128 TYR Chi-restraints excluded: chain V residue 142 ASN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 97 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 279 optimal weight: 30.0000 chunk 163 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 337 optimal weight: 0.0070 chunk 201 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137147 restraints weight = 80099.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140454 restraints weight = 46813.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.141860 restraints weight = 30282.985| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1451 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= 0.207 Angle : 0.547 9.243 67389 Z= 0.293 Chirality : 0.040 0.189 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.209 173.963 8994 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 27.52 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.10), residues: 2671 sheet: -0.88 (0.23), residues: 516 loop : -0.57 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 138 HIS 0.011 0.001 HIS M 388 PHE 0.020 0.001 PHE T 7 TYR 0.024 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 1003 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 826 time to evaluate : 3.532 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 290 LYS cc_start: 0.7357 (ptmm) cc_final: 0.6847 (ptmm) REVERT: J 383 ARG cc_start: 0.6330 (ptp-170) cc_final: 0.5857 (ptp-170) REVERT: J 417 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: M 121 GLU cc_start: 0.7415 (tp30) cc_final: 0.6944 (tp30) REVERT: M 150 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6952 (tp30) REVERT: M 523 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7032 (mp) REVERT: M 612 ARG cc_start: 0.8443 (ptp-170) cc_final: 0.8190 (mtm180) REVERT: M 660 LEU cc_start: 0.7986 (mt) cc_final: 0.7786 (mp) REVERT: N 86 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6289 (tppt) REVERT: N 122 GLN cc_start: 0.7414 (mt0) cc_final: 0.7179 (mt0) REVERT: N 404 TYR cc_start: 0.7367 (t80) cc_final: 0.6805 (t80) REVERT: N 796 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6386 (tp30) REVERT: O 563 SER cc_start: 0.8791 (p) cc_final: 0.8314 (p) REVERT: O 700 MET cc_start: 0.5612 (tmm) cc_final: 0.5191 (tmm) REVERT: O 815 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.5411 (mp10) REVERT: O 834 GLN cc_start: 0.7943 (tp40) cc_final: 0.7519 (tp-100) REVERT: P 713 TYR cc_start: 0.6957 (t80) cc_final: 0.6665 (t80) REVERT: Q 30 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6032 (p-80) REVERT: Q 257 LEU cc_start: 0.4226 (OUTLIER) cc_final: 0.3574 (mm) REVERT: R 19 ARG cc_start: 0.6915 (mpp80) cc_final: 0.6694 (mpt-90) REVERT: S 46 GLU cc_start: 0.6207 (pm20) cc_final: 0.5958 (pm20) REVERT: S 190 ASP cc_start: 0.6955 (m-30) cc_final: 0.6750 (m-30) REVERT: T 242 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7507 (tm-30) REVERT: T 267 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.6729 (p-90) REVERT: T 319 PHE cc_start: 0.7729 (t80) cc_final: 0.7448 (t80) REVERT: T 324 GLU cc_start: 0.6696 (mp0) cc_final: 0.6252 (mp0) REVERT: U 253 GLN cc_start: 0.7398 (tt0) cc_final: 0.7172 (tt0) REVERT: U 327 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7121 (ttp80) REVERT: V 19 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7045 (ptp90) REVERT: V 27 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7240 (m) REVERT: W 71 GLU cc_start: 0.5554 (mt-10) cc_final: 0.5249 (mt-10) REVERT: W 249 LEU cc_start: 0.7813 (mp) cc_final: 0.7578 (mp) outliers start: 177 outliers final: 131 residues processed: 940 average time/residue: 0.5160 time to fit residues: 774.9560 Evaluate side-chains 954 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 814 time to evaluate : 3.480 ------------------------------------------------------------------------------- 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 141 ILE 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 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 66 ILE Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 225 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 738 ILE Chi-restraints excluded: chain M residue 775 PHE 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 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 552 LEU 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 752 ASP Chi-restraints excluded: chain O residue 799 LEU Chi-restraints excluded: chain O residue 815 GLN 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 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 