Starting phenix.real_space_refine on Sat Aug 23 17:43:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrp_36601/08_2025/8jrp_36601.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 78 5.16 5 C 8696 2.51 5 N 2286 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13630 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5622 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "C" Number of atoms: 5622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5622 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" 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: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS B 37 80.733 77.285 94.141 1.00 82.68 S ATOM 266 SG CYS B 40 81.790 74.538 96.437 1.00 85.61 S ATOM 522 SG CYS B 70 83.006 74.518 92.772 1.00 87.38 S ATOM 545 SG CYS B 73 79.491 73.651 93.542 1.00 84.84 S ATOM 864 SG CYS B 110 81.111 74.364 76.450 1.00 80.12 S ATOM 886 SG CYS B 113 83.508 75.932 78.872 1.00 77.59 S ATOM 1148 SG CYS B 143 84.814 74.631 75.547 1.00 94.64 S ATOM 1168 SG CYS B 146 83.667 72.184 78.236 1.00 92.88 S ATOM 7054 SG CYS D 37 62.781 34.099 94.141 1.00 82.68 S ATOM 7079 SG CYS D 40 61.724 36.846 96.437 1.00 85.61 S ATOM 7335 SG CYS D 70 60.508 36.866 92.772 1.00 87.38 S ATOM 7358 SG CYS D 73 64.023 37.733 93.542 1.00 84.84 S ATOM 7677 SG CYS D 110 62.403 37.020 76.450 1.00 80.12 S ATOM 7699 SG CYS D 113 60.006 35.452 78.872 1.00 77.59 S ATOM 7961 SG CYS D 143 58.700 36.753 75.547 1.00 94.64 S ATOM 7981 SG CYS D 146 59.847 39.200 78.236 1.00 92.88 S Time building chain proxies: 2.36, per 1000 atoms: 0.17 Number of scatterers: 13630 At special positions: 0 Unit cell: (144.585, 112.455, 114.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 78 16.00 O 2566 8.00 N 2286 7.00 C 8696 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: 0.86 Conformation dependent library (CDL) restraints added in 540.9 milliseconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " Number of angles added : 24 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 10 sheets defined 62.4% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.527A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.993A pdb=" N ILE B 33 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.508A pdb=" N LYS B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.958A pdb=" N ARG B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 4.847A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 3.598A pdb=" N SER A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.898A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 253 through 274 removed outlier: 4.142A pdb=" N LEU A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.880A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.953A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 4.188A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix removed outlier: 4.036A pdb=" N GLU A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.745A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 353 removed outlier: 3.615A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.144A pdb=" N PHE A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.958A pdb=" N ASN A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 459 through 469 removed outlier: 4.074A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.776A pdb=" N THR A 479 " --> pdb=" O SER A 476 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 515 Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.540A pdb=" N GLU A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.768A pdb=" N LEU A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 removed outlier: 3.514A pdb=" N GLU A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 609 through 626 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.854A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.860A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 710 through 724 removed outlier: 3.566A pdb=" N VAL A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 741 removed outlier: 4.055A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 4.395A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 removed outlier: 3.652A pdb=" N LEU A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 772 " --> pdb=" O GLN A 768 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 796 removed outlier: 3.650A pdb=" N ARG A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 811 removed outlier: 3.606A pdb=" N ARG A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 854 through 867 removed outlier: 3.661A pdb=" N THR A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.527A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.993A pdb=" N ILE D 33 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 70 through 85 removed outlier: 3.508A pdb=" N LYS D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.958A pdb=" N ARG D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 4.847A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 3.598A pdb=" N SER C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 removed outlier: 3.898A pdb=" N LEU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 253 through 274 removed outlier: 4.142A pdb=" N LEU C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.880A pdb=" N ARG C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.953A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 4.188A pdb=" N HIS C 297 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Proline residue: C 299 - end of helix removed outlier: 4.036A pdb=" N GLU C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.745A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 332 through 353 removed outlier: 3.615A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 403 through 414 Processing helix chain 'C' and resid 426 through 433 Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.144A pdb=" N PHE C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 450' Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.958A pdb=" N ASN C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 456' Processing helix chain 'C' and resid 459 through 469 removed outlier: 4.074A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.776A pdb=" N THR C 479 " --> pdb=" O SER C 476 " (cutoff:3.500A) Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 485 through 515 Processing helix chain 'C' and resid 531 through 547 removed outlier: 3.540A pdb=" N GLU C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.768A pdb=" N LEU C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 552 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 583 removed outlier: 3.514A pdb=" N GLU C 573 " --> pdb=" O GLY C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 609 through 626 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.854A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 655 removed outlier: 3.860A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 667 Processing helix chain 'C' and resid 710 through 724 removed outlier: 3.566A pdb=" N VAL C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C 715 " --> pdb=" O LYS C 711 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 719 " --> pdb=" O ASN C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 741 removed outlier: 4.055A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 4.395A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 774 removed outlier: 3.652A pdb=" N LEU C 770 " --> pdb=" O ASP C 766 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 773 " --> pdb=" O ALA C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 796 removed outlier: 3.650A pdb=" N ARG C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 789 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 811 removed outlier: 3.606A pdb=" N ARG C 803 " --> pdb=" O ASP C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 854 through 867 removed outlier: 3.661A pdb=" N THR C 867 " --> pdb=" O LEU C 863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.753A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 525 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 684 Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.434A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 839 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 86 through 90 removed outlier: 3.753A pdb=" N TYR D 88 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 522 through 525 Processing sheet with id=AA8, first strand: chain 'C' and resid 590 through 591 Processing sheet with id=AA9, first strand: chain 'C' and resid 681 through 684 Processing sheet with id=AB1, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.434A pdb=" N GLU C 775 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS C 829 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 777 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 839 " --> pdb=" O LEU C 848 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4476 1.35 - 1.47: 3132 1.47 - 1.58: 6176 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 13904 Sorted by residual: bond pdb=" N TYR C 852 " pdb=" CA TYR C 852 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.34e+00 bond pdb=" N TYR A 852 " pdb=" CA TYR A 852 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.34e+00 bond pdb=" N THR A 798 " pdb=" CA THR A 798 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N THR C 798 " pdb=" CA THR C 798 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.21e-02 6.83e+03 6.75e+00 ... (remaining 13899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 18574 2.35 - 4.70: 176 4.70 - 7.05: 22 7.05 - 9.40: 2 9.40 - 11.75: 2 Bond angle restraints: 18776 Sorted by residual: angle pdb=" CB MET D 144 " pdb=" CG MET D 144 " pdb=" SD MET D 144 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET B 144 " pdb=" CG MET B 144 " pdb=" SD MET B 144 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.54e+01 angle pdb=" N LYS A 420 " pdb=" CA LYS A 420 " pdb=" C LYS A 420 " ideal model delta sigma weight residual 113.61 108.93 4.68 1.50e+00 4.44e-01 9.75e+00 angle pdb=" CA THR A 798 " pdb=" C THR A 798 " pdb=" O THR A 798 " ideal model delta sigma weight residual 121.81 118.36 3.45 1.18e+00 7.18e-01 8.54e+00 angle pdb=" CA THR C 798 " pdb=" C THR C 798 " pdb=" O THR C 798 " ideal model delta sigma weight residual 121.81 118.36 3.45 1.18e+00 7.18e-01 8.54e+00 ... (remaining 18771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 7196 17.14 - 34.28: 1018 34.28 - 51.43: 200 51.43 - 68.57: 52 68.57 - 85.71: 26 Dihedral angle restraints: 8492 sinusoidal: 3576 harmonic: 4916 Sorted by residual: dihedral pdb=" CA ASP C 593 " pdb=" CB ASP C 593 " pdb=" CG ASP C 593 " pdb=" OD1 ASP C 593 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 593 " pdb=" CB ASP A 593 " pdb=" CG ASP A 593 " pdb=" OD1 ASP A 593 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP C 833 " pdb=" CB ASP C 833 " pdb=" CG ASP C 833 " pdb=" OD1 ASP C 833 " ideal model delta sinusoidal sigma weight residual -30.00 -83.72 53.72 1 2.00e+01 2.50e-03 9.80e+00 ... (remaining 8489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1389 0.034 - 0.067: 495 0.067 - 0.101: 122 0.101 - 0.135: 48 0.135 - 0.169: 4 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CA ARG A 418 " pdb=" N ARG A 418 " pdb=" C ARG A 418 " pdb=" CB ARG A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA LYS C 420 " pdb=" N LYS C 420 " pdb=" C LYS C 420 " pdb=" CB LYS C 420 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CG LEU C 163 " pdb=" CB LEU C 163 " pdb=" CD1 LEU C 163 " pdb=" CD2 LEU C 163 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2055 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 56 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C ASP D 56 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP D 56 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 57 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 56 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C ASP B 56 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP B 56 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 57 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 118 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 119 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " -0.019 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1594 2.75 - 3.29: 14115 3.29 - 3.82: 22645 3.82 - 4.36: 26057 4.36 - 4.90: 44784 Nonbonded interactions: 109195 Sorted by model distance: nonbonded pdb=" O LEU A 770 " pdb=" OG1 THR A 774 " model vdw 2.212 3.040 nonbonded pdb=" O LEU C 770 " pdb=" OG1 THR C 774 " model vdw 2.212 3.040 nonbonded pdb=" O ASN A 295 " pdb=" OG SER A 298 " model vdw 2.219 3.040 nonbonded pdb=" O ASN C 295 " pdb=" OG SER C 298 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A 464 " pdb=" OD1 ASP A 496 " model vdw 2.220 3.040 ... (remaining 109190 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13920 Z= 0.157 Angle : 0.547 11.754 18800 Z= 0.289 Chirality : 0.039 0.169 2058 Planarity : 0.003 0.033 2434 Dihedral : 16.575 85.710 5316 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 23.16 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.22), residues: 1648 helix: 0.78 (0.19), residues: 842 sheet: -0.90 (0.61), residues: 68 loop : 0.37 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 788 TYR 0.013 0.001 TYR B 61 PHE 0.011 0.001 PHE C 797 TRP 0.003 0.001 TRP C 791 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00277 (13904) covalent geometry : angle 0.54200 (18776) hydrogen bonds : bond 0.15679 ( 618) hydrogen bonds : angle 5.83872 ( 1752) metal coordination : bond 0.00265 ( 16) metal coordination : angle 2.09374 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 0.396 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: B 19 LEU cc_start: 0.8396 (tp) cc_final: 0.8140 (tp) REVERT: B 22 LEU cc_start: 0.7814 (tp) cc_final: 0.7612 (tp) REVERT: B 26 LEU cc_start: 0.8335 (mp) cc_final: 0.8090 (mp) REVERT: B 41 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7745 (mmtt) REVERT: B 77 TYR cc_start: 0.8202 (m-80) cc_final: 0.7846 (m-80) REVERT: B 84 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7981 (ttm170) REVERT: B 91 TYR cc_start: 0.8581 (m-10) cc_final: 0.7343 (m-10) REVERT: B 94 THR cc_start: 0.8208 (m) cc_final: 0.7946 (p) REVERT: B 96 GLU cc_start: 0.7589 (tp30) cc_final: 0.7235 (tp30) REVERT: B 97 GLN cc_start: 0.7831 (tp40) cc_final: 0.7398 (tp40) REVERT: B 118 SER cc_start: 0.8579 (m) cc_final: 0.8130 (p) REVERT: B 121 GLU cc_start: 0.8135 (mp0) cc_final: 0.7590 (mp0) REVERT: B 124 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7649 (ttp80) REVERT: B 128 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8347 (mtmm) REVERT: B 131 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7801 (mtt90) REVERT: B 135 ILE cc_start: 0.8636 (mm) cc_final: 0.8232 (mm) REVERT: B 138 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7399 (ptp90) REVERT: B 144 MET cc_start: 0.7450 (mmm) cc_final: 0.7202 (mmm) REVERT: A 128 LEU cc_start: 0.8054 (mp) cc_final: 0.7802 (mm) REVERT: A 135 GLU cc_start: 0.7981 (pt0) cc_final: 0.7597 (pp20) REVERT: A 151 ARG cc_start: 0.7005 (ptm160) cc_final: 0.6774 (ptm160) REVERT: A 167 PHE cc_start: 0.7912 (m-80) cc_final: 0.7560 (m-80) REVERT: A 247 LEU cc_start: 0.8033 (mp) cc_final: 0.7611 (tt) REVERT: A 268 GLU cc_start: 0.8228 (tt0) cc_final: 0.7714 (tm-30) REVERT: A 270 ASP cc_start: 0.7840 (t0) cc_final: 0.7638 (t0) REVERT: A 283 TYR cc_start: 0.8184 (t80) cc_final: 0.7799 (t80) REVERT: A 310 CYS cc_start: 0.7884 (m) cc_final: 0.7411 (m) REVERT: A 315 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8028 (mmmm) REVERT: A 327 LEU cc_start: 0.8081 (mt) cc_final: 0.7823 (mt) REVERT: A 328 TRP cc_start: 0.8380 (m-10) cc_final: 0.8097 (m-10) REVERT: A 336 ILE cc_start: 0.8064 (mm) cc_final: 0.7855 (mm) REVERT: A 338 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.7314 (mmm160) REVERT: A 340 MET cc_start: 0.7300 (tmm) cc_final: 0.6891 (tmm) REVERT: A 352 ILE cc_start: 0.8963 (mm) cc_final: 0.8755 (pt) REVERT: A 359 ARG cc_start: 0.7713 (mmp-170) cc_final: 0.7195 (mmp-170) REVERT: A 383 VAL cc_start: 0.8560 (t) cc_final: 0.8251 (p) REVERT: A 387 GLU cc_start: 0.7075 (pm20) cc_final: 0.5496 (mp0) REVERT: A 394 GLU cc_start: 0.7275 (tp30) cc_final: 0.6497 (tp30) REVERT: A 397 ASP cc_start: 0.6759 (p0) cc_final: 0.6073 (p0) REVERT: A 403 GLU cc_start: 0.7691 (pm20) cc_final: 0.7354 (pm20) REVERT: A 406 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 407 LEU cc_start: 0.8908 (mt) cc_final: 0.8637 (mt) REVERT: A 411 GLU cc_start: 0.7872 (tt0) cc_final: 0.7563 (tt0) REVERT: A 428 LEU cc_start: 0.8816 (tp) cc_final: 0.8523 (tp) REVERT: A 448 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 459 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6394 (mm-30) REVERT: A 462 LYS cc_start: 0.7581 (mttm) cc_final: 0.7163 (mtpp) REVERT: A 470 GLU cc_start: 0.7608 (tt0) cc_final: 0.6962 (tt0) REVERT: A 504 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 507 ILE cc_start: 0.8241 (mt) cc_final: 0.8007 (tp) REVERT: A 538 VAL cc_start: 0.8579 (m) cc_final: 0.8310 (p) REVERT: A 541 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7554 (tp30) REVERT: A 558 GLU cc_start: 0.6593 (tm-30) cc_final: 0.5857 (tm-30) REVERT: A 566 ASP cc_start: 0.6481 (t0) cc_final: 0.5967 (t0) REVERT: A 609 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6992 (mp0) REVERT: A 611 GLN cc_start: 0.7855 (mp10) cc_final: 0.7323 (mp10) REVERT: A 621 LEU cc_start: 0.8410 (mt) cc_final: 