Starting phenix.real_space_refine on Thu Jul 31 17:58:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrp_36601/07_2025/8jrp_36601.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrp_36601/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrp_36601/07_2025/8jrp_36601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrp_36601/07_2025/8jrp_36601.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrp_36601/07_2025/8jrp_36601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrp_36601/07_2025/8jrp_36601.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP: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: 7.97, per 1000 atoms: 0.58 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.53 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: 3.90 Time building geometry restraints manager: 3.92 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: 0.07 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.490 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (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 TRP 0.003 0.001 TRP C 791 HIS 0.003 0.001 HIS B 31 PHE 0.011 0.001 PHE C 797 TYR 0.013 0.001 TYR B 61 ARG 0.002 0.000 ARG C 788 Details of bonding type rmsd hydrogen bonds : bond 0.15679 ( 618) hydrogen bonds : angle 5.83872 ( 1752) metal coordination : bond 0.00265 ( 16) metal coordination : angle 2.09374 ( 24) covalent geometry : bond 0.00277 (13904) covalent geometry : angle 0.54200 (18776) *********************** 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 : 1.628 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: 0.8139 (tp) REVERT: B 21 GLN cc_start: 0.7985 (tt0) cc_final: 0.7785 (pt0) REVERT: B 22 LEU cc_start: 0.7814 (tp) cc_final: 0.7610 (tp) REVERT: B 26 LEU cc_start: 0.8335 (mp) cc_final: 0.8089 (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: 0.7847 (m-80) REVERT: B 84 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7982 (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: 0.7945 (p) REVERT: B 96 GLU cc_start: 0.7589 (tp30) cc_final: 0.7236 (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: 0.7591 (mp0) REVERT: B 124 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7650 (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: 0.7800 (mtt90) REVERT: B 135 ILE cc_start: 0.8636 (mm) cc_final: 0.8261 (mm) REVERT: B 138 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7340 (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: 0.7804 (mm) REVERT: A 135 GLU cc_start: 0.7981 (pt0) cc_final: 0.7598 (pp20) REVERT: A 151 ARG cc_start: 0.7005 (ptm160) cc_final: 0.6775 (ptm160) REVERT: A 167 PHE cc_start: 0.7912 (m-80) cc_final: 0.7561 (m-80) REVERT: A 247 LEU cc_start: 0.8033 (mp) cc_final: 0.7612 (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: 0.7637 (t0) REVERT: A 283 TYR cc_start: 0.8184 (t80) cc_final: 0.7798 (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: 0.7822 (mt) REVERT: A 328 TRP cc_start: 0.8380 (m-10) cc_final: 0.8098 (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: 0.6892 (tmm) REVERT: A 352 ILE cc_start: 0.8963 (mm) cc_final: 0.8754 (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: 0.5495 (mp0) REVERT: A 394 GLU cc_start: 0.7275 (tp30) cc_final: 0.6498 (tp30) REVERT: A 397 ASP cc_start: 0.6759 (p0) cc_final: 0.6072 (p0) REVERT: A 403 GLU cc_start: 0.7691 (pm20) cc_final: 0.7357 (pm20) REVERT: A 406 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 407 LEU cc_start: 0.8908 (mt) cc_final: 0.8638 (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: 0.8522 (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: 0.6393 (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: 0.6964 (tt0) REVERT: A 504 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7064 (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: 0.8315 (p) REVERT: A 541 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7553 (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: 0.5969 (t0) REVERT: A 609 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6991 (mp0) REVERT: A 611 GLN cc_start: 0.7855 (mp10) cc_final: 0.7325 (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: 0.8300 (pptt) REVERT: A 677 MET cc_start: 0.5856 (mmm) cc_final: 0.5412 (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: 0.8078 (t80) REVERT: A 738 HIS cc_start: 0.7326 (t70) cc_final: 0.6956 (t70) REVERT: A 747 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7887 (tppt) REVERT: A 757 LEU cc_start: 0.8687 (tp) cc_final: 0.8375 (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: 0.7201 (mp10) REVERT: A 772 GLU cc_start: 0.7286 (mp0) cc_final: 0.6786 (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: 0.8011 (mt) REVERT: A 841 HIS cc_start: 0.8091 (t70) cc_final: 0.7619 (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: 0.7776 (mp0) REVERT: D 26 LEU cc_start: 0.8228 (mp) cc_final: 0.7980 (mp) REVERT: D 41 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7755 (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: 0.7570 (tpp80) REVERT: D 77 TYR cc_start: 0.8287 (m-80) cc_final: 0.7954 (m-80) REVERT: D 84 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7839 (ttm170) REVERT: D 85 HIS cc_start: 0.8692 (m-70) cc_final: 0.8481 (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: 0.7873 (p) REVERT: D 96 GLU cc_start: 0.7679 (tp30) cc_final: 0.7408 (tp30) REVERT: D 103 LEU cc_start: 0.8262 (mm) cc_final: 0.7989 (mt) REVERT: D 123 GLN cc_start: 0.7926 (tp40) cc_final: 0.7264 (tp40) REVERT: D 124 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7566 (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: 0.6989 (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: 0.6714 (mtm110) REVERT: C 239 ILE cc_start: 0.8755 (mm) cc_final: 0.8448 (mm) REVERT: C 241 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7980 (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: 0.7420 (mmm-85) 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: 0.8226 (mm) REVERT: C 310 CYS cc_start: 0.7867 (m) cc_final: 0.7403 (m) REVERT: C 315 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8140 (mmmt) REVERT: C 323 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8312 (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: 0.8150 (m-10) REVERT: C 336 ILE cc_start: 0.8176 (mm) cc_final: 0.7975 (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: 0.8254 (p) REVERT: C 394 GLU cc_start: 0.7165 (tp30) cc_final: 0.5830 (tp30) REVERT: C 403 GLU cc_start: 0.7690 (pm20) cc_final: 0.7315 (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: 0.7652 (tt0) REVERT: C 426 ASP cc_start: 0.8338 (t0) cc_final: 0.8130 (t0) REVERT: C 428 LEU cc_start: 0.8764 (tp) cc_final: 0.8445 (tp) REVERT: C 452 GLU cc_start: 0.7377 (mp0) cc_final: 0.6919 (mp0) REVERT: C 470 GLU cc_start: 0.7505 (tt0) cc_final: 0.7251 (tt0) REVERT: C 501 MET cc_start: 0.6947 (mtm) cc_final: 0.6650 (mtt) REVERT: C 504 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 507 ILE cc_start: 0.8266 (mt) cc_final: 0.8047 (tp) REVERT: C 539 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7404 (tpt-90) REVERT: C 540 LEU cc_start: 0.8504 (mt) cc_final: 0.8220 (mm) REVERT: C 541 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7550 (tp30) REVERT: C 550 ASP cc_start: 0.7777 (t70) cc_final: 0.7380 (t70) REVERT: C 558 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6055 (tm-30) REVERT: C 566 ASP cc_start: 0.6601 (t0) cc_final: 0.6182 (t0) REVERT: C 580 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 609 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7001 (mp0) REVERT: C 611 GLN cc_start: 0.7991 (mp10) cc_final: 0.7384 (mp10) REVERT: C 621 LEU cc_start: 0.8438 (mt) cc_final: 0.8203 (mt) REVERT: C 644 LYS cc_start: 0.8183 (tppt) cc_final: 0.7805 (tppt) REVERT: C 645 LYS cc_start: 0.8329 (mttt) cc_final: 0.7666 (mmtt) REVERT: C 647 THR cc_start: 0.7896 (p) cc_final: 0.7623 (t) REVERT: C 664 ASP cc_start: 0.8607 (m-30) cc_final: 0.8088 (m-30) REVERT: C 677 MET cc_start: 0.5634 (mmm) cc_final: 0.5160 (mmm) REVERT: C 710 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8089 (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: 0.8167 (t80) REVERT: C 728 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8288 (ttpp) REVERT: C 747 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7910 (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: 0.6916 (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: 0.7979 (mtpp) REVERT: C 804 LEU cc_start: 0.8503 (mt) cc_final: 0.8177 (mt) REVERT: C 841 HIS cc_start: 0.8122 (t70) cc_final: 0.7689 (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: 0.8240 (ttmm) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.3544 time to fit residues: 278.5958 Evaluate side-chains 554 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 515 GLN C 517 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.118044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100980 restraints weight = 26968.