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 266 HIS 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 198 MET 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 27 THR Chi-restraints excluded: chain S residue 28 VAL 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 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 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 206 LEU Chi-restraints excluded: chain T residue 228 ILE 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 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 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 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 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 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 d residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 420 optimal weight: 3.9990 chunk 308 optimal weight: 0.0980 chunk 495 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 chunk 390 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 417 optimal weight: 0.8980 chunk 171 optimal weight: 0.0000 chunk 475 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 J 423 ASN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138100 restraints weight = 80153.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141552 restraints weight = 45386.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142624 restraints weight = 29746.664| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 48869 Z= 0.169 Angle : 0.537 8.229 67389 Z= 0.288 Chirality : 0.039 0.212 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.174 174.470 8994 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 3.83 % Allowed : 27.41 % Favored : 68.76 % 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: 2674 sheet: -0.92 (0.23), residues: 476 loop : -0.54 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 284 HIS 0.027 0.001 HIS M 388 PHE 0.020 0.001 PHE T 7 TYR 0.018 0.001 TYR W 271 ARG 0.011 0.000 ARG N 384 *********************** 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 995 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 824 time to evaluate : 3.541 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 46 THR cc_start: 0.6747 (m) cc_final: 0.6021 (p) REVERT: J 60 MET cc_start: 0.5993 (tpp) cc_final: 0.5728 (tpp) REVERT: J 283 LEU cc_start: 0.6489 (mm) cc_final: 0.6277 (mm) REVERT: J 290 LYS cc_start: 0.7356 (ptmm) cc_final: 0.6859 (ptmm) REVERT: J 411 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6877 (tp) REVERT: M 121 GLU cc_start: 0.7400 (tp30) cc_final: 0.6937 (tp30) REVERT: M 150 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6939 (tp30) REVERT: M 235 TYR cc_start: 0.7109 (t80) cc_final: 0.6723 (t80) REVERT: M 612 ARG cc_start: 0.8422 (ptp-170) cc_final: 0.8143 (mtm180) REVERT: M 800 LYS cc_start: 0.7665 (tptp) cc_final: 0.7434 (tptp) REVERT: N 86 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6280 (tppt) REVERT: N 122 GLN cc_start: 0.7393 (mt0) cc_final: 0.7128 (mt0) REVERT: N 126 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7864 (mmtp) REVERT: N 404 TYR cc_start: 0.7376 (t80) cc_final: 0.6874 (t80) REVERT: N 414 LYS cc_start: 0.6581 (mtpt) cc_final: 0.6358 (mtmt) REVERT: N 479 TYR cc_start: 0.7847 (t80) cc_final: 0.7514 (t80) REVERT: N 503 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6652 (mp) REVERT: N 684 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6192 (mt-10) REVERT: N 796 GLU cc_start: 0.7011 (tm-30) cc_final: 0.5881 (tp30) REVERT: N 800 LYS cc_start: 0.7685 (pttt) cc_final: 0.6584 (pttt) REVERT: O 563 SER cc_start: 0.8786 (p) cc_final: 0.8317 (p) REVERT: O 690 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.6086 (pm20) REVERT: O 700 MET cc_start: 0.5649 (tmm) cc_final: 0.5170 (tmm) REVERT: O 815 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5416 (mp10) REVERT: O 834 GLN cc_start: 0.7915 (tp40) cc_final: 0.7524 (tp-100) REVERT: P 713 TYR cc_start: 0.6977 (t80) cc_final: 0.6776 (t80) REVERT: P 805 GLU cc_start: 0.8069 (tp30) cc_final: 0.7865 (tp30) REVERT: Q 28 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8042 (p) REVERT: Q 30 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5855 (p-80) REVERT: Q 232 ARG cc_start: 0.7018 (ptt90) cc_final: 0.6798 (ptt90) REVERT: Q 257 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3547 (mm) REVERT: R 19 ARG cc_start: 0.6870 (mpp80) cc_final: 0.6631 (mpt-90) REVERT: R 24 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5219 (pp20) REVERT: S 190 ASP cc_start: 0.6961 (m-30) cc_final: 0.6730 (m-30) REVERT: T 242 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7481 (tm-30) REVERT: T 267 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6701 (p-90) REVERT: T 319 PHE cc_start: 0.7705 (t80) cc_final: 0.7438 (t80) REVERT: T 324 GLU cc_start: 0.6651 (mp0) cc_final: 0.6231 (mp0) REVERT: U 253 GLN cc_start: 0.7421 (tt0) cc_final: 0.7207 (tt0) REVERT: V 19 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7051 (ptp90) REVERT: V 27 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7252 (m) REVERT: W 71 GLU cc_start: 0.5499 (mt-10) cc_final: 0.4800 (mt-10) REVERT: W 189 LEU cc_start: 0.7523 (mt) cc_final: 0.7123 (mp) REVERT: W 245 LYS cc_start: 0.7833 (ptmt) cc_final: 0.7523 (ptmt) REVERT: W 249 LEU cc_start: 0.7778 (mp) cc_final: 0.7550 (mp) outliers start: 171 outliers final: 119 residues processed: 932 average time/residue: 0.5334 time to fit residues: 788.4986 Evaluate side-chains 947 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 816 time to evaluate : 3.448 ------------------------------------------------------------------------------- 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 141 ILE 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 307 ILE Chi-restraints excluded: chain J residue 405 LEU Chi-restraints excluded: chain J residue 411 LEU 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 225 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 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 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 503 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 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 574 CYS Chi-restraints excluded: chain O residue 601 LEU Chi-restraints excluded: chain O residue 690 GLN 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 726 SER Chi-restraints excluded: chain P residue 771 ILE Chi-restraints excluded: chain Q residue 28 VAL 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 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 275 LEU Chi-restraints excluded: chain Q residue 293 LEU 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 198 MET 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 27 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 125 LYS 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 179 VAL 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 228 ILE 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 189 LEU Chi-restraints excluded: chain U residue 230 PHE 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 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 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 281 LEU 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 436 optimal weight: 6.9990 chunk 116 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 chunk 318 optimal weight: 0.6980 chunk 226 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 378 ASN M 143 GLN M 388 HIS ** 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** ** P 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** V 337 GLN ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.166684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140642 restraints weight = 79530.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143864 restraints weight = 44352.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.145980 restraints weight = 29894.396| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1622 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= 0.193 Angle : 0.549 12.635 67389 Z= 0.294 Chirality : 0.040 0.199 7436 Planarity : 0.004 0.094 7681 Dihedral : 20.174 174.120 8991 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 3.99 % Allowed : 27.32 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2679 sheet: -0.96 (0.23), residues: 500 loop : -0.55 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 284 HIS 0.006 0.001 HIS P 813 PHE 0.019 0.001 PHE T 7 TYR 0.020 0.001 TYR O 742 ARG 0.011 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 1003 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 825 time to evaluate : 3.482 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 268 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.5022 (t0) REVERT: J 283 LEU cc_start: 0.6489 (mm) cc_final: 0.6283 (mm) REVERT: J 290 LYS cc_start: 0.7356 (ptmm) cc_final: 0.6848 (ptmm) REVERT: J 383 ARG cc_start: 0.6356 (ptp-110) cc_final: 0.6154 (ptp-170) REVERT: J 411 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6797 (tp) REVERT: M 121 GLU cc_start: 0.7319 (tp30) cc_final: 0.6866 (tp30) REVERT: M 