0.8198 (mt) REVERT: A 644 LYS cc_start: 0.8220 (tppt) cc_final: 0.7890 (tppt) REVERT: A 645 LYS cc_start: 0.8404 (mttt) cc_final: 0.7642 (mmtt) REVERT: A 663 LYS cc_start: 0.8566 (pttp) cc_final: 0.8299 (pptt) REVERT: A 677 MET cc_start: 0.5856 (mmm) cc_final: 0.5413 (mmm) REVERT: A 684 GLN cc_start: 0.8612 (tt0) cc_final: 0.8259 (tm-30) REVERT: A 711 LYS cc_start: 0.8703 (mppt) cc_final: 0.8431 (mmtt) REVERT: A 713 PHE cc_start: 0.8540 (t80) cc_final: 0.8077 (t80) REVERT: A 738 HIS cc_start: 0.7326 (t70) cc_final: 0.6955 (t70) REVERT: A 747 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7886 (tppt) REVERT: A 757 LEU cc_start: 0.8687 (tp) cc_final: 0.8374 (tt) REVERT: A 764 ASN cc_start: 0.8125 (p0) cc_final: 0.7805 (p0) REVERT: A 768 GLN cc_start: 0.7690 (mp10) cc_final: 0.7200 (mp10) REVERT: A 772 GLU cc_start: 0.7286 (mp0) cc_final: 0.6785 (mp0) REVERT: A 800 GLU cc_start: 0.7490 (tp30) cc_final: 0.7190 (tp30) REVERT: A 802 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7917 (mtpt) REVERT: A 804 LEU cc_start: 0.8372 (mt) cc_final: 0.8012 (mt) REVERT: A 841 HIS cc_start: 0.8091 (t70) cc_final: 0.7617 (t70) REVERT: A 858 LEU cc_start: 0.8624 (tp) cc_final: 0.8399 (tt) REVERT: A 864 LYS cc_start: 0.8541 (tppt) cc_final: 0.8174 (ttmm) REVERT: D 17 ARG cc_start: 0.6831 (mmt180) cc_final: 0.6559 (mmt180) REVERT: D 22 LEU cc_start: 0.7828 (tp) cc_final: 0.7621 (tp) REVERT: D 25 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7775 (mp0) REVERT: D 26 LEU cc_start: 0.8228 (mp) cc_final: 0.7981 (mp) REVERT: D 41 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7754 (mmtt) REVERT: D 52 PHE cc_start: 0.9053 (t80) cc_final: 0.8751 (t80) REVERT: D 62 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7569 (tpp80) REVERT: D 77 TYR cc_start: 0.8287 (m-80) cc_final: 0.7955 (m-80) REVERT: D 84 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7840 (ttm170) REVERT: D 85 HIS cc_start: 0.8692 (m-70) cc_final: 0.8480 (m-70) REVERT: D 91 TYR cc_start: 0.8573 (m-10) cc_final: 0.8117 (m-10) REVERT: D 94 THR cc_start: 0.8116 (m) cc_final: 0.7872 (p) REVERT: D 96 GLU cc_start: 0.7679 (tp30) cc_final: 0.7409 (tp30) REVERT: D 103 LEU cc_start: 0.8262 (mm) cc_final: 0.7988 (mt) REVERT: D 123 GLN cc_start: 0.7926 (tp40) cc_final: 0.7266 (tp40) REVERT: D 124 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7567 (ttp80) REVERT: D 128 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8352 (mtpp) REVERT: D 131 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7946 (ttm110) REVERT: D 144 MET cc_start: 0.7292 (mmm) cc_final: 0.6988 (mmm) REVERT: C 135 GLU cc_start: 0.8169 (pt0) cc_final: 0.7762 (pp20) REVERT: C 144 GLU cc_start: 0.7378 (pm20) cc_final: 0.7133 (pm20) REVERT: C 151 ARG cc_start: 0.6969 (ptm160) cc_final: 0.6713 (mtm110) REVERT: C 239 ILE cc_start: 0.8755 (mm) cc_final: 0.8450 (mm) REVERT: C 241 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: C 243 TYR cc_start: 0.8033 (m-80) cc_final: 0.7532 (m-80) REVERT: C 245 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7419 (mmm-85) REVERT: C 268 GLU cc_start: 0.8085 (tt0) cc_final: 0.7618 (pt0) REVERT: C 283 TYR cc_start: 0.8011 (t80) cc_final: 0.7613 (t80) REVERT: C 289 ILE cc_start: 0.8541 (mm) cc_final: 0.8225 (mm) REVERT: C 310 CYS cc_start: 0.7867 (m) cc_final: 0.7394 (m) REVERT: C 315 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8146 (mmmt) REVERT: C 323 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8311 (ptmt) REVERT: C 327 LEU cc_start: 0.8160 (mt) cc_final: 0.7903 (mt) REVERT: C 328 TRP cc_start: 0.8356 (m-10) cc_final: 0.8151 (m-10) REVERT: C 336 ILE cc_start: 0.8176 (mm) cc_final: 0.7974 (mm) REVERT: C 338 ARG cc_start: 0.7786 (tpp-160) cc_final: 0.7200 (tpt170) REVERT: C 352 ILE cc_start: 0.8872 (mm) cc_final: 0.8665 (pt) REVERT: C 359 ARG cc_start: 0.7706 (mmp-170) cc_final: 0.7197 (mmp80) REVERT: C 383 VAL cc_start: 0.8530 (t) cc_final: 0.8253 (p) REVERT: C 394 GLU cc_start: 0.7165 (tp30) cc_final: 0.5829 (tp30) REVERT: C 403 GLU cc_start: 0.7690 (pm20) cc_final: 0.7314 (pm20) REVERT: C 406 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 407 LEU cc_start: 0.8967 (mt) cc_final: 0.8661 (mt) REVERT: C 411 GLU cc_start: 0.7943 (tt0) cc_final: 0.7651 (tt0) REVERT: C 426 ASP cc_start: 0.8338 (t0) cc_final: 0.8131 (t0) REVERT: C 428 LEU cc_start: 0.8764 (tp) cc_final: 0.8446 (tp) REVERT: C 452 GLU cc_start: 0.7377 (mp0) cc_final: 0.6920 (mp0) REVERT: C 470 GLU cc_start: 0.7505 (tt0) cc_final: 0.7248 (tt0) REVERT: C 501 MET cc_start: 0.6947 (mtm) cc_final: 0.6645 (mtt) REVERT: C 504 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7129 (mm-30) REVERT: C 507 ILE cc_start: 0.8266 (mt) cc_final: 0.8049 (tp) REVERT: C 539 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7407 (tpt-90) REVERT: C 540 LEU cc_start: 0.8504 (mt) cc_final: 0.8215 (mm) REVERT: C 541 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7554 (tp30) REVERT: C 550 ASP cc_start: 0.7777 (t70) cc_final: 0.7387 (t70) REVERT: C 558 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6060 (tm-30) REVERT: C 566 ASP cc_start: 0.6601 (t0) cc_final: 0.6176 (t0) REVERT: C 580 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7382 (mt-10) REVERT: C 582 ILE cc_start: 0.7916 (mt) cc_final: 0.7716 (pt) REVERT: C 609 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7002 (mp0) REVERT: C 611 GLN cc_start: 0.7991 (mp10) cc_final: 0.7393 (mp10) REVERT: C 644 LYS cc_start: 0.8183 (tppt) cc_final: 0.7806 (tppt) REVERT: C 645 LYS cc_start: 0.8329 (mttt) cc_final: 0.7665 (mmtt) REVERT: C 647 THR cc_start: 0.7896 (p) cc_final: 0.7622 (t) REVERT: C 664 ASP cc_start: 0.8607 (m-30) cc_final: 0.8071 (m-30) REVERT: C 677 MET cc_start: 0.5634 (mmm) cc_final: 0.5161 (mmm) REVERT: C 710 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8087 (ptp-170) REVERT: C 712 GLU cc_start: 0.7655 (pm20) cc_final: 0.7331 (pm20) REVERT: C 713 PHE cc_start: 0.8603 (t80) cc_final: 0.8166 (t80) REVERT: C 728 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8290 (ttpp) REVERT: C 747 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7912 (tppt) REVERT: C 757 LEU cc_start: 0.8611 (tp) cc_final: 0.7997 (tt) REVERT: C 764 ASN cc_start: 0.8145 (p0) cc_final: 0.7788 (p0) REVERT: C 768 GLN cc_start: 0.7835 (mp10) cc_final: 0.6803 (mp10) REVERT: C 772 GLU cc_start: 0.7386 (mp0) cc_final: 0.6915 (mp0) REVERT: C 792 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 802 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7978 (mtpp) REVERT: C 804 LEU cc_start: 0.8503 (mt) cc_final: 0.8179 (mt) REVERT: C 841 HIS cc_start: 0.8122 (t70) cc_final: 0.7685 (t70) REVERT: C 851 GLU cc_start: 0.6613 (pm20) cc_final: 0.6306 (mp0) REVERT: C 864 LYS cc_start: 0.8563 (tppt) cc_final: 0.8241 (ttmm) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.1431 time to fit residues: 113.1186 Evaluate side-chains 555 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN C 335 GLN C 490 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.101789 restraints weight = 27038.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105428 restraints weight = 13226.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107813 restraints weight = 7781.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109424 restraints weight = 5205.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110423 restraints weight = 3816.009| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13920 Z= 0.141 Angle : 0.585 10.793 18800 Z= 0.292 Chirality : 0.042 0.162 2058 Planarity : 0.004 0.064 2434 Dihedral : 3.629 15.887 1844 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 25.20 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1648 helix: 0.67 (0.18), residues: 864 sheet: -0.93 (0.60), residues: 68 loop : 0.14 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 649 TYR 0.016 0.001 TYR A 494 PHE 0.023 0.002 PHE C 256 TRP 0.010 0.001 TRP C 791 HIS 0.004 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00299 (13904) covalent geometry : angle 0.57555 (18776) hydrogen bonds : bond 0.03987 ( 618) hydrogen bonds : angle 4.68084 ( 1752) metal coordination : bond 0.00680 ( 16) metal coordination : angle 3.00735 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 576 time to evaluate : 0.314 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: B 17 ARG cc_start: 0.7244 (mmt180) cc_final: 0.7020 (mmt180) REVERT: B 26 LEU cc_start: 0.8529 (mp) cc_final: 0.8263 (mp) REVERT: B 39 TYR cc_start: 0.8085 (m-80) cc_final: 0.7414 (m-80) REVERT: B 41 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7805 (mmtt) REVERT: B 44 LEU cc_start: 0.8722 (mp) cc_final: 0.8506 (mp) REVERT: B 77 TYR cc_start: 0.8216 (m-80) cc_final: 0.7876 (m-80) REVERT: B 85 HIS cc_start: 0.8706 (m90) cc_final: 0.8476 (m-70) REVERT: B 91 TYR cc_start: 0.8745 (m-10) cc_final: 0.8272 (m-10) REVERT: B 94 THR cc_start: 0.8521 (m) cc_final: 0.8273 (p) REVERT: B 96 GLU cc_start: 0.7790 (tp30) cc_final: 0.7473 (tp30) REVERT: B 97 GLN cc_start: 0.8003 (tp40) cc_final: 0.7617 (tp40) REVERT: B 98 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 118 SER cc_start: 0.8382 (m) cc_final: 0.7839 (t) REVERT: B 131 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7993 (mtt90) REVERT: A 128 LEU cc_start: 0.8148 (mp) cc_final: 0.7778 (mp) REVERT: A 135 GLU cc_start: 0.7643 (pt0) cc_final: 0.7432 (pp20) REVERT: A 151 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6783 (ptm160) REVERT: A 243 TYR cc_start: 0.7855 (m-80) cc_final: 0.7421 (m-80) REVERT: A 268 GLU cc_start: 0.8390 (tt0) cc_final: 0.7904 (tm-30) REVERT: A 276 VAL cc_start: 0.8452 (m) cc_final: 0.8177 (m) REVERT: A 306 LEU cc_start: 0.7867 (tp) cc_final: 0.7458 (tp) REVERT: A 310 CYS cc_start: 0.8188 (m) cc_final: 0.7778 (m) REVERT: A 315 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8074 (mmmm) REVERT: A 327 LEU cc_start: 0.8179 (mt) cc_final: 0.7898 (mt) REVERT: A 328 TRP cc_start: 0.8531 (m-10) cc_final: 0.8230 (m-10) REVERT: A 338 ARG cc_start: 0.7894 (tpp-160) cc_final: 0.7367 (mmm160) REVERT: A 340 MET cc_start: 0.7816 (tmm) cc_final: 0.7278 (tmm) REVERT: A 341 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7173 (pt0) REVERT: A 378 VAL cc_start: 0.8741 (t) cc_final: 0.8519 (p) REVERT: A 383 VAL cc_start: 0.8593 (t) cc_final: 0.8278 (p) REVERT: A 387 GLU cc_start: 0.6901 (pm20) cc_final: 0.5810 (mp0) REVERT: A 394 GLU cc_start: 0.7290 (tp30) cc_final: 0.7031 (tp30) REVERT: A 397 ASP cc_start: 0.6718 (p0) cc_final: 0.6154 (p0) REVERT: A 405 SER cc_start: 0.8298 (m) cc_final: 0.7601 (p) REVERT: A 406 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 407 LEU cc_start: 0.8788 (mt) cc_final: 0.8485 (mt) REVERT: A 410 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7053 (tm-30) REVERT: A 435 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8036 (tptp) REVERT: A 459 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6571 (mm-30) REVERT: A 462 LYS cc_start: 0.7860 (mttm) cc_final: 0.7549 (mtmm) REVERT: A 470 GLU cc_start: 0.7933 (tt0) cc_final: 0.7533 (tt0) REVERT: A 504 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 515 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 529 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8173 (ttm-80) REVERT: A 533 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7065 (pt) REVERT: A 541 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7454 (tp30) REVERT: A 577 LEU cc_start: 0.8112 (mm) cc_final: 0.7569 (mm) REVERT: A 580 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7516 (mp0) REVERT: A 581 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 609 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 611 GLN cc_start: 0.7996 (mp10) cc_final: 0.7399 (mp10) REVERT: A 612 PHE cc_start: 0.8563 (m-80) cc_final: 0.8100 (m-10) REVERT: A 644 LYS cc_start: 0.8328 (tppt) cc_final: 0.7687 (tppt) REVERT: A 677 MET cc_start: 0.5385 (mmm) cc_final: 0.5096 (mmm) REVERT: A 713 PHE cc_start: 0.8502 (t80) cc_final: 0.8018 (t80) REVERT: A 717 TYR cc_start: 0.8109 (t80) cc_final: 0.7607 (t80) REVERT: A 738 HIS cc_start: 0.7249 (t70) cc_final: 0.6982 (t70) REVERT: A 747 LYS cc_start: 0.8474 (mmmm) cc_final: 0.7925 (tptt) REVERT: A 754 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 757 LEU cc_start: 0.8719 (tp) cc_final: 0.8443 (tt) REVERT: A 764 ASN cc_start: 0.8170 (p0) cc_final: 0.7917 (p0) REVERT: A 768 GLN cc_start: 0.7772 (mp10) cc_final: 0.7297 (mp10) REVERT: A 772 GLU cc_start: 0.7587 (mp0) cc_final: 0.7032 (mp0) REVERT: A 800 GLU cc_start: 0.7650 (tp30) cc_final: 0.6900 (tp30) REVERT: A 802 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8100 (mtpp) REVERT: A 804 LEU cc_start: 0.8309 (mt) cc_final: 0.7749 (mp) REVERT: A 841 HIS cc_start: 0.7923 (t70) cc_final: 0.7150 (t70) REVERT: A 863 LEU cc_start: 0.8477 (mp) cc_final: 0.8102 (pp) REVERT: A 864 LYS cc_start: 0.8708 (tppt) cc_final: 0.8175 (ttmm) REVERT: D 17 ARG cc_start: 0.7178 (mmt180) cc_final: 0.6711 (mmt180) REVERT: D 22 LEU cc_start: 0.7810 (tp) cc_final: 0.7528 (tp) REVERT: D 25 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7807 (mp0) REVERT: D 26 LEU cc_start: 0.8435 (mp) cc_final: 0.8065 (mp) REVERT: D 41 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7842 (mmtt) REVERT: D 46 ARG cc_start: 0.7671 (mmp-170) cc_final: 0.7461 (mmp-170) REVERT: D 52 PHE cc_start: 0.8976 (t80) cc_final: 0.8666 (t80) REVERT: D 62 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7545 (tpp80) REVERT: D 77 TYR cc_start: 0.8137 (m-80) cc_final: 0.7739 (m-80) REVERT: D 84 ARG cc_start: 0.8134 (ttm170) cc_final: 0.7820 (ttm170) REVERT: D 85 HIS cc_start: 0.8723 (m-70) cc_final: 0.8468 (m-70) REVERT: D 91 TYR cc_start: 0.8717 (m-10) cc_final: 0.8266 (m-10) REVERT: D 94 THR cc_start: 0.8471 (m) cc_final: 0.8223 (p) REVERT: D 96 GLU cc_start: 0.7868 (tp30) cc_final: 0.7607 (tp30) REVERT: D 98 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8078 (tm-30) REVERT: D 101 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8478 (mtmm) REVERT: D 121 GLU cc_start: 0.8190 (mp0) cc_final: 0.7673 (mp0) REVERT: D 124 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7864 (ttp80) REVERT: D 131 ARG cc_start: 0.8283 (ttm110) cc_final: 0.7959 (ttm110) REVERT: C 128 LEU cc_start: 0.8136 (mp) cc_final: 0.7746 (mm) REVERT: C 144 GLU cc_start: 0.7254 (pm20) cc_final: 0.6960 (pm20) REVERT: C 151 ARG cc_start: 0.7020 (ptm160) cc_final: 0.6755 (mtm110) REVERT: C 239 ILE cc_start: 0.8775 (mm) cc_final: 0.8517 (mm) REVERT: C 241 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7865 (mtm-85) REVERT: C 243 TYR cc_start: 0.7927 (m-80) cc_final: 0.7529 (m-80) REVERT: C 245 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7364 (mmm-85) REVERT: C 268 GLU cc_start: 0.8271 (tt0) cc_final: 0.7649 (tm-30) REVERT: C 283 TYR cc_start: 0.7900 (t80) cc_final: 0.7597 (t80) REVERT: C 289 ILE cc_start: 0.8610 (mm) cc_final: 0.8275 (mm) REVERT: C 310 CYS cc_start: 0.8204 (m) cc_final: 0.7749 (m) REVERT: C 311 LYS cc_start: 0.8481 (mttt) cc_final: 0.8201 (mttt) REVERT: C 315 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8108 (mmmm) REVERT: C 323 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8476 (ptmt) REVERT: C 327 LEU cc_start: 0.8351 (mt) cc_final: 0.8013 (mt) REVERT: C 328 TRP cc_start: 0.8547 (m-10) cc_final: 0.8256 (m-10) REVERT: C 336 ILE cc_start: 0.8457 (mm) cc_final: 0.8237 (mm) REVERT: C 338 ARG cc_start: 0.7981 (tpp-160) cc_final: 0.7507 (tpp-160) REVERT: C 345 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7993 (mm110) REVERT: C 359 ARG cc_start: 0.7734 (mmp-170) cc_final: 0.7312 (mmp80) REVERT: C 378 VAL cc_start: 0.8719 (t) cc_final: 0.8502 (p) REVERT: C 383 VAL cc_start: 0.8641 (t) cc_final: 0.8381 (p) REVERT: C 387 GLU cc_start: 0.7212 (pm20) cc_final: 0.6102 (mp0) REVERT: C 395 GLU cc_start: 0.7996 (pp20) cc_final: 0.7658 (pp20) REVERT: C 403 GLU cc_start: 0.7623 (pm20) cc_final: 0.7377 (pm20) REVERT: C 405 SER cc_start: 0.8435 (m) cc_final: 0.7684 (p) REVERT: C 406 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 407 LEU cc_start: 0.8813 (mt) cc_final: 0.8502 (mt) REVERT: C 410 GLN cc_start: 0.7377 (tm-30) cc_final: 0.6856 (tm-30) REVERT: C 411 GLU cc_start: 0.8155 (tt0) cc_final: 0.7886 (tm-30) REVERT: C 426 ASP cc_start: 0.8393 (t0) cc_final: 0.8037 (t0) REVERT: C 428 LEU cc_start: 0.8815 (tp) cc_final: 0.8452 (tp) REVERT: C 452 GLU cc_start: 0.7640 (mp0) cc_final: 0.7100 (mp0) REVERT: C 459 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6519 (mm-30) REVERT: C 470 GLU cc_start: 0.7846 (tt0) cc_final: 0.7454 (tt0) REVERT: C 474 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7913 (mmmt) REVERT: C 490 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7834 (t0) REVERT: C 504 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7361 (mm-30) REVERT: C 507 ILE cc_start: 0.8377 (mt) cc_final: 0.8146 (tp) REVERT: C 515 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7673 (tt0) REVERT: C 518 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6890 (tm-30) REVERT: C 541 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7802 (tp30) REVERT: C 550 ASP cc_start: 0.7979 (t70) cc_final: 0.7656 (t70) REVERT: C 552 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7738 (mmtm) REVERT: C 558 GLU cc_start: 0.6697 (tm-30) cc_final: 0.5980 (tm-30) REVERT: C 577 LEU cc_start: 0.8194 (mm) cc_final: 0.7581 (mm) REVERT: C 580 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 581 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7191 (mt-10) REVERT: C 582 ILE cc_start: 0.8258 (mt) cc_final: 0.7871 (pt) REVERT: C 587 ILE cc_start: 0.8625 (mm) cc_final: 0.8292 (tp) REVERT: C 594 GLU cc_start: 0.7140 (mp0) cc_final: 0.6781 (mp0) REVERT: C 609 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7194 (mp0) REVERT: C 611 GLN cc_start: 0.8086 (mp10) cc_final: 0.7460 (mp10) REVERT: C 612 PHE cc_start: 0.8613 (m-80) cc_final: 0.8176 (m-10) REVERT: C 644 LYS cc_start: 0.8300 (tppt) cc_final: 0.7633 (tppt) REVERT: C 660 GLN cc_start: 0.8650 (pp30) cc_final: 0.8374 (pp30) REVERT: C 677 MET cc_start: 0.5284 (mmm) cc_final: 0.4952 (mmm) REVERT: C 710 ARG cc_start: 0.8330 (ttp-170) cc_final: 0.8104 (ptp-170) REVERT: C 711 LYS cc_start: 0.8848 (mppt) cc_final: 0.8566 (mppt) REVERT: C 712 GLU cc_start: 0.7864 (pm20) cc_final: 0.7507 (pm20) REVERT: C 713 PHE cc_start: 0.8609 (t80) cc_final: 0.8156 (t80) REVERT: C 735 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7876 (ttp80) REVERT: C 738 HIS cc_start: 0.7500 (t70) cc_final: 0.7269 (t70) REVERT: C 747 LYS cc_start: 0.8483 (mmmm) cc_final: 0.7867 (tppt) REVERT: C 757 LEU cc_start: 0.8591 (tp) cc_final: 0.8279 (tt) REVERT: C 764 ASN cc_start: 0.8179 (p0) cc_final: 0.7909 (p0) REVERT: C 768 GLN cc_start: 0.7952 (mp10) cc_final: 0.6939 (mp10) REVERT: C 772 GLU cc_start: 0.7681 (mp0) cc_final: 0.7140 (mp0) REVERT: C 792 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 802 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8073 (mtpt) REVERT: C 804 LEU cc_start: 0.8460 (mt) cc_final: 0.8055 (mt) REVERT: C 841 HIS cc_start: 0.7878 (t70) cc_final: 0.7194 (t70) REVERT: C 851 GLU cc_start: 0.6726 (pm20) cc_final: 0.6372 (mp0) REVERT: C 864 LYS cc_start: 0.8709 (tppt) cc_final: 0.8353 (ttmm) outliers start: 30 outliers final: 10 residues processed: 589 average time/residue: 0.1356 time to fit residues: 105.6757 Evaluate side-chains 563 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 551 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 746 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 75 optimal weight: 0.0980 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 295 ASN A 335 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 684 GLN A 801 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 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 = 0.3693 r_free = 0.3693 target = 0.122117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104573 restraints weight = 27154.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108229 restraints weight = 13210.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110643 restraints weight = 7781.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112233 restraints weight = 5204.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113329 restraints weight = 3837.026| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13920 Z= 0.124 Angle : 0.560 8.985 18800 Z= 0.280 Chirality : 0.041 0.204 2058 Planarity : 0.004 0.055 2434 Dihedral : 3.611 15.838 1844 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.83 % Allowed : 27.24 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.21), residues: 1648 helix: 0.57 (0.18), residues: 872 sheet: -1.16 (0.60), residues: 68 loop : 0.07 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 735 TYR 0.013 0.001 TYR A 494 PHE 0.019 0.002 PHE A 737 TRP 0.011 0.001 TRP A 791 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00267 (13904) covalent geometry : angle 0.54930 (18776) hydrogen bonds : bond 0.03797 ( 618) hydrogen bonds : angle 4.53176 ( 1752) metal coordination : bond 0.00487 ( 16) metal coordination : angle 3.04834 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 552 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ARG cc_start: 0.7383 (mmt180) cc_final: 0.7124 (mmt180) REVERT: B 22 LEU cc_start: 0.7835 (tp) cc_final: 0.7550 (tp) REVERT: B 26 LEU cc_start: 0.8562 (mp) cc_final: 0.8224 (mp) REVERT: B 41 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7836 (mmtt) REVERT: B 44 LEU cc_start: 0.8706 (mp) cc_final: 0.8473 (mp) REVERT: B 76 PHE cc_start: 0.8309 (t80) cc_final: 0.8017 (t80) REVERT: B 77 TYR cc_start: 0.8140 (m-80) cc_final: 0.7723 (m-80) REVERT: B 85 HIS cc_start: 0.8721 (m90) cc_final: 0.8484 (m-70) REVERT: B 91 TYR cc_start: 0.8728 (m-10) cc_final: 0.8311 (m-10) REVERT: B 94 THR cc_start: 0.8475 (m) cc_final: 0.8185 (p) REVERT: B 96 GLU cc_start: 0.7771 (tp30) cc_final: 0.7407 (tp30) REVERT: B 97 GLN cc_start: 0.7984 (tp40) cc_final: 0.7579 (tp40) REVERT: B 118 SER cc_start: 0.8246 (m) cc_final: 0.7931 (p) REVERT: B 121 GLU cc_start: 0.8428 (mp0) cc_final: 0.8159 (mp0) REVERT: B 128 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8590 (mmmm) REVERT: B 131 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7997 (mtt90) REVERT: B 143 CYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7337 (p) REVERT: A 128 LEU cc_start: 0.8200 (mp) cc_final: 0.7931 (mp) REVERT: A 130 GLU cc_start: 0.7453 (pm20) cc_final: 0.7179 (pp20) REVERT: A 135 GLU cc_start: 0.7644 (pt0) cc_final: 0.7390 (pp20) REVERT: A 243 TYR cc_start: 0.7806 (m-80) cc_final: 0.7479 (m-80) REVERT: A 264 SER cc_start: 0.8339 (m) cc_final: 0.8014 (p) REVERT: A 268 GLU cc_start: 0.8434 (tt0) cc_final: 0.7897 (tm-30) REVERT: A 295 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8237 (m110) REVERT: A 306 LEU cc_start: 0.7906 (tp) cc_final: 0.7420 (tp) REVERT: A 310 CYS cc_start: 0.8269 (m) cc_final: 0.7735 (m) REVERT: A 315 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8052 (mmmm) REVERT: A 327 LEU cc_start: 0.8143 (mt) cc_final: 0.7854 (mt) REVERT: A 338 ARG cc_start: 0.7843 (tpp-160) cc_final: 0.7506 (tpt90) REVERT: A 340 MET cc_start: 0.7868 (tmm) cc_final: 0.7269 (tmm) REVERT: A 341 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7099 (pt0) REVERT: A 359 ARG cc_start: 0.7704 (mmp-170) cc_final: 0.7348 (mmp80) REVERT: A 378 VAL cc_start: 0.8725 (t) cc_final: 0.8501 (p) REVERT: A 383 VAL cc_start: 0.8552 (t) cc_final: 0.8233 (p) REVERT: A 387 GLU cc_start: 0.6792 (pm20) cc_final: 0.6025 (mp0) REVERT: A 394 GLU cc_start: 0.7220 (tp30) cc_final: 0.6766 (tp30) REVERT: A 397 ASP cc_start: 0.6611 (p0) cc_final: 0.6121 (p0) REVERT: A 406 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 407 LEU cc_start: 0.8777 (mt) cc_final: 0.8416 (mt) REVERT: A 410 GLN cc_start: 0.7476 (mm-40) cc_final: 0.6963 (tm-30) REVERT: A 411 GLU cc_start: 0.8158 (tt0) cc_final: 0.7572 (tm-30) REVERT: A 435 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7991 (tptp) REVERT: A 440 ARG cc_start: 0.7163 (ttt90) cc_final: 0.6262 (ttt180) REVERT: A 452 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7393 (mp0) REVERT: A 459 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 462 LYS cc_start: 0.7915 (mttm) cc_final: 0.7660 (mtmm) REVERT: A 470 GLU cc_start: 0.7947 (tt0) cc_final: 0.7601 (tt0) REVERT: A 474 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8288 (mmmm) REVERT: A 490 ASN cc_start: 0.7879 (t0) cc_final: 0.7644 (t0) REVERT: A 504 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 533 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7163 (pt) REVERT: A 541 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7468 (tp30) REVERT: A 550 ASP cc_start: 0.7962 (m-30) cc_final: 0.7701 (m-30) REVERT: A 577 LEU cc_start: 0.8066 (mm) cc_final: 0.7461 (mm) REVERT: A 580 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 581 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7064 (mt-10) REVERT: A 587 ILE cc_start: 0.8438 (mm) cc_final: 0.8146 (tp) REVERT: A 589 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6825 (ttp) REVERT: A 609 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7271 (mp0) REVERT: A 611 GLN cc_start: 0.7962 (mp10) cc_final: 0.7377 (mp10) REVERT: A 612 PHE cc_start: 0.8542 (m-80) cc_final: 0.8045 (m-10) REVERT: A 644 LYS cc_start: 0.8328 (tppt) cc_final: 0.7713 (tppt) REVERT: A 645 LYS cc_start: 0.8179 (mttt) cc_final: 0.7218 (mtpp) REVERT: A 649 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7842 (mtp180) REVERT: A 660 GLN cc_start: 0.8494 (pp30) cc_final: 0.8126 (pp30) REVERT: A 663 LYS cc_start: 0.8664 (pttp) cc_final: 0.8317 (pptt) REVERT: A 664 ASP cc_start: 0.8390 (m-30) cc_final: 0.7940 (m-30) REVERT: A 710 ARG cc_start: 0.8431 (ptm160) cc_final: 0.7677 (ptt180) REVERT: A 711 LYS cc_start: 0.8840 (mppt) cc_final: 0.8414 (mmtm) REVERT: A 713 PHE cc_start: 0.8536 (t80) cc_final: 0.8036 (t80) REVERT: A 717 TYR cc_start: 0.8178 (t80) cc_final: 0.7805 (t80) REVERT: A 738 HIS cc_start: 0.7278 (t70) cc_final: 0.6973 (t70) REVERT: A 747 LYS cc_start: 0.8507 (mmmm) cc_final: 0.7938 (tptt) REVERT: A 754 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7394 (mp0) REVERT: A 757 LEU cc_start: 0.8716 (tp) cc_final: 0.8456 (tt) REVERT: A 763 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7112 (ttp80) REVERT: A 764 ASN cc_start: 0.8185 (p0) cc_final: 0.7925 (p0) REVERT: A 768 GLN cc_start: 0.7791 (mp10) cc_final: 0.6827 (mp10) REVERT: A 772 GLU cc_start: 0.7627 (mp0) cc_final: 0.7058 (mp0) REVERT: A 798 THR cc_start: 0.8218 (m) cc_final: 0.7991 (p) REVERT: A 800 GLU cc_start: 0.7644 (tp30) cc_final: 0.6950 (tp30) REVERT: A 802 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8022 (mtpp) REVERT: A 804 LEU cc_start: 0.8307 (mt) cc_final: 0.7721 (mp) REVERT: A 836 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7739 (mtt90) REVERT: A 841 HIS cc_start: 0.7878 (t70) cc_final: 0.7168 (t70) REVERT: A 863 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8088 (pp) REVERT: A 864 LYS cc_start: 0.8694 (tppt) cc_final: 0.8160 (ttmm) REVERT: D 17 ARG cc_start: 0.7249 (mmt180) cc_final: 0.6794 (mmt180) REVERT: D 22 LEU cc_start: 0.7801 (tp) cc_final: 0.7496 (tp) REVERT: D 25 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7850 (mp0) REVERT: D 26 LEU cc_start: 0.8487 (mp) cc_final: 0.8101 (mp) REVERT: D 41 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7916 (mmtt) REVERT: D 52 PHE cc_start: 0.8964 (t80) cc_final: 0.8630 (t80) REVERT: D 57 LEU cc_start: 0.8553 (mt) cc_final: 0.8348 (mp) REVERT: D 62 ARG cc_start: 0.7834 (tpp80) cc_final: 0.7518 (tpp80) REVERT: D 77 TYR cc_start: 0.8016 (m-80) cc_final: 0.7734 (m-80) REVERT: D 84 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7801 (ttm170) REVERT: D 91 TYR cc_start: 0.8727 (m-10) cc_final: 0.8217 (m-10) REVERT: D 94 THR cc_start: 0.8430 (m) cc_final: 0.8165 (p) REVERT: D 95 LEU cc_start: 0.8978 (tp) cc_final: 0.8774 (tp) REVERT: D 96 GLU cc_start: 0.7846 (tp30) cc_final: 0.7567 (tp30) REVERT: D 121 GLU cc_start: 0.8208 (mp0) cc_final: 0.7705 (mp0) REVERT: D 124 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7899 (ttp80) REVERT: D 128 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8546 (mtpp) REVERT: D 131 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7937 (ttm110) REVERT: D 143 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7257 (p) REVERT: C 128 LEU cc_start: 0.8205 (mp) cc_final: 0.7752 (mm) REVERT: C 151 ARG cc_start: 0.6988 (ptm160) cc_final: 0.6754 (mtm110) REVERT: C 239 ILE cc_start: 0.8820 (mm) cc_final: 0.8601 (mm) REVERT: C 243 TYR cc_start: 0.7987 (m-80) cc_final: 0.7550 (m-80) REVERT: C 245 ARG cc_start: 0.7848 (tpp80) cc_final: 0.7492 (mmm-85) REVERT: C 247 LEU cc_start: 0.8038 (mp) cc_final: 0.7712 (mp) REVERT: C 268 GLU cc_start: 0.8283 (tt0) cc_final: 0.7598 (tm-30) REVERT: C 283 TYR cc_start: 0.7907 (t80) cc_final: 0.7568 (t80) REVERT: C 289 ILE cc_start: 0.8605 (mm) cc_final: 0.8285 (mm) REVERT: C 310 CYS cc_start: 0.8257 (m) cc_final: 0.7791 (m) REVERT: C 311 LYS cc_start: 0.8476 (mttt) cc_final: 0.8206 (mttm) REVERT: C 315 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8095 (mmmm) REVERT: C 323 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8073 (ttmt) REVERT: C 327 LEU cc_start: 0.8372 (mt) cc_final: 0.8126 (mt) REVERT: C 328 TRP cc_start: 0.8511 (m-10) cc_final: 0.8233 (m-10) REVERT: C 336 ILE cc_start: 0.8469 (mm) cc_final: 0.8232 (mm) REVERT: C 338 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7544 (mmm160) REVERT: C 340 MET cc_start: 0.7572 (tmm) cc_final: 0.7110 (tmm) REVERT: C 341 GLU cc_start: 0.7797 (pt0) cc_final: 0.7261 (pt0) REVERT: C 345 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7932 (mm110) REVERT: C 359 ARG cc_start: 0.7738 (mmp-170) cc_final: 0.7327 (mmp80) REVERT: C 378 VAL cc_start: 0.8712 (t) cc_final: 0.8488 (p) REVERT: C 394 GLU cc_start: 0.7463 (tp30) cc_final: 0.6847 (tp30) REVERT: C 403 GLU cc_start: 0.7615 (pm20) cc_final: 0.7310 (pm20) REVERT: C 405 SER cc_start: 0.8339 (m) cc_final: 0.7772 (p) REVERT: C 406 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 407 LEU cc_start: 0.8821 (mt) cc_final: 0.8461 (mt) REVERT: C 410 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6751 (tm-30) REVERT: C 411 GLU cc_start: 0.8230 (tt0) cc_final: 0.7862 (tm-30) REVERT: C 426 ASP cc_start: 0.8407 (t0) cc_final: 0.8125 (t0) REVERT: C 428 LEU cc_start: 0.8815 (tp) cc_final: 0.8437 (tp) REVERT: C 452 GLU cc_start: 0.7722 (mp0) cc_final: 0.7240 (mp0) REVERT: C 459 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6582 (mm-30) REVERT: C 462 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7781 (mtmm) REVERT: C 470 GLU cc_start: 0.7801 (tt0) cc_final: 0.7309 (tt0) REVERT: C 490 ASN cc_start: 0.7874 (t0) cc_final: 0.7665 (t0) REVERT: C 504 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7378 (mm-30) REVERT: C 507 ILE cc_start: 0.8372 (mt) cc_final: 0.8133 (tp) REVERT: C 515 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7668 (tt0) REVERT: C 518 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6875 (tm-30) REVERT: C 539 ARG cc_start: 0.8005 (tpt-90) cc_final: 0.7634 (tpt-90) REVERT: C 541 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7856 (tp30) REVERT: C 550 ASP cc_start: 0.7910 (t70) cc_final: 0.7586 (t70) REVERT: C 552 LYS cc_start: 0.8043 (mmtm) cc_final: 0.7706 (mmtm) REVERT: C 558 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6062 (tm-30) REVERT: C 577 LEU cc_start: 0.8138 (mm) cc_final: 0.7521 (mm) REVERT: C 580 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 581 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7229 (mt-10) REVERT: C 582 ILE cc_start: 0.8318 (mt) cc_final: 0.7847 (pt) REVERT: C 587 ILE cc_start: 0.8612 (mm) cc_final: 0.8351 (tp) REVERT: C 594 GLU cc_start: 0.7154 (mp0) cc_final: 0.6785 (mp0) REVERT: C 609 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7268 (mp0) REVERT: C 611 GLN cc_start: 0.8061 (mp10) cc_final: 0.7493 (mp10) REVERT: C 612 PHE cc_start: 0.8580 (m-80) cc_final: 0.8113 (m-10) REVERT: C 635 MET cc_start: 0.7334 (mmm) cc_final: 0.6395 (mmm) REVERT: C 644 LYS cc_start: 0.8305 (tppt) cc_final: 0.7590 (tppt) REVERT: C 645 LYS cc_start: 0.8257 (mttt) cc_final: 0.7460 (mmtt) REVERT: C 660 GLN cc_start: 0.8594 (pp30) cc_final: 0.8354 (pp30) REVERT: C 677 MET cc_start: 0.5272 (mmm) cc_final: 0.4950 (mmm) REVERT: C 710 ARG cc_start: 0.8315 (ttp-170) cc_final: 0.8090 (ptp-170) REVERT: C 712 GLU cc_start: 0.7880 (pm20) cc_final: 0.7466 (pm20) REVERT: C 713 PHE cc_start: 0.8619 (t80) cc_final: 0.8142 (t80) REVERT: C 735 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7875 (ttp80) REVERT: C 747 LYS cc_start: 0.8495 (mmmm) cc_final: 0.7861 (tppt) REVERT: C 753 GLU cc_start: 0.7957 (mp0) cc_final: 0.7520 (mm-30) REVERT: C 757 LEU cc_start: 0.8600 (tp) cc_final: 0.8320 (tt) REVERT: C 764 ASN cc_start: 0.8177 (p0) cc_final: 0.7903 (p0) REVERT: C 768 GLN cc_start: 0.7966 (mp10) cc_final: 0.6895 (mp10) REVERT: C 772 GLU cc_start: 0.7705 (mp0) cc_final: 0.7146 (mp0) REVERT: C 782 ARG cc_start: 0.7144 (tpt90) cc_final: 0.5841 (tpt90) REVERT: C 788 ARG cc_start: 0.6850 (mmm-85) cc_final: 0.6413 (tpp80) REVERT: C 792 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 802 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8063 (mtpp) REVERT: C 804 LEU cc_start: 0.8446 (mt) cc_final: 0.8078 (mt) REVERT: C 836 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7445 (mtt90) REVERT: C 841 HIS cc_start: 0.7872 (t70) cc_final: 0.7102 (t70) REVERT: C 851 GLU cc_start: 0.6705 (pm20) cc_final: 0.6375 (mp0) REVERT: C 864 LYS cc_start: 0.8709 (tppt) cc_final: 0.8364 (ttmm) outliers start: 43 outliers final: 19 residues processed: 569 average time/residue: 0.1335 time to fit residues: 101.3665 Evaluate side-chains 566 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 540 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.0570 chunk 138 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103404 restraints weight = 27011.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107019 restraints weight = 13135.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109417 restraints weight = 7708.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110944 restraints weight = 5134.