150 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6902 (tp30) REVERT: M 235 TYR cc_start: 0.7128 (t80) cc_final: 0.6800 (t80) REVERT: M 411 ARG cc_start: 0.6882 (ptp-110) cc_final: 0.6648 (ptp-170) REVERT: M 612 ARG cc_start: 0.8419 (ptp-170) cc_final: 0.8057 (mtm110) REVERT: M 800 LYS cc_start: 0.7713 (tptp) cc_final: 0.7412 (tptp) REVERT: N 86 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6393 (tppt) REVERT: N 122 GLN cc_start: 0.7447 (mt0) cc_final: 0.7182 (mt0) REVERT: N 126 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7858 (mmtp) REVERT: N 404 TYR cc_start: 0.7431 (t80) cc_final: 0.6936 (t80) REVERT: N 779 GLN cc_start: 0.7211 (tp40) cc_final: 0.6347 (mt0) REVERT: N 796 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6442 (tp30) REVERT: O 563 SER cc_start: 0.8750 (p) cc_final: 0.8298 (p) REVERT: O 690 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5904 (pm20) REVERT: O 700 MET cc_start: 0.5593 (tmm) cc_final: 0.5071 (tmm) REVERT: O 834 GLN cc_start: 0.7912 (tp40) cc_final: 0.7524 (tp-100) REVERT: P 713 TYR cc_start: 0.6952 (t80) cc_final: 0.6747 (t80) REVERT: Q 30 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.5898 (p-80) REVERT: Q 193 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7528 (mmtt) REVERT: Q 232 ARG cc_start: 0.7059 (ptt90) cc_final: 0.6842 (ptt90) REVERT: Q 257 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3574 (mm) REVERT: R 19 ARG cc_start: 0.6793 (mpp80) cc_final: 0.6589 (mpt-90) REVERT: R 24 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.5116 (pp20) REVERT: S 190 ASP cc_start: 0.6966 (m-30) cc_final: 0.6756 (m-30) REVERT: S 270 PHE cc_start: 0.7851 (m-80) cc_final: 0.7538 (m-80) REVERT: T 198 MET cc_start: 0.8107 (mtp) cc_final: 0.7852 (mtt) REVERT: T 242 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7509 (tm-30) REVERT: T 267 TRP cc_start: 0.6988 (OUTLIER) cc_final: 0.6729 (p-90) REVERT: T 319 PHE cc_start: 0.7676 (t80) cc_final: 0.7419 (t80) REVERT: T 324 GLU cc_start: 0.6694 (mp0) cc_final: 0.6255 (mp0) REVERT: U 253 GLN cc_start: 0.7452 (tt0) cc_final: 0.7244 (tt0) REVERT: V 19 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7002 (ptp90) REVERT: V 27 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7266 (m) REVERT: W 223 ARG cc_start: 0.7152 (ptt90) cc_final: 0.6699 (ptt90) REVERT: W 245 LYS cc_start: 0.7850 (ptmt) cc_final: 0.7549 (ptmt) REVERT: W 249 LEU cc_start: 0.7761 (mp) cc_final: 0.7537 (mp) outliers start: 178 outliers final: 137 residues processed: 935 average time/residue: 0.5188 time to fit residues: 776.1251 Evaluate side-chains 968 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 821 time to evaluate : 3.602 ------------------------------------------------------------------------------- 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 141 ILE 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 307 ILE 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 225 ILE Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 388 HIS 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 M residue 738 ILE 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 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 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 361 LEU 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 552 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 799 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 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 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 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 275 LEU 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 166 ASP Chi-restraints excluded: chain R residue 198 MET 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 27 THR 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 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 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 206 LEU Chi-restraints excluded: chain T residue 228 ILE 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 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 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 311 SER 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 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 218 SER Chi-restraints excluded: chain W residue 231 ARG 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 357 optimal weight: 0.9980 chunk 392 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 489 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 360 optimal weight: 0.8980 chunk 267 optimal weight: 0.9990 chunk 525 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 379 optimal weight: 0.6980 chunk 413 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS O 815 GLN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139924 restraints weight = 79968.