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112076 restraints weight = 3786.208| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13920 Z= 0.155 Angle : 0.575 8.889 18800 Z= 0.292 Chirality : 0.042 0.219 2058 Planarity : 0.003 0.038 2434 Dihedral : 3.702 15.906 1844 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.82 % Allowed : 26.97 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.21), residues: 1648 helix: 0.68 (0.18), residues: 848 sheet: -1.21 (0.61), residues: 68 loop : 0.20 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 649 TYR 0.016 0.001 TYR A 273 PHE 0.026 0.002 PHE D 76 TRP 0.011 0.002 TRP C 791 HIS 0.010 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00325 (13904) covalent geometry : angle 0.56341 (18776) hydrogen bonds : bond 0.03863 ( 618) hydrogen bonds : angle 4.57957 ( 1752) metal coordination : bond 0.00659 ( 16) metal coordination : angle 3.32800 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 552 time to evaluate : 0.579 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: B 26 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 41 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7970 (mmtt) REVERT: B 44 LEU cc_start: 0.8825 (mp) cc_final: 0.8565 (mp) REVERT: B 76 PHE cc_start: 0.8302 (t80) cc_final: 0.8064 (t80) REVERT: B 77 TYR cc_start: 0.8055 (m-80) cc_final: 0.7768 (m-80) REVERT: B 85 HIS cc_start: 0.8761 (m90) cc_final: 0.8514 (m-70) REVERT: B 91 TYR cc_start: 0.8766 (m-10) cc_final: 0.8094 (m-10) REVERT: B 94 THR cc_start: 0.8514 (m) cc_final: 0.8294 (p) REVERT: B 96 GLU cc_start: 0.7738 (tp30) cc_final: 0.7371 (tp30) REVERT: B 98 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 118 SER cc_start: 0.8536 (m) cc_final: 0.8051 (p) REVERT: B 121 GLU cc_start: 0.8391 (mp0) cc_final: 0.8134 (mp0) REVERT: B 128 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8624 (mmmm) REVERT: B 131 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7657 (ttm110) REVERT: B 143 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7437 (p) REVERT: A 128 LEU cc_start: 0.8268 (mp) cc_final: 0.7853 (mm) REVERT: A 130 GLU cc_start: 0.7495 (pm20) cc_final: 0.7220 (pp20) REVERT: A 135 GLU cc_start: 0.7665 (pt0) cc_final: 0.7386 (pp20) REVERT: A 241 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7664 (mpp80) REVERT: A 243 TYR cc_start: 0.7811 (m-80) cc_final: 0.7182 (m-80) REVERT: A 247 LEU cc_start: 0.8111 (mp) cc_final: 0.7605 (tt) REVERT: A 264 SER cc_start: 0.8429 (m) cc_final: 0.8162 (p) REVERT: A 267 VAL cc_start: 0.8956 (t) cc_final: 0.8724 (p) REVERT: A 268 GLU cc_start: 0.8402 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 273 TYR cc_start: 0.8002 (m-80) cc_final: 0.7790 (m-80) REVERT: A 306 LEU cc_start: 0.7856 (tp) cc_final: 0.7421 (tp) REVERT: A 310 CYS cc_start: 0.8269 (m) cc_final: 0.7759 (m) REVERT: A 311 LYS cc_start: 0.8487 (mttt) cc_final: 0.8265 (mptt) REVERT: A 315 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8124 (mmmm) REVERT: A 327 LEU cc_start: 0.8124 (mt) cc_final: 0.7834 (mt) REVERT: A 336 ILE cc_start: 0.8406 (mm) cc_final: 0.8201 (mm) REVERT: A 338 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7507 (tpt90) REVERT: A 340 MET cc_start: 0.7996 (tmm) cc_final: 0.7343 (tmm) REVERT: A 341 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7119 (pt0) REVERT: A 342 THR cc_start: 0.8772 (m) cc_final: 0.8554 (m) REVERT: A 359 ARG cc_start: 0.7672 (mmp-170) cc_final: 0.7328 (mmp80) REVERT: A 387 GLU cc_start: 0.6843 (pm20) cc_final: 0.6017 (mp0) REVERT: A 394 GLU cc_start: 0.7286 (tp30) cc_final: 0.6386 (tp30) REVERT: A 397 ASP cc_start: 0.6678 (p0) cc_final: 0.6235 (p0) REVERT: A 406 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 407 LEU cc_start: 0.8737 (mt) cc_final: 0.8395 (mt) REVERT: A 410 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6901 (tm-30) REVERT: A 411 GLU cc_start: 0.8184 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 435 LYS cc_start: 0.8309 (tmtt) cc_final: 0.8091 (tptp) REVERT: A 452 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7425 (mp0) REVERT: A 459 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6508 (mm-30) REVERT: A 470 GLU cc_start: 0.7883 (tt0) cc_final: 0.7387 (tt0) REVERT: A 533 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 541 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7436 (tp30) REVERT: A 550 ASP cc_start: 0.7941 (m-30) cc_final: 0.7660 (m-30) REVERT: A 577 LEU cc_start: 0.8169 (mm) cc_final: 0.7607 (mm) REVERT: A 580 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 581 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 589 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6864 (ttp) REVERT: A 598 LEU cc_start: 0.8615 (mt) cc_final: 0.8286 (mt) REVERT: A 609 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 611 GLN cc_start: 0.7942 (mp10) cc_final: 0.7341 (mp10) REVERT: A 612 PHE cc_start: 0.8526 (m-80) cc_final: 0.8071 (m-10) REVERT: A 644 LYS cc_start: 0.8412 (tppt) cc_final: 0.7719 (tppt) REVERT: A 645 LYS cc_start: 0.8170 (mttt) cc_final: 0.7376 (mmtt) REVERT: A 660 GLN cc_start: 0.8441 (pp30) cc_final: 0.8063 (pp30) REVERT: A 663 LYS cc_start: 0.8718 (pttp) cc_final: 0.8331 (pptt) REVERT: A 664 ASP cc_start: 0.8336 (m-30) cc_final: 0.7889 (m-30) REVERT: A 665 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 710 ARG cc_start: 0.8417 (ptm160) cc_final: 0.7626 (ptt180) REVERT: A 711 LYS cc_start: 0.8837 (mppt) cc_final: 0.8370 (mmtm) REVERT: A 713 PHE cc_start: 0.8530 (t80) cc_final: 0.8077 (t80) REVERT: A 717 TYR cc_start: 0.8282 (t80) cc_final: 0.7907 (t80) REVERT: A 738 HIS cc_start: 0.7271 (t70) cc_final: 0.6909 (t70) REVERT: A 747 LYS cc_start: 0.8533 (mmmm) cc_final: 0.8035 (tppp) REVERT: A 754 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7370 (mp0) REVERT: A 757 LEU cc_start: 0.8689 (tp) cc_final: 0.8420 (tt) REVERT: A 764 ASN cc_start: 0.8197 (p0) cc_final: 0.7795 (p0) REVERT: A 768 GLN cc_start: 0.7832 (mp10) cc_final: 0.6802 (mp10) REVERT: A 772 GLU cc_start: 0.7677 (mp0) cc_final: 0.7137 (mp0) REVERT: A 798 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7941 (p) REVERT: A 800 GLU cc_start: 0.7693 (tp30) cc_final: 0.7121 (tp30) REVERT: A 802 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8056 (mtpp) REVERT: A 804 LEU cc_start: 0.8267 (mt) cc_final: 0.7792 (mt) REVERT: A 829 LYS cc_start: 0.8407 (tttt) cc_final: 0.8105 (ttpp) REVERT: A 836 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7676 (mtt-85) REVERT: A 841 HIS cc_start: 0.7848 (t70) cc_final: 0.7164 (t70) REVERT: D 17 ARG cc_start: 0.7322 (mmt180) cc_final: 0.6826 (mmt180) REVERT: D 22 LEU cc_start: 0.7815 (tp) cc_final: 0.7471 (tp) REVERT: D 26 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 39 TYR cc_start: 0.7984 (m-80) cc_final: 0.7558 (m-80) REVERT: D 41 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7976 (mmtt) REVERT: D 48 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7426 (mp0) REVERT: D 52 PHE cc_start: 0.8980 (t80) cc_final: 0.8767 (t80) REVERT: D 62 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7537 (tpp80) REVERT: D 77 TYR cc_start: 0.8003 (m-80) cc_final: 0.7627 (m-80) REVERT: D 84 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7860 (ttm170) REVERT: D 91 TYR cc_start: 0.8763 (m-10) cc_final: 0.8201 (m-10) REVERT: D 94 THR cc_start: 0.8494 (m) cc_final: 0.8261 (p) REVERT: D 96 GLU cc_start: 0.7785 (tp30) cc_final: 0.7524 (tp30) REVERT: D 98 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 101 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8472 (mttm) REVERT: D 121 GLU cc_start: 0.8199 (mp0) cc_final: 0.7719 (mp0) REVERT: D 124 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7919 (ttp80) REVERT: D 131 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7958 (ttm110) REVERT: D 143 CYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7245 (p) REVERT: C 128 LEU cc_start: 0.8214 (mp) cc_final: 0.7968 (mp) REVERT: C 151 ARG cc_start: 0.7023 (ptm160) cc_final: 0.6780 (mtm110) REVERT: C 239 ILE cc_start: 0.8850 (mm) cc_final: 0.8596 (mm) REVERT: C 241 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7722 (mtm-85) REVERT: C 243 TYR cc_start: 0.7881 (m-80) cc_final: 0.7532 (m-80) REVERT: C 245 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7508 (mmm-85) REVERT: C 247 LEU cc_start: 0.8076 (mp) cc_final: 0.7735 (mm) REVERT: C 268 GLU cc_start: 0.8315 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 283 TYR cc_start: 0.7885 (t80) cc_final: 0.7564 (t80) REVERT: C 289 ILE cc_start: 0.8639 (mm) cc_final: 0.8312 (mm) REVERT: C 310 CYS cc_start: 0.8305 (m) cc_final: 0.7791 (m) REVERT: C 311 LYS cc_start: 0.8513 (mttt) cc_final: 0.8246 (mttm) REVERT: C 315 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8163 (mmmm) REVERT: C 323 LYS cc_start: 0.8655 (ptmt) cc_final: 0.8000 (tttt) REVERT: C 327 LEU cc_start: 0.8269 (mt) cc_final: 0.8058 (mt) REVERT: C 336 ILE cc_start: 0.8495 (mm) cc_final: 0.8257 (mm) REVERT: C 340 MET cc_start: 0.7690 (tmm) cc_final: 0.7245 (tmm) REVERT: C 341 GLU cc_start: 0.7850 (pt0) cc_final: 0.7363 (pt0) REVERT: C 359 ARG cc_start: 0.7740 (mmp-170) cc_final: 0.7377 (mmp80) REVERT: C 366 ASP cc_start: 0.7700 (p0) cc_final: 0.7435 (p0) REVERT: C 394 GLU cc_start: 0.7522 (tp30) cc_final: 0.7006 (tp30) REVERT: C 403 GLU cc_start: 0.7576 (pm20) cc_final: 0.7283 (pm20) REVERT: C 406 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 407 LEU cc_start: 0.8808 (mt) cc_final: 0.8461 (mt) REVERT: C 410 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6856 (tm-30) REVERT: C 411 GLU cc_start: 0.8221 (tt0) cc_final: 0.7852 (tm-30) REVERT: C 426 ASP cc_start: 0.8381 (t0) cc_final: 0.8091 (t0) REVERT: C 428 LEU cc_start: 0.8807 (tp) cc_final: 0.8419 (tp) REVERT: C 452 GLU cc_start: 0.7741 (mp0) cc_final: 0.7258 (mp0) REVERT: C 462 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7800 (mtmm) REVERT: C 470 GLU cc_start: 0.7837 (tt0) cc_final: 0.7357 (tt0) REVERT: C 474 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8296 (mmmt) REVERT: C 490 ASN cc_start: 0.7917 (t0) cc_final: 0.7715 (t0) REVERT: C 504 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 507 ILE cc_start: 0.8390 (mt) cc_final: 0.8180 (tp) REVERT: C 515 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7638 (tt0) REVERT: C 539 ARG cc_start: 0.7987 (tpt-90) cc_final: 0.7637 (tpt-90) REVERT: C 541 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7794 (tp30) REVERT: C 546 GLU cc_start: 0.7566 (tp30) cc_final: 0.7359 (tp30) REVERT: C 550 ASP cc_start: 0.8015 (t70) cc_final: 0.7604 (t70) REVERT: C 552 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7660 (mmtm) REVERT: C 572 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7540 (mtmm) REVERT: C 577 LEU cc_start: 0.8196 (mm) cc_final: 0.7667 (mm) REVERT: C 580 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 582 ILE cc_start: 0.8409 (mt) cc_final: 0.8023 (pt) REVERT: C 594 GLU cc_start: 0.7225 (mp0) cc_final: 0.6885 (mp0) REVERT: C 609 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7222 (mp0) REVERT: C 611 GLN cc_start: 0.8039 (mp10) cc_final: 0.7425 (mp10) REVERT: C 635 MET cc_start: 0.7468 (mmm) cc_final: 0.6492 (mmm) REVERT: C 644 LYS cc_start: 0.8384 (tppt) cc_final: 0.7619 (tppt) REVERT: C 645 LYS cc_start: 0.8304 (mttt) cc_final: 0.7509 (mmtt) REVERT: C 677 MET cc_start: 0.5311 (mmm) cc_final: 0.5019 (mmm) REVERT: C 712 GLU cc_start: 0.7906 (pm20) cc_final: 0.7490 (pm20) REVERT: C 713 PHE cc_start: 0.8635 (t80) cc_final: 0.8169 (t80) REVERT: C 735 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7817 (ttp80) REVERT: C 747 LYS cc_start: 0.8529 (mmmm) cc_final: 0.7904 (tppt) REVERT: C 757 LEU cc_start: 0.8590 (tp) cc_final: 0.8316 (tt) REVERT: C 763 ARG cc_start: 0.7355 (ptp-110) cc_final: 0.7138 (ptp-110) REVERT: C 764 ASN cc_start: 0.8194 (p0) cc_final: 0.7895 (p0) REVERT: C 768 GLN cc_start: 0.7974 (mp10) cc_final: 0.6932 (mp10) REVERT: C 772 GLU cc_start: 0.7801 (mp0) cc_final: 0.7208 (mp0) REVERT: C 782 ARG cc_start: 0.7158 (tpt90) cc_final: 0.5800 (tpt90) REVERT: C 788 ARG cc_start: 0.6915 (mmm-85) cc_final: 0.6548 (tpp80) REVERT: C 792 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 799 ASP cc_start: 0.7459 (t0) cc_final: 0.7222 (t0) REVERT: C 802 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8161 (mtpp) REVERT: C 804 LEU cc_start: 0.8396 (mt) cc_final: 0.7948 (mt) REVERT: C 836 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7631 (mtt90) REVERT: C 841 HIS cc_start: 0.7853 (t70) cc_final: 0.7180 (t70) REVERT: C 864 LYS cc_start: 0.8750 (tppt) cc_final: 0.8537 (ttmm) outliers start: 58 outliers final: 28 residues processed: 573 average time/residue: 0.1698 time to fit residues: 129.5162 Evaluate side-chains 583 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 545 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 127 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096324 restraints weight = 27463.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099863 restraints weight = 13303.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102143 restraints weight = 7817.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103736 restraints weight = 5260.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104795 restraints weight = 3897.468| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13920 Z= 0.145 Angle : 0.579 9.512 18800 Z= 0.290 Chirality : 0.041 0.141 2058 Planarity : 0.003 0.035 2434 Dihedral : 3.702 15.099 1844 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.42 % Allowed : 28.16 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1648 helix: 0.71 (0.18), residues: 848 sheet: -1.55 (0.57), residues: 72 loop : 0.16 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 763 TYR 0.018 0.001 TYR C 277 PHE 0.021 0.002 PHE C 612 TRP 0.011 0.001 TRP A 791 HIS 0.012 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00308 (13904) covalent geometry : angle 0.56728 (18776) hydrogen bonds : bond 0.03773 ( 618) hydrogen bonds : angle 4.51654 ( 1752) metal coordination : bond 0.00620 ( 16) metal coordination : angle 3.31759 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 560 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6724 (mmt180) REVERT: B 26 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 41 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8055 (mmtt) REVERT: B 44 LEU cc_start: 0.8805 (mp) cc_final: 0.8599 (mp) REVERT: B 77 TYR cc_start: 0.8028 (m-80) cc_final: 0.7733 (m-80) REVERT: B 91 TYR cc_start: 0.8744 (m-10) cc_final: 0.8325 (m-10) REVERT: B 94 THR cc_start: 0.8440 (m) cc_final: 0.8212 (p) REVERT: B 96 GLU cc_start: 0.7642 (tp30) cc_final: 0.7323 (tp30) REVERT: B 98 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7937 (tm-30) REVERT: B 118 SER cc_start: 0.8595 (m) cc_final: 0.8084 (p) REVERT: B 121 GLU cc_start: 0.8336 (mp0) cc_final: 0.7864 (mp0) REVERT: B 124 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7863 (ttp80) REVERT: B 131 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7999 (mtt90) REVERT: B 143 CYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7414 (p) REVERT: A 128 LEU cc_start: 0.8212 (mp) cc_final: 0.7826 (mm) REVERT: A 135 GLU cc_start: 0.7606 (pt0) cc_final: 0.7346 (pp20) REVERT: A 241 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7592 (mpp80) REVERT: A 243 TYR cc_start: 0.7622 (m-80) cc_final: 0.7242 (m-80) REVERT: A 264 SER cc_start: 0.8369 (m) cc_final: 0.8065 (p) REVERT: A 267 VAL cc_start: 0.8978 (t) cc_final: 0.8681 (p) REVERT: A 268 GLU cc_start: 0.8401 (tt0) cc_final: 0.7845 (tm-30) REVERT: A 283 TYR cc_start: 0.8017 (t80) cc_final: 0.7698 (t80) REVERT: A 300 GLU cc_start: 0.8119 (pm20) cc_final: 0.7892 (pm20) REVERT: A 306 LEU cc_start: 0.7891 (tp) cc_final: 0.7334 (tp) REVERT: A 310 CYS cc_start: 0.8224 (m) cc_final: 0.7658 (m) REVERT: A 315 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8081 (mmmm) REVERT: A 327 LEU cc_start: 0.8080 (mt) cc_final: 0.7775 (mt) REVERT: A 336 ILE cc_start: 0.8383 (mm) cc_final: 0.8182 (mm) REVERT: A 338 ARG cc_start: 0.7783 (tpp-160) cc_final: 0.7191 (tpt90) REVERT: A 340 MET cc_start: 0.7983 (tmm) cc_final: 0.7288 (tmm) REVERT: A 341 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7074 (pt0) REVERT: A 359 ARG cc_start: 0.7591 (mmp-170) cc_final: 0.7278 (mmp80) REVERT: A 387 GLU cc_start: 0.6871 (pm20) cc_final: 0.6298 (mp0) REVERT: A 397 ASP cc_start: 0.6571 (p0) cc_final: 0.6082 (p0) REVERT: A 406 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 407 LEU cc_start: 0.8765 (mt) cc_final: 0.8426 (mt) REVERT: A 410 GLN cc_start: 0.7504 (mm-40) cc_final: 0.6947 (tm-30) REVERT: A 411 GLU cc_start: 0.8135 (tt0) cc_final: 0.7482 (tm-30) REVERT: A 435 LYS cc_start: 0.8280 (tmtt) cc_final: 0.8051 (tptp) REVERT: A 447 GLU cc_start: 0.7543 (mp0) cc_final: 0.7149 (mp0) REVERT: A 448 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 452 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7309 (mp0) REVERT: A 459 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6527 (mm-30) REVERT: A 470 GLU cc_start: 0.7818 (tt0) cc_final: 0.7526 (tt0) REVERT: A 490 ASN cc_start: 0.7834 (t0) cc_final: 0.7604 (t0) REVERT: A 533 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7082 (pt) REVERT: A 541 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 550 ASP cc_start: 0.7958 (m-30) cc_final: 0.7657 (m-30) REVERT: A 577 LEU cc_start: 0.8190 (mm) cc_final: 0.7637 (mm) REVERT: A 580 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 581 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7154 (mt-10) REVERT: A 598 LEU cc_start: 0.8621 (mt) cc_final: 0.8312 (mt) REVERT: A 611 GLN cc_start: 0.7896 (mp10) cc_final: 0.7293 (mp10) REVERT: A 645 LYS cc_start: 0.8321 (mttt) cc_final: 0.7513 (mmtt) REVERT: A 649 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: A 660 GLN cc_start: 0.8360 (pp30) cc_final: 0.8001 (pp30) REVERT: A 663 LYS cc_start: 0.8733 (pttp) cc_final: 0.8349 (pptt) REVERT: A 664 ASP cc_start: 0.8238 (m-30) cc_final: 0.7774 (m-30) REVERT: A 665 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 676 MET cc_start: 0.5665 (pmm) cc_final: 0.5121 (pmm) REVERT: A 710 ARG cc_start: 0.8350 (ptm160) cc_final: 0.7583 (ptt180) REVERT: A 711 LYS cc_start: 0.8848 (mppt) cc_final: 0.8375 (mmtm) REVERT: A 713 PHE cc_start: 0.8460 (t80) cc_final: 0.8110 (t80) REVERT: A 717 TYR cc_start: 0.8209 (t80) cc_final: 0.7820 (t80) REVERT: A 738 HIS cc_start: 0.7177 (t70) cc_final: 0.6791 (t70) REVERT: A 747 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8018 (tppp) REVERT: A 754 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7353 (mp0) REVERT: A 757 LEU cc_start: 0.8686 (tp) cc_final: 0.8191 (tt) REVERT: A 764 ASN cc_start: 0.8078 (p0) cc_final: 0.7790 (p0) REVERT: A 768 GLN cc_start: 0.7790 (mp10) cc_final: 0.6804 (mp10) REVERT: A 772 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7084 (mp0) REVERT: A 800 GLU cc_start: 0.7697 (tp30) cc_final: 0.7160 (tp30) REVERT: A 802 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8128 (mtpp) REVERT: A 804 LEU cc_start: 0.8330 (mt) cc_final: 0.7856 (mt) REVERT: A 829 LYS cc_start: 0.8417 (tttt) cc_final: 0.8106 (ttpp) REVERT: A 836 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7562 (mtt-85) REVERT: D 15 ARG cc_start: 0.7398 (mtp85) cc_final: 0.7149 (mtp85) REVERT: D 17 ARG cc_start: 0.7301 (mmt180) cc_final: 0.6856 (mmt180) REVERT: D 22 LEU cc_start: 0.7816 (tp) cc_final: 0.7455 (tp) REVERT: D 25 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 26 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8138 (mp) REVERT: D 39 TYR cc_start: 0.8125 (m-80) cc_final: 0.7622 (m-80) REVERT: D 41 LYS cc_start: 0.8276 (mmtt) cc_final: 0.8044 (mmtt) REVERT: D 48 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7323 (mp0) REVERT: D 62 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7525 (tpp80) REVERT: D 77 TYR cc_start: 0.8038 (m-80) cc_final: 0.7626 (m-80) REVERT: D 91 TYR cc_start: 0.8713 (m-10) cc_final: 0.8277 (m-10) REVERT: D 98 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7972 (tm-30) REVERT: D 101 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8452 (mttm) REVERT: D 103 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8434 (tt) REVERT: D 121 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: D 124 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7870 (ttp80) REVERT: D 131 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8029 (ttm110) REVERT: D 143 CYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7457 (p) REVERT: C 128 LEU cc_start: 0.8177 (mp) cc_final: 0.7917 (mp) REVERT: C 151 ARG cc_start: 0.6950 (ptm160) cc_final: 0.6749 (mtm110) REVERT: C 161 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7780 (pm20) REVERT: C 239 ILE cc_start: 0.8789 (mm) cc_final: 0.8562 (mm) REVERT: C 241 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7845 (mtm-85) REVERT: C 243 TYR cc_start: 0.7759 (m-80) cc_final: 0.7389 (m-80) REVERT: C 245 ARG cc_start: 0.7812 (tpp80) cc_final: 0.7473 (mmm-85) REVERT: C 247 LEU cc_start: 0.7964 (mp) cc_final: 0.7643 (mm) REVERT: C 268 GLU cc_start: 0.8271 (tt0) cc_final: 0.7722 (tm-30) REVERT: C 283 TYR cc_start: 0.7911 (t80) cc_final: 0.7562 (t80) REVERT: C 289 ILE cc_start: 0.8550 (mm) cc_final: 0.8244 (mm) REVERT: C 291 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6886 (tmm) REVERT: C 310 CYS cc_start: 0.8301 (m) cc_final: 0.7826 (m) REVERT: C 311 LYS cc_start: 0.8506 (mttt) cc_final: 0.8239 (mttm) REVERT: C 315 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8154 (mmmm) REVERT: C 323 LYS cc_start: 0.8624 (ptmt) cc_final: 0.7930 (tttt) REVERT: C 327 LEU cc_start: 0.8200 (mt) cc_final: 0.7986 (mt) REVERT: C 336 ILE cc_start: 0.8465 (mm) cc_final: 0.8233 (mm) REVERT: C 338 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7641 (tpp-160) REVERT: C 340 MET cc_start: 0.7609 (tmm) cc_final: 0.7007 (tmm) REVERT: C 341 GLU cc_start: 0.7777 (pt0) cc_final: 0.7185 (pt0) REVERT: C 359 ARG cc_start: 0.7658 (mmp-170) cc_final: 0.7347 (mmp80) REVERT: C 366 ASP cc_start: 0.7663 (p0) cc_final: 0.7426 (p0) REVERT: C 394 GLU cc_start: 0.7476 (tp30) cc_final: 0.7148 (mm-30) REVERT: C 403 GLU cc_start: 0.7638 (pm20) cc_final: 0.7240 (pm20) REVERT: C 407 LEU cc_start: 0.8808 (mt) cc_final: 0.8533 (mt) REVERT: C 410 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6675 (tm-30) REVERT: C 411 GLU cc_start: 0.8187 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 426 ASP cc_start: 0.8259 (t0) cc_final: 0.7966 (t0) REVERT: C 428 LEU cc_start: 0.8755 (tp) cc_final: 0.8364 (tp) REVERT: C 452 GLU cc_start: 0.7681 (mp0) cc_final: 0.7240 (mp0) REVERT: C 470 GLU cc_start: 0.7768 (tt0) cc_final: 0.7469 (tt0) REVERT: C 490 ASN cc_start: 0.7940 (t0) cc_final: 0.7700 (t0) REVERT: C 504 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7388 (mm-30) REVERT: C 507 ILE cc_start: 0.8407 (mt) cc_final: 0.8196 (tp) REVERT: C 521 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8269 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7954 (tpt-90) cc_final: 0.7688 (tpt-90) REVERT: C 541 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7785 (tp30) REVERT: C 546 GLU cc_start: 0.7543 (tp30) cc_final: 0.7309 (tp30) REVERT: C 552 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7662 (mmtm) REVERT: C 558 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6118 (tm-30) REVERT: C 572 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7487 (mtmm) REVERT: C 577 LEU cc_start: 0.8233 (mm) cc_final: 0.7712 (mm) REVERT: C 580 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7521 (mt-10) REVERT: C 582 ILE cc_start: 0.8457 (mt) cc_final: 0.8066 (pt) REVERT: C 594 GLU cc_start: 0.7238 (mp0) cc_final: 0.6907 (mp0) REVERT: C 609 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7090 (mp0) REVERT: C 644 LYS cc_start: 0.8440 (tppt) cc_final: 0.7667 (tppt) REVERT: C 645 LYS cc_start: 0.8307 (mttt) cc_final: 0.7370 (mttt) REVERT: C 712 GLU cc_start: 0.7876 (pm20) cc_final: 0.7605 (pm20) REVERT: C 713 PHE cc_start: 0.8551 (t80) cc_final: 0.8135 (t80) REVERT: C 724 LYS cc_start: 0.8166 (ptpp) cc_final: 0.7857 (ptpp) REVERT: C 735 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7761 (ttp80) REVERT: C 741 THR cc_start: 0.8258 (t) cc_final: 0.7951 (p) REVERT: C 747 LYS cc_start: 0.8527 (mmmm) cc_final: 0.7983 (tppp) REVERT: C 757 LEU cc_start: 0.8583 (tp) cc_final: 0.8242 (tt) REVERT: C 763 ARG cc_start: 0.7313 (ptp-110) cc_final: 0.7099 (ptp-110) REVERT: C 764 ASN cc_start: 0.8156 (p0) cc_final: 0.7849 (p0) REVERT: C 766 ASP cc_start: 0.7154 (t0) cc_final: 0.6628 (t0) REVERT: C 768 GLN cc_start: 0.7930 (mp10) cc_final: 0.6826 (mp10) REVERT: C 772 GLU cc_start: 0.7728 (mp0) cc_final: 0.7186 (mp0) REVERT: C 782 ARG cc_start: 0.7119 (tpt90) cc_final: 0.5753 (tpt90) REVERT: C 788 ARG cc_start: 0.6841 (mmm-85) cc_final: 0.6392 (tpp80) REVERT: C 799 ASP cc_start: 0.7427 (t0) cc_final: 0.7226 (t0) REVERT: C 802 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7946 (mtpp) REVERT: C 804 LEU cc_start: 0.8391 (mt) cc_final: 0.8017 (mt) REVERT: C 836 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7562 (mtt90) REVERT: C 864 LYS cc_start: 0.8761 (tppt) cc_final: 0.8496 (ttmm) outliers start: 52 outliers final: 29 residues processed: 580 average time/residue: 0.1523 time to fit residues: 118.3632 Evaluate side-chains 577 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 538 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 137 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 0.0470 chunk 106 optimal weight: 0.9980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS D 85 HIS ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098378 restraints weight = 27200.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102032 restraints weight = 13392.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104441 restraints weight = 7967.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106070 restraints weight = 5376.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107130 restraints weight = 3991.472| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13920 Z= 0.146 Angle : 0.604 9.262 18800 Z= 0.301 Chirality : 0.042 0.248 2058 Planarity : 0.003 0.034 2434 Dihedral : 3.749 15.945 1844 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.49 % Allowed : 28.62 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.21), residues: 1648 helix: 0.69 (0.18), residues: 846 sheet: -1.65 (0.56), residues: 72 loop : 0.23 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 763 TYR 0.016 0.001 TYR C 277 PHE 0.029 0.002 PHE B 76 TRP 0.011 0.001 TRP A 791 HIS 0.010 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00313 (13904) covalent geometry : angle 0.59312 (18776) hydrogen bonds : bond 0.03804 ( 618) hydrogen bonds : angle 4.41126 ( 1752) metal coordination : bond 0.00612 ( 16) metal coordination : angle 3.23705 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 551 time to evaluate : 0.516 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: B 15 ARG cc_start: 0.7346 (mtp85) cc_final: 0.6834 (mmt180) REVERT: B 25 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 26 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 41 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8030 (mmtt) REVERT: B 44 LEU cc_start: 0.8821 (mp) cc_final: 0.8566 (mp) REVERT: B 77 TYR cc_start: 0.7877 (m-80) cc_final: 0.7644 (m-80) REVERT: B 91 TYR cc_start: 0.8749 (m-10) cc_final: 0.8265 (m-10) REVERT: B 94 THR cc_start: 0.8529 (m) cc_final: 0.8284 (p) REVERT: B 96 GLU cc_start: 0.7673 (tp30) cc_final: 0.7388 (tp30) REVERT: B 98 GLN cc_start: 0.8234 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 118 SER cc_start: 0.8557 (m) cc_final: 0.7988 (p) REVERT: B 121 GLU cc_start: 0.8387 (mp0) cc_final: 0.7874 (mp0) REVERT: B 124 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7836 (ttp80) REVERT: B 131 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7996 (mtt90) REVERT: B 143 CYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7293 (p) REVERT: A 128 LEU cc_start: 0.8286 (mp) cc_final: 0.7856 (mm) REVERT: A 135 GLU cc_start: 0.7711 (pt0) cc_final: 0.7391 (pp20) REVERT: A 241 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7701 (mpp80) REVERT: A 243 TYR cc_start: 0.7645 (m-80) cc_final: 0.7273 (m-80) REVERT: A 264 SER cc_start: 0.8447 (m) cc_final: 0.8141 (p) REVERT: A 267 VAL cc_start: 0.8941 (t) cc_final: 0.8671 (p) REVERT: A 268 GLU cc_start: 0.8424 (tt0) cc_final: 0.7908 (tm-30) REVERT: A 283 TYR cc_start: 0.7949 (t80) cc_final: 0.7732 (t80) REVERT: A 291 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6799 (tmm) REVERT: A 306 LEU cc_start: 0.7816 (tp) cc_final: 0.7284 (tp) REVERT: A 310 CYS cc_start: 0.8257 (m) cc_final: 0.7698 (m) REVERT: A 315 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8030 (mmmm) REVERT: A 327 LEU cc_start: 0.8122 (mt) cc_final: 0.7813 (mt) REVERT: A 336 ILE cc_start: 0.8395 (mm) cc_final: 0.8193 (mm) REVERT: A 338 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.7298 (tpt90) REVERT: A 340 MET cc_start: 0.8012 (tmm) cc_final: 0.7394 (tmm) REVERT: A 341 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 387 GLU cc_start: 0.6832 (pm20) cc_final: 0.6241 (mp0) REVERT: A 392 HIS cc_start: 0.7573 (m-70) cc_final: 0.6777 (m-70) REVERT: A 397 ASP cc_start: 0.6584 (p0) cc_final: 0.6255 (p0) REVERT: A 406 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 407 LEU cc_start: 0.8699 (mt) cc_final: 0.8363 (mt) REVERT: A 411 GLU cc_start: 0.8170 (tt0) cc_final: 0.7471 (tm-30) REVERT: A 429 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: A 435 LYS cc_start: 0.8294 (tmtt) cc_final: 0.8023 (tptp) REVERT: A 447 GLU cc_start: 0.7616 (mp0) cc_final: 0.7260 (mp0) REVERT: A 448 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7924 (mt-10) REVERT: A 452 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7384 (mp0) REVERT: A 462 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7548 (mtmm) REVERT: A 470 GLU cc_start: 0.7812 (tt0) cc_final: 0.7539 (tt0) REVERT: A 490 ASN cc_start: 0.7869 (t0) cc_final: 0.7621 (t0) REVERT: A 504 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 533 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.6975 (tt) REVERT: A 541 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7390 (tp30) REVERT: A 550 ASP cc_start: 0.7969 (m-30) cc_final: 0.7644 (m-30) REVERT: A 577 LEU cc_start: 0.8208 (mm) cc_final: 0.7753 (mm) REVERT: A 580 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 581 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7569 (pt0) REVERT: A 598 LEU cc_start: 0.8645 (mt) cc_final: 0.8363 (mt) REVERT: A 611 GLN cc_start: 0.7908 (mp10) cc_final: 0.7334 (mp10) REVERT: A 644 LYS cc_start: 0.8468 (tppt) cc_final: 0.7748 (tppp) REVERT: A 660 GLN cc_start: 0.8339 (pp30) cc_final: 0.7990 (pp30) REVERT: A 663 LYS cc_start: 0.8790 (pttp) cc_final: 0.8401 (pptt) REVERT: A 664 ASP cc_start: 0.8246 (m-30) cc_final: 0.7736 (m-30) REVERT: A 665 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 710 ARG cc_start: 0.8527 (ptm160) cc_final: 0.7832 (ptt180) REVERT: A 712 GLU cc_start: 0.7955 (pm20) cc_final: 0.7685 (pm20) REVERT: A 713 PHE cc_start: 0.8481 (t80) cc_final: 0.8133 (t80) REVERT: A 724 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8071 (ptpp) REVERT: A 738 HIS cc_start: 0.7159 (t-90) cc_final: 0.6778 (t-90) REVERT: A 739 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7418 (tpp) REVERT: A 747 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8070 (tptt) REVERT: A 754 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7395 (mp0) REVERT: A 757 LEU cc_start: 0.8563 (tp) cc_final: 0.8255 (tt) REVERT: A 764 ASN cc_start: 0.8062 (p0) cc_final: 0.7828 (p0) REVERT: A 768 GLN cc_start: 0.7818 (mp10) cc_final: 0.7349 (mp10) REVERT: A 772 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7138 (mp0) REVERT: A 788 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6694 (tpp-160) REVERT: A 800 GLU cc_start: 0.7783 (tp30) cc_final: 0.7416 (tp30) REVERT: A 802 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8141 (mtpp) REVERT: A 804 LEU cc_start: 0.8313 (mt) cc_final: 0.7957 (mt) REVERT: A 807 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 829 LYS cc_start: 0.8405 (tttt) cc_final: 0.8078 (ttpp) REVERT: A 836 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7525 (mtt90) REVERT: A 841 HIS cc_start: 0.7839 (t70) cc_final: 0.7311 (t70) REVERT: D 17 ARG cc_start: 0.7311 (mmt180) cc_final: 0.6855 (mmt180) REVERT: D 22 LEU cc_start: 0.7800 (tp) cc_final: 0.7454 (tp) REVERT: D 25 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8177 (mm-30) REVERT: D 26 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8189 (mp) REVERT: D 41 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8051 (mmtt) REVERT: D 48 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: D 62 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7522 (tpp80) REVERT: D 77 TYR cc_start: 0.7989 (m-80) cc_final: 0.7724 (m-80) REVERT: D 91 TYR cc_start: 0.8579 (m-10) cc_final: 0.8346 (m-10) REVERT: D 103 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8415 (tt) REVERT: D 104 SER cc_start: 0.8508 (m) cc_final: 0.8271 (p) REVERT: D 115 LYS cc_start: 0.8668 (tttm) cc_final: 0.8161 (ptmm) REVERT: D 121 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: D 124 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7796 (ttp80) REVERT: D 131 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7971 (ttm110) REVERT: D 143 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7218 (p) REVERT: C 151 ARG cc_start: 0.7031 (ptm160) cc_final: 0.6783 (mtm110) REVERT: C 161 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7889 (pm20) REVERT: C 239 ILE cc_start: 0.8865 (mm) cc_final: 0.8661 (mm) REVERT: C 241 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7921 (mtm-85) REVERT: C 243 TYR cc_start: 0.7880 (m-80) cc_final: 0.7575 (m-80) REVERT: C 245 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7540 (mmm-85) REVERT: C 268 GLU cc_start: 0.8316 (tt0) cc_final: 0.7741 (tm-30) REVERT: C 283 TYR cc_start: 0.7954 (t80) cc_final: 0.7620 (t80) REVERT: C 289 ILE cc_start: 0.8570 (mm) cc_final: 0.8314 (mm) REVERT: C 291 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.6900 (tmm) REVERT: C 310 CYS cc_start: 0.8351 (m) cc_final: 0.7871 (m) REVERT: C 311 LYS cc_start: 0.8552 (mttt) cc_final: 0.8293 (mttm) REVERT: C 315 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8128 (mmmm) REVERT: C 323 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8206 (tttt) REVERT: C 327 LEU cc_start: 0.8214 (mt) cc_final: 0.7993 (mt) REVERT: C 336 ILE cc_start: 0.8503 (mm) cc_final: 0.8266 (mm) REVERT: C 338 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7440 (tpt170) REVERT: C 340 MET cc_start: 0.7650 (tmm) cc_final: 0.6979 (tmm) REVERT: C 341 GLU cc_start: 0.7831 (pt0) cc_final: 0.7218 (pt0) REVERT: C 394 GLU cc_start: 0.7523 (tp30) cc_final: 0.7295 (tp30) REVERT: C 403 GLU cc_start: 0.7505 (pm20) cc_final: 0.7169 (pm20) REVERT: C 407 LEU cc_start: 0.8801 (mt) cc_final: 0.8505 (mt) REVERT: C 410 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6688 (tm-30) REVERT: C 411 GLU cc_start: 0.8216 (tt0) cc_final: 0.7814 (tm-30) REVERT: C 426 ASP cc_start: 0.8293 (t0) cc_final: 0.7955 (t0) REVERT: C 428 LEU cc_start: 0.8775 (tp) cc_final: 0.8369 (tp) REVERT: C 447 GLU cc_start: 0.7637 (mp0) cc_final: 0.7082 (mp0) REVERT: C 452 GLU cc_start: 0.7776 (mp0) cc_final: 0.7251 (mp0) REVERT: C 470 GLU cc_start: 0.7758 (tt0) cc_final: 0.7502 (tt0) REVERT: C 490 ASN cc_start: 0.7968 (t0) cc_final: 0.7702 (t0) REVERT: C 504 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 521 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.8269 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7979 (tpt-90) cc_final: 0.7613 (tpt-90) REVERT: C 541 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7449 (tp30) REVERT: C 547 ASN cc_start: 0.7775 (m-40) cc_final: 0.7423 (m-40) REVERT: C 550 ASP cc_start: 0.7992 (m-30) cc_final: 0.7752 (m-30) REVERT: C 552 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7398 (mmtm) REVERT: C 572 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7513 (mtmm) REVERT: C 577 LEU cc_start: 0.8243 (mm) cc_final: 0.7723 (mm) REVERT: C 580 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7537 (mt-10) REVERT: C 582 ILE cc_start: 0.8520 (mt) cc_final: 0.8103 (pt) REVERT: C 594 GLU cc_start: 0.7339 (mp0) cc_final: 0.6978 (mp0) REVERT: C 609 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7292 (mp0) REVERT: C 611 GLN cc_start: 0.8187 (mp-120) cc_final: 0.7607 (mp10) REVERT: C 644 LYS cc_start: 0.8369 (tppt) cc_final: 0.7630 (tppt) REVERT: C 645 LYS cc_start: 0.8238 (mttt) cc_final: 0.7353 (mtpp) REVERT: C 710 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8061 (ptp-170) REVERT: C 711 LYS cc_start: 0.8828 (mppt) cc_final: 0.8533 (mppt) REVERT: C 712 GLU cc_start: 0.7910 (pm20) cc_final: 0.7469 (pm20) REVERT: C 713 PHE cc_start: 0.8581 (t80) cc_final: 0.8235 (t80) REVERT: C 735 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7791 (ttp80) REVERT: C 741 THR cc_start: 0.8136 (t) cc_final: 0.7847 (p) REVERT: C 747 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8017 (tppp) REVERT: C 757 LEU cc_start: 0.8564 (tp) cc_final: 0.8245 (tt) REVERT: C 763 ARG cc_start: 0.7344 (ptp-110) cc_final: 0.7141 (ptp-110) REVERT: C 764 ASN cc_start: 0.8119 (p0) cc_final: 0.7807 (p0) REVERT: C 768 GLN cc_start: 0.7955 (mp10) cc_final: 0.6854 (mp10) REVERT: C 772 GLU cc_start: 0.7767 (mp0) cc_final: 0.7205 (mp0) REVERT: C 782 ARG cc_start: 0.7132 (tpt90) cc_final: 0.5631 (tpt90) REVERT: C 788 ARG cc_start: 0.6980 (mmm-85) cc_final: 0.6535 (tpp80) REVERT: C 799 ASP cc_start: 0.7487 (t0) cc_final: 0.7277 (t0) REVERT: C 802 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8169 (mtpp) REVERT: C 804 LEU cc_start: 0.8378 (mt) cc_final: 0.7966 (mt) REVERT: C 836 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7610 (mtt90) REVERT: C 841 HIS cc_start: 0.7930 (t70) cc_final: 0.7291 (t70) REVERT: C 864 LYS cc_start: 0.8741 (tppt) cc_final: 0.8533 (ttmm) outliers start: 53 outliers final: 33 residues processed: 571 average time/residue: 0.1438 time to fit residues: 110.2800 Evaluate side-chains 582 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 534 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 105 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 345 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 801 GLN D 98 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101220 restraints weight = 27227.