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143272 restraints weight = 43303.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145422 restraints weight = 28729.622| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 48869 Z= 0.233 Angle : 0.573 13.870 67389 Z= 0.307 Chirality : 0.041 0.252 7436 Planarity : 0.005 0.094 7681 Dihedral : 20.212 174.273 8991 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 3.65 % Allowed : 27.72 % Favored : 68.62 % 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: 0.13 (0.12), residues: 5088 helix: 0.83 (0.10), residues: 2677 sheet: -0.93 (0.22), residues: 540 loop : -0.53 (0.15), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 389 HIS 0.045 0.001 HIS M 388 PHE 0.024 0.001 PHE M 851 TYR 0.019 0.001 TYR N 159 ARG 0.011 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 988 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 825 time to evaluate : 3.451 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: J 133 ARG cc_start: 0.7280 (mtt-85) cc_final: 0.6995 (mtt90) REVERT: J 144 GLN cc_start: 0.6593 (mp10) cc_final: 0.6136 (mp-120) REVERT: J 268 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.5036 (t0) REVERT: J 290 LYS cc_start: 0.7343 (ptmm) cc_final: 0.6835 (ptmm) REVERT: J 383 ARG cc_start: 0.6296 (ptp-110) cc_final: 0.5943 (ptp-170) REVERT: J 411 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6807 (tp) REVERT: M 121 GLU cc_start: 0.7363 (tp30) cc_final: 0.6903 (tp30) REVERT: M 150 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6937 (tp30) REVERT: M 388 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7938 (t-170) REVERT: M 411 ARG cc_start: 0.6929 (ptp-110) cc_final: 0.6677 (ptp-170) REVERT: M 612 ARG cc_start: 0.8414 (ptp-170) cc_final: 0.8067 (mtm110) REVERT: M 800 LYS cc_start: 0.7696 (tptp) cc_final: 0.7397 (tptp) REVERT: N 86 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5996 (tppt) REVERT: N 122 GLN cc_start: 0.7569 (mt0) cc_final: 0.7280 (mt0) REVERT: N 126 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7898 (mmtp) REVERT: N 404 TYR cc_start: 0.7447 (t80) cc_final: 0.6951 (t80) REVERT: N 414 LYS cc_start: 0.6540 (mtmt) cc_final: 0.6326 (mtmt) REVERT: N 479 TYR cc_start: 0.7900 (t80) cc_final: 0.7506 (t80) REVERT: N 649 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6739 (mtp85) REVERT: N 756 GLU cc_start: 0.6980 (tt0) cc_final: 0.6642 (tt0) REVERT: N 779 GLN cc_start: 0.7251 (tp40) cc_final: 0.6441 (mt0) REVERT: N 796 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6498 (tp30) REVERT: O 563 SER cc_start: 0.8752 (p) cc_final: 0.8304 (p) REVERT: O 690 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.5968 (pm20) REVERT: O 700 MET cc_start: 0.5599 (tmm) cc_final: 0.5082 (tmm) REVERT: O 834 GLN cc_start: 0.7912 (tp40) cc_final: 0.7509 (tp-100) REVERT: P 565 ARG cc_start: 0.8111 (mpt180) cc_final: 0.7861 (mpt180) REVERT: P 618 ARG cc_start: 0.4553 (OUTLIER) cc_final: 0.4345 (mtt180) REVERT: P 713 TYR cc_start: 0.6968 (t80) cc_final: 0.6734 (t80) REVERT: P 805 GLU cc_start: 0.8130 (tp30) cc_final: 0.7926 (tp30) REVERT: Q 30 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.5968 (p-80) REVERT: Q 69 ARG cc_start: 0.7131 (tpt-90) cc_final: 0.6668 (tpt-90) REVERT: Q 193 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7614 (mmtt) REVERT: Q 257 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3341 (mm) REVERT: R 24 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5140 (pp20) REVERT: S 46 GLU cc_start: 0.6598 (pm20) cc_final: 0.6313 (pm20) REVERT: S 224 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5520 (mtp85) REVERT: S 270 PHE cc_start: 0.7813 (m-80) cc_final: 0.7453 (m-80) REVERT: T 242 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7538 (tm-30) REVERT: T 267 TRP cc_start: 0.6990 (OUTLIER) cc_final: 0.6675 (p-90) REVERT: U 253 GLN cc_start: 0.7475 (tt0) cc_final: 0.7255 (tt0) REVERT: V 19 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7026 (ptp90) REVERT: V 27 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7207 (m) REVERT: W 223 ARG cc_start: 0.7264 (ptt90) cc_final: 0.6708 (ptt90) REVERT: W 245 LYS cc_start: 0.7849 (ptmt) cc_final: 0.7527 (ptmt) REVERT: W 249 LEU cc_start: 0.7772 (mp) cc_final: 0.7543 (mp) outliers start: 163 outliers final: 130 residues processed: 