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104751 restraints weight = 13259.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107129 restraints weight = 7868.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108688 restraints weight = 5235.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109614 restraints weight = 3864.411| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13920 Z= 0.130 Angle : 0.619 10.408 18800 Z= 0.304 Chirality : 0.042 0.249 2058 Planarity : 0.003 0.032 2434 Dihedral : 3.718 16.398 1844 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.82 % Allowed : 29.67 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.21), residues: 1648 helix: 0.71 (0.18), residues: 838 sheet: -1.79 (0.55), residues: 72 loop : 0.29 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 649 TYR 0.015 0.001 TYR A 659 PHE 0.022 0.001 PHE B 76 TRP 0.012 0.001 TRP A 791 HIS 0.016 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00288 (13904) covalent geometry : angle 0.60951 (18776) hydrogen bonds : bond 0.03642 ( 618) hydrogen bonds : angle 4.39158 ( 1752) metal coordination : bond 0.00498 ( 16) metal coordination : angle 3.11313 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 542 time to evaluate : 0.414 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: B 15 ARG cc_start: 0.7361 (mtp85) cc_final: 0.6846 (mmt180) REVERT: B 25 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8088 (mm-30) REVERT: B 26 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8301 (mp) REVERT: B 41 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8026 (mmtt) REVERT: B 44 LEU cc_start: 0.8807 (mp) cc_final: 0.8544 (mp) REVERT: B 77 TYR cc_start: 0.7833 (m-80) cc_final: 0.7609 (m-80) REVERT: B 91 TYR cc_start: 0.8741 (m-10) cc_final: 0.8250 (m-10) REVERT: B 94 THR cc_start: 0.8556 (m) cc_final: 0.8296 (p) REVERT: B 96 GLU cc_start: 0.7710 (tp30) cc_final: 0.7422 (tp30) REVERT: B 118 SER cc_start: 0.8549 (m) cc_final: 0.7973 (p) REVERT: B 121 GLU cc_start: 0.8322 (mp0) cc_final: 0.8082 (mp0) REVERT: B 131 ARG cc_start: 0.8289 (ttm110) cc_final: 0.8014 (mtt90) REVERT: B 143 CYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 144 MET cc_start: 0.7285 (mmm) cc_final: 0.6917 (mmm) REVERT: A 128 LEU cc_start: 0.8288 (mp) cc_final: 0.7874 (mm) REVERT: A 135 GLU cc_start: 0.7742 (pt0) cc_final: 0.7355 (pp20) REVERT: A 143 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7849 (mmm160) REVERT: A 241 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7660 (mpp80) REVERT: A 243 TYR cc_start: 0.7655 (m-80) cc_final: 0.7335 (m-80) REVERT: A 264 SER cc_start: 0.8446 (m) cc_final: 0.8125 (p) REVERT: A 267 VAL cc_start: 0.8906 (t) cc_final: 0.8629 (p) REVERT: A 268 GLU cc_start: 0.8483 (tt0) cc_final: 0.7804 (tm-30) REVERT: A 291 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6858 (tmm) REVERT: A 306 LEU cc_start: 0.7805 (tp) cc_final: 0.7285 (tp) REVERT: A 310 CYS cc_start: 0.8189 (m) cc_final: 0.7624 (m) REVERT: A 313 MET cc_start: 0.8313 (ttm) cc_final: 0.8048 (mtp) REVERT: A 315 LYS cc_start: 0.8526 (mmtt) cc_final: 0.7976 (mmmm) REVERT: A 327 LEU cc_start: 0.8094 (mt) cc_final: 0.7790 (mt) REVERT: A 336 ILE cc_start: 0.8379 (mm) cc_final: 0.8167 (mm) REVERT: A 338 ARG cc_start: 0.7899 (tpp-160) cc_final: 0.7352 (tpt90) REVERT: A 340 MET cc_start: 0.8042 (tmm) cc_final: 0.7390 (tmm) REVERT: A 341 GLU cc_start: 0.7932 (mt-10) cc_final: 0.6949 (mt-10) REVERT: A 387 GLU cc_start: 0.6816 (pm20) cc_final: 0.6306 (mp0) REVERT: A 392 HIS cc_start: 0.7485 (m-70) cc_final: 0.6682 (m-70) REVERT: A 397 ASP cc_start: 0.6593 (p0) cc_final: 0.6273 (p0) REVERT: A 406 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 407 LEU cc_start: 0.8701 (mt) cc_final: 0.8347 (mt) REVERT: A 411 GLU cc_start: 0.8170 (tt0) cc_final: 0.7457 (tm-30) REVERT: A 429 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: A 435 LYS cc_start: 0.8284 (tmtt) cc_final: 0.8033 (tptp) REVERT: A 447 GLU cc_start: 0.7573 (mp0) cc_final: 0.7268 (mp0) REVERT: A 448 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7944 (mt-10) REVERT: A 452 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7261 (mp0) REVERT: A 470 GLU cc_start: 0.7796 (tt0) cc_final: 0.7535 (tt0) REVERT: A 504 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 533 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.6955 (tt) REVERT: A 541 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7385 (tp30) REVERT: A 550 ASP cc_start: 0.8008 (m-30) cc_final: 0.7679 (m-30) REVERT: A 577 LEU cc_start: 0.8166 (mm) cc_final: 0.7678 (mm) REVERT: A 580 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 581 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7512 (pt0) REVERT: A 590 PHE cc_start: 0.8548 (m-80) cc_final: 0.8287 (m-80) REVERT: A 611 GLN cc_start: 0.7800 (mp10) cc_final: 0.7120 (mp10) REVERT: A 644 LYS cc_start: 0.8474 (tppt) cc_final: 0.7736 (tppp) REVERT: A 645 LYS cc_start: 0.8271 (mttt) cc_final: 0.7164 (mmtm) REVERT: A 660 GLN cc_start: 0.8336 (pp30) cc_final: 0.7950 (pp30) REVERT: A 663 LYS cc_start: 0.8799 (pttp) cc_final: 0.8447 (pptt) REVERT: A 664 ASP cc_start: 0.8269 (m-30) cc_final: 0.7786 (m-30) REVERT: A 665 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 710 ARG cc_start: 0.8525 (ptm160) cc_final: 0.7599 (ptt180) REVERT: A 711 LYS cc_start: 0.8783 (mppt) cc_final: 0.8340 (mmtm) REVERT: A 712 GLU cc_start: 0.7908 (pm20) cc_final: 0.7614 (pm20) REVERT: A 713 PHE cc_start: 0.8504 (t80) cc_final: 0.8138 (t80) REVERT: A 721 ILE cc_start: 0.8806 (tp) cc_final: 0.8563 (tt) REVERT: A 724 LYS cc_start: 0.8309 (ptpp) cc_final: 0.8081 (ptpp) REVERT: A 738 HIS cc_start: 0.7147 (t-90) cc_final: 0.6761 (t-90) REVERT: A 739 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7384 (tpp) REVERT: A 747 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8078 (tptt) REVERT: A 754 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7381 (mp0) REVERT: A 757 LEU cc_start: 0.8569 (tp) cc_final: 0.8276 (tt) REVERT: A 764 ASN cc_start: 0.8079 (p0) cc_final: 0.7862 (p0) REVERT: A 768 GLN cc_start: 0.7817 (mp10) cc_final: 0.6809 (mp10) REVERT: A 772 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7125 (mp0) REVERT: A 788 ARG cc_start: 0.7036 (mmm-85) cc_final: 0.6678 (tpp-160) REVERT: A 800 GLU cc_start: 0.7769 (tp30) cc_final: 0.7208 (tp30) REVERT: A 802 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8130 (mtpp) REVERT: A 804 LEU cc_start: 0.8329 (mt) cc_final: 0.7885 (mt) REVERT: A 829 LYS cc_start: 0.8425 (tttt) cc_final: 0.8093 (ttpt) REVERT: A 836 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7558 (mtt90) REVERT: A 841 HIS cc_start: 0.7845 (t70) cc_final: 0.7301 (t70) REVERT: D 15 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7202 (mtp85) REVERT: D 17 ARG cc_start: 0.7339 (mmt180) cc_final: 0.6885 (mmt180) REVERT: D 22 LEU cc_start: 0.7804 (tp) cc_final: 0.7458 (tp) REVERT: D 25 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8185 (mm-30) REVERT: D 26 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8182 (mp) REVERT: D 41 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8034 (mmtt) REVERT: D 48 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: D 62 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7515 (tpp80) REVERT: D 76 PHE cc_start: 0.8131 (t80) cc_final: 0.7871 (t80) REVERT: D 77 TYR cc_start: 0.7960 (m-80) cc_final: 0.7682 (m-80) REVERT: D 89 SER cc_start: 0.8352 (p) cc_final: 0.8055 (t) REVERT: D 91 TYR cc_start: 0.8546 (m-10) cc_final: 0.8334 (m-10) REVERT: D 96 GLU cc_start: 0.7688 (tp30) cc_final: 0.7421 (tp30) REVERT: D 115 LYS cc_start: 0.8631 (tttm) cc_final: 0.8143 (ptmm) REVERT: D 121 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: D 124 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7807 (ttp80) REVERT: D 131 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7740 (ttm110) REVERT: D 143 CYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7267 (p) REVERT: C 128 LEU cc_start: 0.8167 (mp) cc_final: 0.7884 (mp) REVERT: C 161 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7898 (pm20) REVERT: C 241 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: C 243 TYR cc_start: 0.7808 (m-80) cc_final: 0.7465 (m-80) REVERT: C 245 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7534 (mmm-85) REVERT: C 268 GLU cc_start: 0.8332 (tt0) cc_final: 0.7750 (tm-30) REVERT: C 283 TYR cc_start: 0.7962 (t80) cc_final: 0.7598 (t80) REVERT: C 289 ILE cc_start: 0.8569 (mm) cc_final: 0.8344 (mm) REVERT: C 291 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6911 (tmm) REVERT: C 310 CYS cc_start: 0.8287 (m) cc_final: 0.7813 (m) REVERT: C 311 LYS cc_start: 0.8461 (mttt) cc_final: 0.8241 (mttm) REVERT: C 315 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8103 (mmmm) REVERT: C 323 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8276 (tttt) REVERT: C 327 LEU cc_start: 0.8172 (mt) cc_final: 0.7954 (mt) REVERT: C 336 ILE cc_start: 0.8503 (mm) cc_final: 0.8267 (mm) REVERT: C 338 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7486 (tpt170) REVERT: C 340 MET cc_start: 0.7645 (tmm) cc_final: 0.6973 (tmm) REVERT: C 341 GLU cc_start: 0.7847 (pt0) cc_final: 0.7148 (pt0) REVERT: C 394 GLU cc_start: 0.7565 (tp30) cc_final: 0.7352 (tp30) REVERT: C 401 ILE cc_start: 0.8707 (mm) cc_final: 0.8410 (pt) REVERT: C 403 GLU cc_start: 0.7489 (pm20) cc_final: 0.7142 (pm20) REVERT: C 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8513 (mt) REVERT: C 410 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6653 (tm-30) REVERT: C 411 GLU cc_start: 0.8221 (tt0) cc_final: 0.7803 (tm-30) REVERT: C 426 ASP cc_start: 0.8280 (t0) cc_final: 0.7962 (t0) REVERT: C 428 LEU cc_start: 0.8761 (tp) cc_final: 0.8366 (tp) REVERT: C 447 GLU cc_start: 0.7627 (mp0) cc_final: 0.7059 (mp0) REVERT: C 452 GLU cc_start: 0.7762 (mp0) cc_final: 0.7280 (mp0) REVERT: C 470 GLU cc_start: 0.7761 (tt0) cc_final: 0.7541 (tt0) REVERT: C 490 ASN cc_start: 0.7933 (t0) cc_final: 0.7624 (t0) REVERT: C 504 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 521 PRO cc_start: 0.8512 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: C 526 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7582 (tmtt) REVERT: C 539 ARG cc_start: 0.8023 (tpt-90) cc_final: 0.7646 (tpt-90) REVERT: C 541 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7443 (tp30) REVERT: C 546 GLU cc_start: 0.7531 (tp30) cc_final: 0.6969 (tp30) REVERT: C 550 ASP cc_start: 0.7954 (m-30) cc_final: 0.7727 (m-30) REVERT: C 552 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7401 (mmtm) REVERT: C 558 GLU cc_start: 0.6551 (tm-30) cc_final: 0.6199 (tm-30) REVERT: C 572 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7481 (mtmm) REVERT: C 577 LEU cc_start: 0.8243 (mm) cc_final: 0.7715 (mm) REVERT: C 580 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 594 GLU cc_start: 0.7340 (mp0) cc_final: 0.6971 (mp0) REVERT: C 609 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7263 (mp0) REVERT: C 611 GLN cc_start: 0.7781 (mp-120) cc_final: 0.7576 (mp10) REVERT: C 644 LYS cc_start: 0.8298 (tppt) cc_final: 0.7608 (tppt) REVERT: C 645 LYS cc_start: 0.8271 (mttt) cc_final: 0.7350 (mtpp) REVERT: C 664 ASP cc_start: 0.8124 (m-30) cc_final: 0.7849 (m-30) REVERT: C 710 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8069 (ptp-170) REVERT: C 711 LYS cc_start: 0.8833 (mppt) cc_final: 0.8555 (mppt) REVERT: C 712 GLU cc_start: 0.7909 (pm20) cc_final: 0.7472 (pm20) REVERT: C 713 PHE cc_start: 0.8575 (t80) cc_final: 0.8226 (t80) REVERT: C 735 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7765 (ttp80) REVERT: C 743 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7004 (mt-10) REVERT: C 747 LYS cc_start: 0.8539 (mmmm) cc_final: 0.7983 (tppp) REVERT: C 757 LEU cc_start: 0.8540 (tp) cc_final: 0.8234 (tt) REVERT: C 763 ARG cc_start: 0.7353 (ptp-110) cc_final: 0.7150 (ptp-110) REVERT: C 764 ASN cc_start: 0.8106 (p0) cc_final: 0.7790 (p0) REVERT: C 768 GLN cc_start: 0.7950 (mp10) cc_final: 0.6840 (mp10) REVERT: C 772 GLU cc_start: 0.7765 (mp0) cc_final: 0.7196 (mp0) REVERT: C 800 GLU cc_start: 0.7680 (tp30) cc_final: 0.7096 (tp30) REVERT: C 802 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8175 (mtpp) REVERT: C 804 LEU cc_start: 0.8399 (mt) cc_final: 0.7771 (mt) REVERT: C 836 ARG cc_start: 0.7938 (mtt-85) cc_final: 0.7485 (mtt90) REVERT: C 841 HIS cc_start: 0.7864 (t70) cc_final: 0.7303 (t70) REVERT: C 855 LYS cc_start: 0.7806 (ttpp) cc_final: 0.7555 (ttpp) REVERT: C 864 LYS cc_start: 0.8732 (tppt) cc_final: 0.8530 (ttmm) outliers start: 58 outliers final: 34 residues processed: 565 average time/residue: 0.1500 time to fit residues: 113.1108 Evaluate side-chains 583 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 536 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099762 restraints weight = 27266.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103253 restraints weight = 13308.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105540 restraints weight = 7897.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107175 restraints weight = 5304.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108194 restraints weight = 3870.053| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13920 Z= 0.197 Angle : 0.663 9.954 18800 Z= 0.333 Chirality : 0.044 0.266 2058 Planarity : 0.004 0.035 2434 Dihedral : 3.915 17.606 1844 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.62 % Allowed : 30.20 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.21), residues: 1648 helix: 0.58 (0.18), residues: 848 sheet: -1.90 (0.55), residues: 72 loop : 0.20 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 639 TYR 0.017 0.001 TYR A 659 PHE 0.031 0.002 PHE B 76 TRP 0.010 0.001 TRP A 791 HIS 0.005 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00406 (13904) covalent geometry : angle 0.65063 (18776) hydrogen bonds : bond 0.04181 ( 618) hydrogen bonds : angle 4.56787 ( 1752) metal coordination : bond 0.00909 ( 16) metal coordination : angle 3.57243 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 548 time to evaluate : 0.531 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: B 15 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7075 (mmt180) REVERT: B 25 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 26 LEU cc_start: 0.8595 (mp) cc_final: 0.8297 (mp) REVERT: B 41 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8016 (mmtt) REVERT: B 44 LEU cc_start: 0.8866 (mp) cc_final: 0.8582 (mp) REVERT: B 77 TYR cc_start: 0.7993 (m-80) cc_final: 0.7741 (m-80) REVERT: B 91 TYR cc_start: 0.8769 (m-10) cc_final: 0.8246 (m-10) REVERT: B 94 THR cc_start: 0.8641 (m) cc_final: 0.8402 (p) REVERT: B 96 GLU cc_start: 0.7673 (tp30) cc_final: 0.7353 (tp30) REVERT: B 118 SER cc_start: 0.8663 (m) cc_final: 0.8344 (t) REVERT: B 121 GLU cc_start: 0.8401 (mp0) cc_final: 0.8135 (mp0) REVERT: B 123 GLN cc_start: 0.8257 (tp40) cc_final: 0.7804 (tp40) REVERT: B 124 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7882 (ttp80) REVERT: B 131 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8042 (mtt90) REVERT: B 143 CYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7353 (p) REVERT: A 128 LEU cc_start: 0.8343 (mp) cc_final: 0.7923 (mm) REVERT: A 135 GLU cc_start: 0.7740 (pt0) cc_final: 0.7418 (pp20) REVERT: A 241 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: A 243 TYR cc_start: 0.7692 (m-80) cc_final: 0.7316 (m-80) REVERT: A 247 LEU cc_start: 0.8381 (mp) cc_final: 0.8110 (mm) REVERT: A 264 SER cc_start: 0.8396 (m) cc_final: 0.8025 (p) REVERT: A 267 VAL cc_start: 0.8870 (t) cc_final: 0.8599 (p) REVERT: A 268 GLU cc_start: 0.8508 (tt0) cc_final: 0.7825 (tm-30) REVERT: A 291 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6865 (tmm) REVERT: A 310 CYS cc_start: 0.8331 (m) cc_final: 0.7770 (m) REVERT: A 315 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8045 (mmmm) REVERT: A 327 LEU cc_start: 0.8098 (mt) cc_final: 0.7792 (mt) REVERT: A 336 ILE cc_start: 0.8370 (mm) cc_final: 0.8168 (mm) REVERT: A 338 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7357 (tpt90) REVERT: A 340 MET cc_start: 0.8040 (tmm) cc_final: 0.7384 (tmm) REVERT: A 341 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 387 GLU cc_start: 0.6849 (pm20) cc_final: 0.6286 (mp0) REVERT: A 392 HIS cc_start: 0.7506 (m-70) cc_final: 0.6852 (m-70) REVERT: A 394 GLU cc_start: 0.7454 (tp30) cc_final: 0.6217 (tp30) REVERT: A 397 ASP cc_start: 0.6602 (p0) cc_final: 0.6374 (p0) REVERT: A 406 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 407 LEU cc_start: 0.8727 (mt) cc_final: 0.8381 (mt) REVERT: A 411 GLU cc_start: 0.8154 (tt0) cc_final: 0.7807 (tt0) REVERT: A 429 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: A 435 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7937 (tptp) REVERT: A 447 GLU cc_start: 0.7652 (mp0) cc_final: 0.7423 (mp0) REVERT: A 452 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7335 (mp0) REVERT: A 470 GLU cc_start: 0.7828 (tt0) cc_final: 0.7526 (tt0) REVERT: A 550 ASP cc_start: 0.7971 (m-30) cc_final: 0.7669 (m-30) REVERT: A 577 LEU cc_start: 0.8238 (mm) cc_final: 0.7884 (mm) REVERT: A 580 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 581 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7691 (tm-30) REVERT: A 611 GLN cc_start: 0.7893 (mp10) cc_final: 0.7240 (mp10) REVERT: A 627 CYS cc_start: 0.8102 (m) cc_final: 0.7869 (m) REVERT: A 644 LYS cc_start: 0.8515 (tppt) cc_final: 0.7728 (tppt) REVERT: A 645 LYS cc_start: 0.8311 (mttt) cc_final: 0.7472 (mmtt) REVERT: A 660 GLN cc_start: 0.8342 (pp30) cc_final: 0.7941 (pp30) REVERT: A 663 LYS cc_start: 0.8819 (pttp) cc_final: 0.8427 (pptt) REVERT: A 664 ASP cc_start: 0.8267 (m-30) cc_final: 0.7765 (m-30) REVERT: A 665 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 708 GLU cc_start: 0.7371 (pp20) cc_final: 0.7121 (pp20) REVERT: A 710 ARG cc_start: 0.8553 (ptm160) cc_final: 0.8128 (ptp-170) REVERT: A 711 LYS cc_start: 0.8826 (mppt) cc_final: 0.8411 (mmtm) REVERT: A 712 GLU cc_start: 0.7954 (pm20) cc_final: 0.7688 (pm20) REVERT: A 713 PHE cc_start: 0.8505 (t80) cc_final: 0.8157 (t80) REVERT: A 717 TYR cc_start: 0.8349 (t80) cc_final: 0.7975 (t80) REVERT: A 724 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8082 (ptpp) REVERT: A 738 HIS cc_start: 0.7205 (t-90) cc_final: 0.6887 (t-90) REVERT: A 747 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8050 (mmtt) REVERT: A 754 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7430 (mp0) REVERT: A 757 LEU cc_start: 0.8551 (tp) cc_final: 0.8253 (tt) REVERT: A 768 GLN cc_start: 0.7866 (mp10) cc_final: 0.6861 (mp10) REVERT: A 772 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7189 (mp0) REVERT: A 788 ARG cc_start: 0.7127 (mmm-85) cc_final: 0.6739 (tpp-160) REVERT: A 800 GLU cc_start: 0.7839 (tp30) cc_final: 0.7465 (tp30) REVERT: A 802 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8141 (mtpp) REVERT: A 804 LEU cc_start: 0.8353 (mt) cc_final: 0.7983 (mt) REVERT: A 829 LYS cc_start: 0.8450 (tttt) cc_final: 0.8119 (ttpp) REVERT: A 836 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7537 (mtt90) REVERT: A 841 HIS cc_start: 0.7815 (t70) cc_final: 0.7212 (t70) REVERT: D 17 ARG cc_start: 0.7360 (mmt180) cc_final: 0.6969 (mmt180) REVERT: D 22 LEU cc_start: 0.7866 (tp) cc_final: 0.7511 (tp) REVERT: D 25 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8196 (mm-30) REVERT: D 26 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8122 (mp) REVERT: D 41 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8061 (mmtt) REVERT: D 48 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: D 76 PHE cc_start: 0.8181 (t80) cc_final: 0.7937 (t80) REVERT: D 77 TYR cc_start: 0.7976 (m-80) cc_final: 0.7708 (m-80) REVERT: D 89 SER cc_start: 0.8376 (p) cc_final: 0.8102 (t) REVERT: D 96 GLU cc_start: 0.7755 (tp30) cc_final: 0.7503 (tp30) REVERT: D 103 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8449 (tt) REVERT: D 104 SER cc_start: 0.8577 (m) cc_final: 0.8340 (p) REVERT: D 115 LYS cc_start: 0.8649 (tttm) cc_final: 0.8199 (ptmm) REVERT: D 121 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: D 124 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7845 (ttp80) REVERT: D 131 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7776 (ttm110) REVERT: D 143 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7272 (p) REVERT: C 123 LYS cc_start: 0.7998 (tptp) cc_final: 0.7559 (tppt) REVERT: C 151 ARG cc_start: 0.7165 (ptp-110) cc_final: 0.6873 (mtm110) REVERT: C 161 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7939 (pm20) REVERT: C 241 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7985 (mtm110) REVERT: C 268 GLU cc_start: 0.8345 (tt0) cc_final: 0.7822 (tm-30) REVERT: C 283 TYR cc_start: 0.7956 (t80) cc_final: 0.7579 (t80) REVERT: C 289 ILE cc_start: 0.8586 (mm) cc_final: 0.8363 (mm) REVERT: C 291 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.6926 (tmm) REVERT: C 310 CYS cc_start: 0.8389 (m) cc_final: 0.7819 (m) REVERT: C 315 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8115 (mmmm) REVERT: C 323 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8128 (tttt) REVERT: C 327 LEU cc_start: 0.8250 (mt) cc_final: 0.8030 (mt) REVERT: C 336 ILE cc_start: 0.8609 (mm) cc_final: 0.8369 (mm) REVERT: C 338 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7371 (tpt170) REVERT: C 340 MET cc_start: 0.7709 (tmm) cc_final: 0.7032 (tmm) REVERT: C 342 THR cc_start: 0.8604 (m) cc_final: 0.8358 (m) REVERT: C 397 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6668 (p0) REVERT: C 403 GLU cc_start: 0.7540 (pm20) cc_final: 0.7203 (pm20) REVERT: C 407 LEU cc_start: 0.8790 (mt) cc_final: 0.8502 (mt) REVERT: C 410 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6656 (tm-30) REVERT: C 411 GLU cc_start: 0.8228 (tt0) cc_final: 0.7802 (tm-30) REVERT: C 426 ASP cc_start: 0.8256 (t0) cc_final: 0.7909 (t0) REVERT: C 428 LEU cc_start: 0.8775 (tp) cc_final: 0.8361 (tp) REVERT: C 447 GLU cc_start: 0.7656 (mp0) cc_final: 0.7129 (mp0) REVERT: C 452 GLU cc_start: 0.7780 (mp0) cc_final: 0.7280 (mp0) REVERT: C 458 LEU cc_start: 0.8414 (tp) cc_final: 0.8102 (tt) REVERT: C 504 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 515 GLN cc_start: 0.8090 (tp40) cc_final: 0.7880 (mm-40) REVERT: C 521 PRO cc_start: 0.8530 (Cg_endo) cc_final: 0.8295 (Cg_exo) REVERT: C 526 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7563 (tmtt) REVERT: C 539 ARG cc_start: 0.7993 (tpt-90) cc_final: 0.7608 (tpt-90) REVERT: C 541 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 546 GLU cc_start: 0.7499 (tp30) cc_final: 0.6970 (tp30) REVERT: C 552 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7541 (mmtm) REVERT: C 558 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6151 (tm-30) REVERT: C 572 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7588 (mtmm) REVERT: C 577 LEU cc_start: 0.8311 (mm) cc_final: 0.7800 (mm) REVERT: C 580 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 581 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7886 (tm-30) REVERT: C 582 ILE cc_start: 0.8554 (mt) cc_final: 0.7479 (pt) REVERT: C 609 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7187 (mp0) REVERT: C 611 GLN cc_start: 0.7900 (mp-120) cc_final: 0.7585 (mp10) REVERT: C 644 LYS cc_start: 0.8396 (tppt) cc_final: 0.7623 (tppt) REVERT: C 645 LYS cc_start: 0.8358 (mttt) cc_final: 0.7439 (mtpp) REVERT: C 710 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.7992 (ptp-170) REVERT: C 711 LYS cc_start: 0.8781 (mppt) cc_final: 0.8485 (mppt) REVERT: C 712 GLU cc_start: 0.7933 (pm20) cc_final: 0.7510 (pm20) REVERT: C 713 PHE cc_start: 0.8583 (t80) cc_final: 0.8245 (t80) REVERT: C 735 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7881 (ttp80) REVERT: C 743 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6905 (mt-10) REVERT: C 747 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8091 (mmmm) REVERT: C 757 LEU cc_start: 0.8554 (tp) cc_final: 0.8271 (tt) REVERT: C 764 ASN cc_start: 0.8012 (p0) cc_final: 0.7729 (p0) REVERT: C 766 ASP cc_start: 0.7150 (t0) cc_final: 0.6539 (t0) REVERT: C 768 GLN cc_start: 0.7974 (mp10) cc_final: 0.6890 (mp10) REVERT: C 772 GLU cc_start: 0.7793 (mp0) cc_final: 0.7258 (mp0) REVERT: C 800 GLU cc_start: 0.7696 (tp30) cc_final: 0.7147 (tp30) REVERT: C 802 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8155 (mtpp) REVERT: C 804 LEU cc_start: 0.8361 (mt) cc_final: 0.7781 (mp) REVERT: C 836 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7644 (mtt90) REVERT: C 860 GLU cc_start: 0.7957 (tt0) cc_final: 0.7512 (mt-10) REVERT: C 864 LYS cc_start: 0.8791 (tppt) cc_final: 0.8565 (ttmm) outliers start: 55 outliers final: 35 residues processed: 568 average time/residue: 0.1611 time to fit residues: 121.8364 Evaluate side-chains 583 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 536 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 839 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 138 optimal weight: 0.0060 chunk 2 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098386 restraints weight = 26986.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101959 restraints weight = 13219.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104335 restraints weight = 7860.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105953 restraints weight = 5305.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106993 restraints weight = 3939.960| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13920 Z= 0.125 Angle : 0.663 10.303 18800 Z= 0.326 Chirality : 0.042 0.263 2058 Planarity : 0.004 0.037 2434 Dihedral : 3.815 16.799 1844 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.03 % Allowed : 30.99 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.21), residues: 1648 helix: 0.67 (0.18), residues: 844 sheet: -3.33 (0.57), residues: 48 loop : 0.25 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 763 TYR 0.017 0.001 TYR A 659 PHE 0.026 0.002 PHE C 287 TRP 0.014 0.002 TRP A 328 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00286 (13904) covalent geometry : angle 0.65455 (18776) hydrogen bonds : bond 0.03638 ( 618) hydrogen bonds : angle 4.38570 ( 1752) metal coordination : bond 0.00358 ( 16) metal coordination : angle 2.95262 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 551 time to evaluate : 0.375 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: B 15 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7119 (mmt180) REVERT: B 25 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 26 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 41 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 44 LEU cc_start: 0.8826 (mp) cc_final: 0.8559 (mp) REVERT: B 77 TYR cc_start: 0.7814 (m-80) cc_final: 0.7597 (m-80) REVERT: B 91 TYR cc_start: 0.8696 (m-10) cc_final: 0.8263 (m-10) REVERT: B 94 THR cc_start: 0.8542 (m) cc_final: 0.8295 (p) REVERT: B 96 GLU cc_start: 0.7661 (tp30) cc_final: 0.7354 (tp30) REVERT: B 118 SER cc_start: 0.8546 (m) cc_final: 0.7984 (p) REVERT: B 121 GLU cc_start: 0.8287 (mp0) cc_final: 0.8070 (mp0) REVERT: B 123 GLN cc_start: 0.8168 (tp40) cc_final: 0.7646 (tp40) REVERT: B 128 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8559 (mmmm) REVERT: B 131 ARG cc_start: 0.8328 (ttm110) cc_final: 0.8055 (mtt90) REVERT: A 128 LEU cc_start: 0.8303 (mp) cc_final: 0.7991 (mp) REVERT: A 135 GLU cc_start: 0.7604 (pt0) cc_final: 0.7336 (pp20) REVERT: A 241 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: A 243 TYR cc_start: 0.7672 (m-80) cc_final: 0.7334 (m-80) REVERT: A 247 LEU cc_start: 0.8384 (mp) cc_final: 0.8134 (mm) REVERT: A 264 SER cc_start: 0.8398 (m) cc_final: 0.7979 (p) REVERT: A 267 VAL cc_start: 0.8916 (t) cc_final: 0.8661 (p) REVERT: A 268 GLU cc_start: 0.8450 (tt0) cc_final: 0.7775 (tm-30) REVERT: A 291 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6978 (tmm) REVERT: A 297 HIS cc_start: 0.6927 (t-170) cc_final: 0.5625 (t-170) REVERT: A 310 CYS cc_start: 0.8293 (m) cc_final: 0.7717 (m) REVERT: A 313 MET cc_start: 0.8193 (mtp) cc_final: 0.7913 (ttm) REVERT: A 315 LYS cc_start: 0.8495 (mmtt) cc_final: 0.7957 (mmmm) REVERT: A 327 LEU cc_start: 0.7964 (mt) cc_final: 0.7683 (mt) REVERT: A 336 ILE cc_start: 0.8386 (mm) cc_final: 0.8181 (mm) REVERT: A 338 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7400 (tpt90) REVERT: A 340 MET cc_start: 0.7925 (tmm) cc_final: 0.7289 (tmm) REVERT: A 387 GLU cc_start: 0.6770 (pm20) cc_final: 0.6153 (mp0) REVERT: A 392 HIS cc_start: 0.7427 (m-70) cc_final: 0.6812 (m-70) REVERT: A 394 GLU cc_start: 0.7408 (tp30) cc_final: 0.6218 (tp30) REVERT: A 397 ASP cc_start: 0.6519 (p0) cc_final: 0.6247 (p0) REVERT: A 406 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 407 LEU cc_start: 0.8711 (mt) cc_final: 0.8382 (mt) REVERT: A 411 GLU cc_start: 0.8130 (tt0) cc_final: 0.7466 (tm-30) REVERT: A 429 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 435 LYS cc_start: 0.8282 (tmtt) cc_final: 0.8028 (tptp) REVERT: A 452 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 462 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7487 (mttm) REVERT: A 463 ASP cc_start: 0.8076 (t0) cc_final: 0.7753 (t0) REVERT: A 470 GLU cc_start: 0.7778 (tt0) cc_final: 0.7514 (tt0) REVERT: A 478 MET cc_start: 0.7311 (mtp) cc_final: 0.7034 (mtm) REVERT: A 504 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 510 LEU cc_start: 0.8535 (tp) cc_final: 0.8309 (tp) REVERT: A 518 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 533 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.6997 (tt) REVERT: A 542 MET cc_start: 0.7352 (ptp) cc_final: 0.6927 (ptp) REVERT: A 577 LEU cc_start: 0.8164 (mm) cc_final: 0.7670 (mm) REVERT: A 580 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 581 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7495 (pt0) REVERT: A 611 GLN cc_start: 0.7768 (mp10) cc_final: 0.7056 (mp10) REVERT: A 627 CYS cc_start: 0.8144 (m) cc_final: 0.7920 (m) REVERT: A 644 LYS cc_start: 0.8492 (tppt) cc_final: 0.7756 (tppt) REVERT: A 645 LYS cc_start: 0.8287 (mttt) cc_final: 0.7521 (mmtt) REVERT: A 648 PHE cc_start: 0.8088 (t80) cc_final: 0.7474 (t80) REVERT: A 660 GLN cc_start: 0.8309 (pp30) cc_final: 0.7870 (pp30) REVERT: A 663 LYS cc_start: 0.8820 (pttp) cc_final: 0.8358 (pptt) REVERT: A 664 ASP cc_start: 0.8227 (m-30) cc_final: 0.7729 (m-30) REVERT: A 708 GLU cc_start: 0.7377 (pp20) cc_final: 0.7106 (pp20) REVERT: A 710 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8150 (ptp-170) REVERT: A 711 LYS cc_start: 0.8788 (mppt) cc_final: 0.8387 (mmtm) REVERT: A 712 GLU cc_start: 0.7901 (pm20) cc_final: 0.7587 (pm20) REVERT: A 713 PHE cc_start: 0.8445 (t80) cc_final: 0.8108 (t80) REVERT: A 717 TYR cc_start: 0.8268 (t80) cc_final: 0.7877 (t80) REVERT: A 724 LYS cc_start: 0.8330 (ptpp) cc_final: 0.8067 (ptpp) REVERT: A 738 HIS cc_start: 0.7076 (t-90) cc_final: 0.6731 (t-90) REVERT: A 747 LYS cc_start: 0.8576 (mmmm) cc_final: 0.7986 (mmtm) REVERT: A 754 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7372 (mp0) REVERT: A 757 LEU cc_start: 0.8541 (tp) cc_final: 0.8250 (tt) REVERT: A 768 GLN cc_start: 0.7791 (mp10) cc_final: 0.7310 (mp10) REVERT: A 772 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7079 (mp0) REVERT: A 786 LEU cc_start: 0.8973 (tp) cc_final: 0.8739 (tp) REVERT: A 788 ARG cc_start: 0.6929 (mmm-85) cc_final: 0.6589 (tpp-160) REVERT: A 800 GLU cc_start: 0.7711 (tp30) cc_final: 0.7165 (tp30) REVERT: A 802 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7991 (mtpt) REVERT: A 804 LEU cc_start: 0.8400 (mt) cc_final: 0.7976 (mt) REVERT: A 829 LYS cc_start: 0.8427 (tttt) cc_final: 0.8126 (ttpt) REVERT: A 836 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7549 (mtt90) REVERT: A 841 HIS cc_start: 0.7891 (t70) cc_final: 0.7309 (t70) REVERT: A 855 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7718 (tttm) REVERT: D 17 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6892 (mmt180) REVERT: D 22 LEU cc_start: 0.7853 (tp) cc_final: 0.7493 (tp) REVERT: D 25 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8170 (mm-30) REVERT: D 26 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8111 (mp) REVERT: D 41 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8054 (mmtt) REVERT: D 48 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: D 77 TYR cc_start: 0.7957 (m-80) cc_final: 0.7673 (m-80) REVERT: D 89 SER cc_start: 0.8325 (p) cc_final: 0.8037 (t) REVERT: D 91 TYR cc_start: 0.8593 (m-10) cc_final: 0.8361 (m-10) REVERT: D 96 GLU cc_start: 0.7610 (tp30) cc_final: 0.7353 (tp30) REVERT: D 115 LYS cc_start: 0.8664 (tttm) cc_final: 0.8191 (ptmm) REVERT: D 121 