928 average time/residue: 0.5206 time to fit residues: 769.1872 Evaluate side-chains 956 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 813 time to evaluate : 3.415 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain J residue 268 ASN 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 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 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 M residue 738 ILE 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 138 SER Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 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 361 LEU 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 799 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 600 THR 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 664 THR Chi-restraints excluded: chain P residue 667 LEU Chi-restraints excluded: chain P residue 771 ILE 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 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 275 LEU 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 198 MET 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 41 MET 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 128 TYR 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 224 ARG 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 206 LEU Chi-restraints excluded: chain T residue 228 ILE 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 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 302 LEU Chi-restraints excluded: chain V residue 311 SER 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 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 218 SER Chi-restraints excluded: chain W residue 231 ARG 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 121 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 428 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 148 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 328 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 O 815 GLN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.166984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140792 restraints weight = 80307.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144178 restraints weight = 43425.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146340 restraints weight = 28628.174| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1728 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= 0.187 Angle : 0.563 12.447 67389 Z= 0.301 Chirality : 0.040 0.316 7436 Planarity : 0.005 0.094 7681 Dihedral : 20.184 174.659 8991 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 3.38 % Allowed : 28.17 % 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: 0.17 (0.12), residues: 5088 helix: 0.87 (0.10), residues: 2679 sheet: -0.94 (0.23), residues: 500 loop : -0.54 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 284 HIS 0.032 0.001 HIS M 388 PHE 0.019 0.001 PHE T 7 TYR 0.034 0.001 TYR M 67 ARG 0.011 0.000 ARG N 384 ********************** 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 965 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 814 time to evaluate : 3.559 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: 0.6748 (m) cc_final: 0.6001 (p) REVERT: J 144 GLN cc_start: 0.6485 (mp10) cc_final: 0.6155 (mp10) REVERT: J 268 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.5000 (t0) REVERT: J 290 LYS cc_start: 0.7329 (ptmm) cc_final: 0.6829 (ptmm) REVERT: J 383 ARG cc_start: 0.6278 (ptp-110) cc_final: 0.5931 (ptp-170) REVERT: J 411 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6777 (tp) REVERT: M 121 GLU cc_start: 0.7356 (tp30) cc_final: 0.6890 (tp30) REVERT: M 150 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6925 (tp30) REVERT: M 411 ARG cc_start: 0.6919 (ptp-110) cc_final: 0.6679 (ptp-170) REVERT: M 612 ARG cc_start: 0.8376 (ptp-170) cc_final: 0.8083 (mtm180) REVERT: M 727 GLU cc_start: 0.6465 (mp0) cc_final: 0.6208 (mp0) REVERT: M 800 LYS cc_start: 0.7705 (tptp) cc_final: 0.7379 (tptp) REVERT: N 122 GLN cc_start: 0.7531 (mt0) cc_final: 0.7242 (mt0) REVERT: N 126 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7923 (mmtp) REVERT: N 404 TYR cc_start: 0.7439 (t80) cc_final: 0.6894 (t80) REVERT: N 414 LYS cc_start: 0.6525 (mtmt) cc_final: 0.6309 (mtpt) REVERT: N 479 TYR cc_start: 0.7890 (t80) cc_final: 0.7511 (t80) REVERT: N 756 GLU cc_start: 0.6904 (tt0) cc_final: 0.6558 (tt0) REVERT: N 779 GLN cc_start: 0.7213 (tp40) cc_final: 0.6380 (mt0) REVERT: N 796 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6488 (tp30) REVERT: O 563 SER cc_start: 0.8739 (p) cc_final: 0.8302 (p) REVERT: O 700 MET cc_start: 0.5593 (tmm) cc_final: 0.5052 (tmm) REVERT: O 834 GLN cc_start: 0.7897 (tp40) cc_final: 0.7502 (tp-100) REVERT: P 618 ARG cc_start: 0.4536 (OUTLIER) cc_final: 0.4334 (mtt180) REVERT: P 713 TYR cc_start: 0.6956 (t80) cc_final: 0.6736 (t80) REVERT: Q 30 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.5889 (p-80) REVERT: Q 69 ARG cc_start: 0.7132 (tpt-90) cc_final: 0.6641 (tpt-90) REVERT: Q 193 LYS cc_start: 0.7774 (mmtt) cc_final: 0.7573 (mmtt) REVERT: Q 257 LEU cc_start: 0.4211 (OUTLIER) cc_final: 0.3504 (mm) REVERT: R 24 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5114 (pp20) REVERT: S 46 GLU cc_start: 0.6500 (pm20) cc_final: 0.6120 (pm20) REVERT: S 224 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5517 (mtp85) REVERT: S 270 PHE cc_start: 0.7799 (m-80) cc_final: 0.7465 (m-80) REVERT: T 198 MET cc_start: 0.8299 (mtt) cc_final: 0.7954 (mtp) REVERT: T 242 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7498 (tm-30) REVERT: T 267 TRP cc_start: 0.7000 (OUTLIER) cc_final: 0.6681 (p-90) REVERT: T 324 GLU cc_start: 0.6695 (mp0) cc_final: 0.6216 (mp0) REVERT: U 253 GLN cc_start: 0.7401 (tt0) cc_final: 0.7180 (tt0) REVERT: V 19 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7009 (ptp90) REVERT: V 27 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7195 (m) REVERT: W 245 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7464 (ptmt) REVERT: W 249 LEU cc_start: 0.7764 (mp) cc_final: 0.7537 (mp) outliers start: 151 outliers final: 126 residues processed: 909 average time/residue: 0.5155 time to fit residues: 745.6717 Evaluate side-chains 938 residues out of total 4462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 802 time to evaluate : 3.459 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain J residue 268 ASN 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 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 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 M residue 738 ILE 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 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 361 LEU 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 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 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 618 ARG 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 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 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 275 LEU 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 198 MET 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 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 128 TYR 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 224 ARG 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 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 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 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 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 337 GLN 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 205 LEU Chi-restraints excluded: chain W residue 210 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 349 optimal weight: 0.6980 chunk 450 optimal weight: 0.0020 chunk 145 optimal weight: 0.8980 chunk 434 optimal weight: 2.9990 chunk 506 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 520 optimal weight: 4.9990 chunk 464 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 155 GLN N 594 HIS O 815 GLN ** P 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.166282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140220 restraints weight = 79108.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143414 restraints weight = 44369.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145513 restraints weight = 30073.932| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 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= 0.211 Angle : 0.573 12.806 67389 Z= 0.306 Chirality : 0.041 0.286 7436 Planarity : 0.005 0.093 7681 Dihedral : 20.197 174.329 8991 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 3.38 % Allowed : 28.17 % 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: 0.14 (0.12), residues: 5088 helix: 0.84 (0.10), residues: 2679 sheet: -0.93 (0.23), residues: 500 loop : -0.57 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 284 HIS 0.013 0.001 HIS M 388 PHE 0.028 0.001 PHE M 851 TYR 0.021 0.001 TYR M 67 ARG 0.011 0.000 ARG M 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16184.06 seconds wall clock time: 280 minutes 11.21 seconds (16811.21 seconds total)