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: D 124 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7727 (ttp80) REVERT: D 131 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7774 (ttm110) REVERT: C 123 LYS cc_start: 0.7965 (tptp) cc_final: 0.7530 (tppt) REVERT: C 161 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7912 (pm20) REVERT: C 268 GLU cc_start: 0.8300 (tt0) cc_final: 0.7781 (tm-30) REVERT: C 283 TYR cc_start: 0.7995 (t80) cc_final: 0.7593 (t80) REVERT: C 291 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6974 (tmm) REVERT: C 310 CYS cc_start: 0.8314 (m) cc_final: 0.7647 (m) REVERT: C 315 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8014 (mmmm) REVERT: C 321 GLN cc_start: 0.8379 (mt0) cc_final: 0.8093 (mt0) REVERT: C 323 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8062 (tttt) REVERT: C 327 LEU cc_start: 0.8153 (mt) cc_final: 0.7915 (mt) REVERT: C 336 ILE cc_start: 0.8524 (mm) cc_final: 0.8283 (mm) REVERT: C 338 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7358 (tpt170) REVERT: C 340 MET cc_start: 0.7636 (tmm) cc_final: 0.6893 (tmm) REVERT: C 397 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6666 (p0) REVERT: C 401 ILE cc_start: 0.8737 (mm) cc_final: 0.8461 (pt) REVERT: C 403 GLU cc_start: 0.7478 (pm20) cc_final: 0.7137 (pm20) REVERT: C 407 LEU cc_start: 0.8817 (mt) cc_final: 0.8526 (mt) REVERT: C 410 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6663 (tm-30) REVERT: C 411 GLU cc_start: 0.8185 (tt0) cc_final: 0.7769 (tm-30) REVERT: C 426 ASP cc_start: 0.8284 (t0) cc_final: 0.7928 (t0) REVERT: C 428 LEU cc_start: 0.8747 (tp) cc_final: 0.8356 (tp) REVERT: C 447 GLU cc_start: 0.7566 (mp0) cc_final: 0.7079 (mp0) REVERT: C 452 GLU cc_start: 0.7708 (mp0) cc_final: 0.7243 (mp0) REVERT: C 470 GLU cc_start: 0.7887 (tt0) cc_final: 0.7601 (tm-30) REVERT: C 515 GLN cc_start: 0.8067 (tp40) cc_final: 0.7864 (mm-40) REVERT: C 521 PRO cc_start: 0.8520 (Cg_endo) cc_final: 0.8241 (Cg_exo) REVERT: C 526 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7539 (tmtt) REVERT: C 539 ARG cc_start: 0.8008 (tpt-90) cc_final: 0.7635 (tpt-90) REVERT: C 541 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7428 (tp30) REVERT: C 547 ASN cc_start: 0.7594 (m-40) cc_final: 0.7172 (p0) REVERT: C 550 ASP cc_start: 0.7890 (m-30) cc_final: 0.6768 (m-30) REVERT: C 552 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7395 (mmtm) REVERT: C 558 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6125 (tm-30) REVERT: C 572 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7488 (mtmm) REVERT: C 577 LEU cc_start: 0.8226 (mm) cc_final: 0.7738 (mm) REVERT: C 580 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 581 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7813 (tm-30) REVERT: C 582 ILE cc_start: 0.8501 (mt) cc_final: 0.7446 (pt) REVERT: C 609 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7197 (mp0) REVERT: C 644 LYS cc_start: 0.8301 (tppt) cc_final: 0.7767 (tppt) REVERT: C 645 LYS cc_start: 0.8307 (mttt) cc_final: 0.7490 (mmtt) REVERT: C 663 LYS cc_start: 0.8938 (pttp) cc_final: 0.8593 (pptt) REVERT: C 664 ASP cc_start: 0.8133 (m-30) cc_final: 0.7801 (m-30) REVERT: C 712 GLU cc_start: 0.7884 (pm20) cc_final: 0.7458 (pm20) REVERT: C 713 PHE cc_start: 0.8547 (t80) cc_final: 0.8200 (t80) REVERT: C 735 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7870 (ttp80) REVERT: C 743 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6967 (mt-10) REVERT: C 747 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8095 (mmmm) REVERT: C 754 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7325 (mp0) REVERT: C 757 LEU cc_start: 0.8525 (tp) cc_final: 0.8248 (tt) REVERT: C 764 ASN cc_start: 0.8081 (p0) cc_final: 0.7808 (p0) REVERT: C 766 ASP cc_start: 0.7045 (t0) cc_final: 0.6485 (t0) REVERT: C 768 GLN cc_start: 0.7922 (mp10) cc_final: 0.7027 (mp10) REVERT: C 772 GLU cc_start: 0.7728 (mp0) cc_final: 0.7203 (mp0) REVERT: C 800 GLU cc_start: 0.7655 (tp30) cc_final: 0.7064 (tp30) REVERT: C 802 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8162 (mtpp) REVERT: C 804 LEU cc_start: 0.8414 (mt) cc_final: 0.7796 (mp) REVERT: C 836 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7431 (mtt90) outliers start: 46 outliers final: 30 residues processed: 567 average time/residue: 0.1625 time to fit residues: 122.5872 Evaluate side-chains 578 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 538 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.114534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097499 restraints weight = 27402.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101093 restraints weight = 13378.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103434 restraints weight = 7870.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105015 restraints weight = 5286.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106071 restraints weight = 3918.518| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13920 Z= 0.142 Angle : 0.683 9.915 18800 Z= 0.336 Chirality : 0.043 0.270 2058 Planarity : 0.004 0.031 2434 Dihedral : 3.845 16.891 1844 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.89 % Allowed : 31.64 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1648 helix: 0.60 (0.18), residues: 846 sheet: -3.40 (0.57), residues: 48 loop : 0.27 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 649 TYR 0.019 0.001 TYR A 659 PHE 0.026 0.002 PHE B 76 TRP 0.024 0.002 TRP A 328 HIS 0.004 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00320 (13904) covalent geometry : angle 0.67424 (18776) hydrogen bonds : bond 0.03747 ( 618) hydrogen bonds : angle 4.41034 ( 1752) metal coordination : bond 0.00489 ( 16) metal coordination : angle 3.08808 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 545 time to evaluate : 0.505 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: B 15 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7160 (mmt180) REVERT: B 25 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 26 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 41 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8042 (mmtt) REVERT: B 77 TYR cc_start: 0.7869 (m-80) cc_final: 0.7609 (m-80) REVERT: B 91 TYR cc_start: 0.8714 (m-10) cc_final: 0.8266 (m-10) REVERT: B 94 THR cc_start: 0.8526 (m) cc_final: 0.8263 (p) REVERT: B 96 GLU cc_start: 0.7572 (tp30) cc_final: 0.7279 (tp30) REVERT: B 118 SER cc_start: 0.8601 (m) cc_final: 0.7983 (p) REVERT: B 121 GLU cc_start: 0.8346 (mp0) cc_final: 0.8056 (mp0) REVERT: B 123 GLN cc_start: 0.8173 (tp40) cc_final: 0.7645 (tp40) REVERT: B 131 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8057 (mtt90) REVERT: A 128 LEU cc_start: 0.8279 (mp) cc_final: 0.7981 (mp) REVERT: A 135 GLU cc_start: 0.7541 (pt0) cc_final: 0.7326 (pp20) REVERT: A 241 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: A 243 TYR cc_start: 0.7637 (m-80) cc_final: 0.7321 (m-80) REVERT: A 245 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7467 (mmp80) REVERT: A 247 LEU cc_start: 0.8402 (mp) cc_final: 0.8159 (mm) REVERT: A 264 SER cc_start: 0.8427 (m) cc_final: 0.8020 (p) REVERT: A 267 VAL cc_start: 0.8903 (t) cc_final: 0.8636 (p) REVERT: A 268 GLU cc_start: 0.8425 (tt0) cc_final: 0.7794 (tm-30) REVERT: A 291 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: A 310 CYS cc_start: 0.8229 (m) cc_final: 0.7662 (m) REVERT: A 313 MET cc_start: 0.8076 (mtp) cc_final: 0.7840 (ttm) REVERT: A 315 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8050 (mmmm) REVERT: A 338 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7383 (tpt90) REVERT: A 340 MET cc_start: 0.7932 (tmm) cc_final: 0.7273 (tmm) REVERT: A 341 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 387 GLU cc_start: 0.6788 (pm20) cc_final: 0.6151 (mp0) REVERT: A 392 HIS cc_start: 0.7385 (m-70) cc_final: 0.7011 (m-70) REVERT: A 394 GLU cc_start: 0.7399 (tp30) cc_final: 0.6275 (tp30) REVERT: A 397 ASP cc_start: 0.6564 (p0) cc_final: 0.6266 (p0) REVERT: A 406 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 407 LEU cc_start: 0.8732 (mt) cc_final: 0.8404 (mt) REVERT: A 411 GLU cc_start: 0.8120 (tt0) cc_final: 0.7516 (tm-30) REVERT: A 429 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7107 (tp30) REVERT: A 435 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7950 (tptp) REVERT: A 452 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7281 (mp0) REVERT: A 462 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7302 (mtmm) REVERT: A 470 GLU cc_start: 0.7757 (tt0) cc_final: 0.7480 (tt0) REVERT: A 504 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 533 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7013 (tt) REVERT: A 542 MET cc_start: 0.7272 (ptp) cc_final: 0.6866 (ptp) REVERT: A 577 LEU cc_start: 0.8169 (mm) cc_final: 0.7685 (mm) REVERT: A 580 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 581 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7531 (pt0) REVERT: A 611 GLN cc_start: 0.7624 (mp10) cc_final: 0.7041 (mp10) REVERT: A 627 CYS cc_start: 0.8131 (m) cc_final: 0.7915 (m) REVERT: A 645 LYS cc_start: 0.8379 (mttt) cc_final: 0.7638 (mmtt) REVERT: A 648 PHE cc_start: 0.8074 (t80) cc_final: 0.7434 (t80) REVERT: A 660 GLN cc_start: 0.8269 (pp30) cc_final: 0.7775 (pp30) REVERT: A 663 LYS cc_start: 0.8769 (pttp) cc_final: 0.8368 (pptt) REVERT: A 664 ASP cc_start: 0.8125 (m-30) cc_final: 0.7643 (m-30) REVERT: A 708 GLU cc_start: 0.7365 (pp20) cc_final: 0.7059 (pp20) REVERT: A 710 ARG cc_start: 0.8447 (ptm160) cc_final: 0.8121 (ptp-170) REVERT: A 712 GLU cc_start: 0.7870 (pm20) cc_final: 0.7580 (pm20) REVERT: A 713 PHE cc_start: 0.8400 (t80) cc_final: 0.8073 (t80) REVERT: A 717 TYR cc_start: 0.8255 (t80) cc_final: 0.7881 (t80) REVERT: A 724 LYS cc_start: 0.8338 (ptpp) cc_final: 0.8034 (ptpp) REVERT: A 738 HIS cc_start: 0.7085 (t-90) cc_final: 0.6719 (t-90) REVERT: A 747 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8022 (mmtm) REVERT: A 754 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7387 (mp0) REVERT: A 757 LEU cc_start: 0.8550 (tp) cc_final: 0.8264 (tt) REVERT: A 768 GLN cc_start: 0.7757 (mp10) cc_final: 0.6750 (mp10) REVERT: A 772 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7064 (mp0) REVERT: A 786 LEU cc_start: 0.8971 (tp) cc_final: 0.8753 (tp) REVERT: A 788 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6618 (tpp-160) REVERT: A 800 GLU cc_start: 0.7712 (tp30) cc_final: 0.7213 (tp30) REVERT: A 802 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8077 (mtpp) REVERT: A 804 LEU cc_start: 0.8427 (mt) cc_final: 0.8014 (mt) REVERT: A 829 LYS cc_start: 0.8445 (tttt) cc_final: 0.8075 (ttpp) REVERT: A 836 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7545 (mtt90) REVERT: A 841 HIS cc_start: 0.7897 (t70) cc_final: 0.7349 (t70) REVERT: A 855 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7705 (tttm) REVERT: D 17 ARG cc_start: 0.7318 (mmt180) cc_final: 0.6896 (mmt180) REVERT: D 22 LEU cc_start: 0.7840 (tp) cc_final: 0.7486 (tp) REVERT: D 25 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 26 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8083 (mp) REVERT: D 41 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8060 (mmtt) REVERT: D 48 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: D 77 TYR cc_start: 0.7970 (m-80) cc_final: 0.7710 (m-80) REVERT: D 89 SER cc_start: 0.8372 (p) cc_final: 0.8072 (t) REVERT: D 96 GLU cc_start: 0.7550 (tp30) cc_final: 0.7342 (tp30) REVERT: D 103 LEU cc_start: 0.8803 (mm) cc_final: 0.8468 (tt) REVERT: D 115 LYS cc_start: 0.8693 (tttm) cc_final: 0.8228 (ptmm) REVERT: D 121 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: D 124 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7742 (ttp80) REVERT: D 131 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7867 (ttm110) REVERT: C 123 LYS cc_start: 0.7966 (tptp) cc_final: 0.7524 (tppt) REVERT: C 241 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7834 (mtm-85) REVERT: C 251 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7825 (mtmm) REVERT: C 268 GLU cc_start: 0.8265 (tt0) cc_final: 0.7789 (tm-30) REVERT: C 283 TYR cc_start: 0.7963 (t80) cc_final: 0.7619 (t80) REVERT: C 291 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6871 (tmm) REVERT: C 310 CYS cc_start: 0.8211 (m) cc_final: 0.7666 (m) REVERT: C 313 MET cc_start: 0.8044 (ttp) cc_final: 0.7815 (ttt) REVERT: C 315 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8083 (mmmm) REVERT: C 321 GLN cc_start: 0.8349 (mt0) cc_final: 0.8117 (mt0) REVERT: C 323 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8088 (tttt) REVERT: C 327 LEU cc_start: 0.8148 (mt) cc_final: 0.7929 (mt) REVERT: C 336 ILE cc_start: 0.8538 (mm) cc_final: 0.8310 (mm) REVERT: C 338 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7399 (tpt170) REVERT: C 340 MET cc_start: 0.7552 (tmm) cc_final: 0.6810 (tmm) REVERT: C 341 GLU cc_start: 0.7730 (pt0) cc_final: 0.6937 (pt0) REVERT: C 395 GLU cc_start: 0.8296 (pp20) cc_final: 0.7846 (pp20) REVERT: C 397 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6580 (p0) REVERT: C 401 ILE cc_start: 0.8747 (mm) cc_final: 0.8476 (pt) REVERT: C 403 GLU cc_start: 0.7491 (pm20) cc_final: 0.7132 (pm20) REVERT: C 407 LEU cc_start: 0.8814 (mt) cc_final: 0.8512 (mt) REVERT: C 410 GLN cc_start: 0.7482 (mm-40) cc_final: 0.6668 (tm-30) REVERT: C 411 GLU cc_start: 0.8157 (tt0) cc_final: 0.7793 (tm-30) REVERT: C 426 ASP cc_start: 0.8236 (t0) cc_final: 0.8026 (t0) REVERT: C 428 LEU cc_start: 0.8733 (tp) cc_final: 0.8349 (tp) REVERT: C 447 GLU cc_start: 0.7573 (mp0) cc_final: 0.7064 (mp0) REVERT: C 452 GLU cc_start: 0.7725 (mp0) cc_final: 0.7266 (mp0) REVERT: C 521 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8258 (Cg_exo) REVERT: C 526 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7592 (tmtt) REVERT: C 539 ARG cc_start: 0.7984 (tpt-90) cc_final: 0.7616 (tpt-90) REVERT: C 541 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7442 (tp30) REVERT: C 547 ASN cc_start: 0.7263 (m-40) cc_final: 0.6330 (m-40) REVERT: C 550 ASP cc_start: 0.7896 (m-30) cc_final: 0.7670 (m-30) REVERT: C 552 LYS cc_start: 0.7752 (mmtm) cc_final: 0.7414 (mmtm) REVERT: C 558 GLU cc_start: 0.6466 (tm-30) cc_final: 0.6111 (tm-30) REVERT: C 572 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7505 (mtmm) REVERT: C 577 LEU cc_start: 0.8233 (mm) cc_final: 0.7722 (mm) REVERT: C 580 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 582 ILE cc_start: 0.8483 (mt) cc_final: 0.8250 (pt) REVERT: C 594 GLU cc_start: 0.7233 (mp0) cc_final: 0.6871 (mp0) REVERT: C 609 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7097 (mp0) REVERT: C 644 LYS cc_start: 0.8338 (tppt) cc_final: 0.7785 (tppt) REVERT: C 645 LYS cc_start: 0.8322 (mttt) cc_final: 0.7340 (mmmm) REVERT: C 660 GLN cc_start: 0.8460 (pp30) cc_final: 0.8233 (pp30) REVERT: C 663 LYS cc_start: 0.8921 (pttp) cc_final: 0.8575 (pptt) REVERT: C 664 ASP cc_start: 0.8050 (m-30) cc_final: 0.7838 (m-30) REVERT: C 712 GLU cc_start: 0.7869 (pm20) cc_final: 0.7459 (pm20) REVERT: C 713 PHE cc_start: 0.8489 (t80) cc_final: 0.8151 (t80) REVERT: C 735 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7887 (ttp80) REVERT: C 743 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 747 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8086 (mmmm) REVERT: C 754 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7361 (mp0) REVERT: C 757 LEU cc_start: 0.8539 (tp) cc_final: 0.8276 (tt) REVERT: C 764 ASN cc_start: 0.8059 (p0) cc_final: 0.7796 (p0) REVERT: C 766 ASP cc_start: 0.7034 (t0) cc_final: 0.6465 (t0) REVERT: C 768 GLN cc_start: 0.7902 (mp10) cc_final: 0.6916 (mp10) REVERT: C 772 GLU cc_start: 0.7699 (mp0) cc_final: 0.7113 (mp0) REVERT: C 800 GLU cc_start: 0.7679 (tp30) cc_final: 0.7115 (tp30) REVERT: C 802 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8177 (mtpp) REVERT: C 804 LEU cc_start: 0.8441 (mt) cc_final: 0.7818 (mp) REVERT: C 836 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7399 (mtt90) outliers start: 44 outliers final: 33 residues processed: 560 average time/residue: 0.1648 time to fit residues: 122.9265 Evaluate side-chains 587 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 544 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097397 restraints weight = 27437.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100992 restraints weight = 13388.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103308 restraints weight = 7879.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104890 restraints weight = 5298.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105950 restraints weight = 3931.516| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13920 Z= 0.145 Angle : 0.686 10.381 18800 Z= 0.337 Chirality : 0.043 0.270 2058 Planarity : 0.004 0.037 2434 Dihedral : 3.854 16.907 1844 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.76 % Allowed : 31.32 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1648 helix: 0.62 (0.18), residues: 844 sheet: -3.51 (0.55), residues: 48 loop : 0.25 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 763 TYR 0.021 0.001 TYR B 99 PHE 0.027 0.002 PHE A 606 TRP 0.029 0.002 TRP A 328 HIS 0.004 0.001 HIS C 738 Details of bonding type rmsd covalent geometry : bond 0.00326 (13904) covalent geometry : angle 0.67744 (18776) hydrogen bonds : bond 0.03750 ( 618) hydrogen bonds : angle 4.40640 ( 1752) metal coordination : bond 0.00509 ( 16) metal coordination : angle 3.17385 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.24 seconds wall clock time: 48 minutes 45.18 seconds (2925.18 seconds total)