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104589 restraints weight = 13197.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106953 restraints weight = 7766.947| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1998 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= 0.160 Angle : 0.588 10.552 18800 Z= 0.295 Chirality : 0.042 0.165 2058 Planarity : 0.004 0.069 2434 Dihedral : 3.657 15.667 1844 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.24 % Allowed : 25.07 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1648 helix: 0.67 (0.18), residues: 864 sheet: -0.98 (0.60), residues: 68 loop : 0.14 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 791 HIS 0.003 0.001 HIS C 738 PHE 0.021 0.002 PHE C 256 TYR 0.016 0.001 TYR A 494 ARG 0.006 0.000 ARG C 649 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 618) hydrogen bonds : angle 4.70806 ( 1752) metal coordination : bond 0.00779 ( 16) metal coordination : angle 3.16495 ( 24) covalent geometry : bond 0.00332 (13904) covalent geometry : angle 0.57737 (18776) *********************** 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 611 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 577 time to evaluate : 1.494 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: 0.8550 (mp) cc_final: 0.8267 (mp) REVERT: B 41 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7818 (mmtt) REVERT: B 44 LEU cc_start: 0.8759 (mp) cc_final: 0.8541 (mp) REVERT: B 77 TYR cc_start: 0.8255 (m-80) cc_final: 0.7997 (m-80) REVERT: B 85 HIS cc_start: 0.8727 (m90) cc_final: 0.8508 (m-70) REVERT: B 91 TYR cc_start: 0.8746 (m-10) cc_final: 0.8490 (m-10) REVERT: B 94 THR cc_start: 0.8563 (m) cc_final: 0.8314 (p) REVERT: B 96 GLU cc_start: 0.7815 (tp30) cc_final: 0.7498 (tp30) REVERT: B 97 GLN cc_start: 0.8018 (tp40) cc_final: 0.7631 (tp40) REVERT: B 98 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 118 SER cc_start: 0.8413 (m) cc_final: 0.7875 (t) REVERT: B 121 GLU cc_start: 0.8353 (mp0) cc_final: 0.7825 (mp0) REVERT: B 124 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7745 (ttp80) REVERT: B 131 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7943 (ttm110) REVERT: A 128 LEU cc_start: 0.8181 (mp) cc_final: 0.7851 (mt) REVERT: A 135 GLU cc_start: 0.7681 (pt0) cc_final: 0.7446 (pp20) REVERT: A 151 ARG cc_start: 0.7079 (ptm160) cc_final: 0.6844 (ptm160) REVERT: A 243 TYR cc_start: 0.7876 (m-80) cc_final: 0.7425 (m-80) REVERT: A 268 GLU cc_start: 0.8399 (tt0) cc_final: 0.7916 (tm-30) REVERT: A 270 ASP cc_start: 0.7889 (t0) cc_final: 0.7664 (t0) REVERT: A 276 VAL cc_start: 0.8498 (m) cc_final: 0.8221 (m) REVERT: A 306 LEU cc_start: 0.7927 (tp) cc_final: 0.7510 (tp) REVERT: A 310 CYS cc_start: 0.8204 (m) cc_final: 0.7800 (m) REVERT: A 315 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8128 (mmmm) REVERT: A 321 GLN cc_start: 0.8421 (mt0) cc_final: 0.8200 (mt0) REVERT: A 327 LEU cc_start: 0.8184 (mt) cc_final: 0.7904 (mt) REVERT: A 328 TRP cc_start: 0.8568 (m-10) cc_final: 0.8252 (m-10) REVERT: A 338 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7325 (mmm160) REVERT: A 340 MET cc_start: 0.7854 (tmm) cc_final: 0.7279 (tmm) REVERT: A 341 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7136 (pt0) REVERT: A 378 VAL cc_start: 0.8719 (t) cc_final: 0.8502 (p) REVERT: A 383 VAL cc_start: 0.8600 (t) cc_final: 0.8282 (p) REVERT: A 387 GLU cc_start: 0.6938 (pm20) cc_final: 0.5978 (mp0) REVERT: A 394 GLU cc_start: 0.7354 (tp30) cc_final: 0.6238 (tp30) REVERT: A 397 ASP cc_start: 0.6759 (p0) cc_final: 0.6191 (p0) REVERT: A 405 SER cc_start: 0.8254 (m) cc_final: 0.7618 (p) REVERT: A 406 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 407 LEU cc_start: 0.8795 (mt) cc_final: 0.8494 (mt) REVERT: A 409 LEU cc_start: 0.8387 (tp) cc_final: 0.8158 (tp) REVERT: A 410 GLN cc_start: 0.7378 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 435 LYS cc_start: 0.8320 (tmtt) cc_final: 0.8066 (tptp) REVERT: A 459 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6600 (mm-30) REVERT: A 462 LYS cc_start: 0.7865 (mttm) cc_final: 0.7586 (mtmm) REVERT: A 470 GLU cc_start: 0.7945 (tt0) cc_final: 0.7696 (tt0) REVERT: A 504 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 515 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 533 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7124 (pt) REVERT: A 541 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7453 (tp30) REVERT: A 566 ASP cc_start: 0.6549 (t0) cc_final: 0.6322 (t0) REVERT: A 577 LEU cc_start: 0.8135 (mm) cc_final: 0.7574 (mm) REVERT: A 580 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 581 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 609 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7201 (mp0) REVERT: A 611 GLN cc_start: 0.8014 (mp10) cc_final: 0.7341 (mp10) REVERT: A 612 PHE cc_start: 0.8573 (m-80) cc_final: 0.8119 (m-10) REVERT: A 644 LYS cc_start: 0.8339 (tppt) cc_final: 0.7735 (tppt) REVERT: A 645 LYS cc_start: 0.8277 (mttt) cc_final: 0.7433 (mmtt) REVERT: A 677 MET cc_start: 0.5483 (mmm) cc_final: 0.5158 (mmm) REVERT: A 713 PHE cc_start: 0.8502 (t80) cc_final: 0.8010 (t80) REVERT: A 717 TYR cc_start: 0.8137 (t80) cc_final: 0.7616 (t80) REVERT: A 738 HIS cc_start: 0.7293 (t70) cc_final: 0.7032 (t70) REVERT: A 747 LYS cc_start: 0.8469 (mmmm) cc_final: 0.7816 (tptt) REVERT: A 754 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 757 LEU cc_start: 0.8761 (tp) cc_final: 0.8486 (tt) REVERT: A 764 ASN cc_start: 0.8207 (p0) cc_final: 0.7939 (p0) REVERT: A 768 GLN cc_start: 0.7810 (mp10) cc_final: 0.7318 (mp10) REVERT: A 772 GLU cc_start: 0.7708 (mp0) cc_final: 0.7145 (mp0) REVERT: A 800 GLU cc_start: 0.7705 (tp30) cc_final: 0.7066 (tp30) REVERT: A 802 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8105 (mtpp) REVERT: A 804 LEU cc_start: 0.8320 (mt) cc_final: 0.7874 (mt) REVERT: A 841 HIS cc_start: 0.7910 (t70) cc_final: 0.7150 (t70) REVERT: A 863 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8129 (pp) REVERT: A 864 LYS cc_start: 0.8740 (tppt) cc_final: 0.8209 (ttmm) REVERT: D 17 ARG cc_start: 0.7169 (mmt180) cc_final: 0.6721 (mmt180) REVERT: D 22 LEU cc_start: 0.7835 (tp) cc_final: 0.7563 (tp) REVERT: D 25 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7839 (mp0) REVERT: D 26 LEU cc_start: 0.8447 (mp) cc_final: 0.8096 (mp) REVERT: D 41 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7850 (mmtt) REVERT: D 46 ARG cc_start: 0.7672 (mmp-170) cc_final: 0.7450 (mmp-170) REVERT: D 62 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7548 (tpp80) REVERT: D 77 TYR cc_start: 0.8165 (m-80) cc_final: 0.7785 (m-80) REVERT: D 84 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7791 (ttm170) REVERT: D 85 HIS cc_start: 0.8739 (m-70) cc_final: 0.8500 (m-70) REVERT: D 91 TYR cc_start: 0.8724 (m-10) cc_final: 0.8274 (m-10) REVERT: D 94 THR cc_start: 0.8485 (m) cc_final: 0.8239 (p) REVERT: D 96 GLU cc_start: 0.7878 (tp30) cc_final: 0.7620 (tp30) REVERT: D 98 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 121 GLU cc_start: 0.8235 (mp0) cc_final: 0.7693 (mp0) REVERT: D 124 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7856 (ttp80) REVERT: D 131 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7990 (ttm110) REVERT: C 128 LEU cc_start: 0.8193 (mp) cc_final: 0.7800 (mm) REVERT: C 135 GLU cc_start: 0.7856 (pt0) cc_final: 0.7646 (pp20) REVERT: C 144 GLU cc_start: 0.7331 (pm20) cc_final: 0.7049 (pm20) REVERT: C 151 ARG cc_start: 0.7099 (ptm160) cc_final: 0.6803 (mtm110) REVERT: C 239 ILE cc_start: 0.8832 (mm) cc_final: 0.8565 (mm) REVERT: C 241 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: C 243 TYR cc_start: 0.7963 (m-80) cc_final: 0.7550 (m-80) REVERT: C 245 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7503 (mmm-85) REVERT: C 268 GLU cc_start: 0.8267 (tt0) cc_final: 0.7659 (tm-30) REVERT: C 283 TYR cc_start: 0.7896 (t80) cc_final: 0.7576 (t80) REVERT: C 289 ILE cc_start: 0.8594 (mm) cc_final: 0.8287 (mm) REVERT: C 310 CYS cc_start: 0.8208 (m) cc_final: 0.7773 (m) REVERT: C 311 LYS cc_start: 0.8537 (mttt) cc_final: 0.8258 (mttt) REVERT: C 315 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8179 (mmmm) REVERT: C 323 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8479 (ptmt) REVERT: C 327 LEU cc_start: 0.8328 (mt) cc_final: 0.8019 (mt) REVERT: C 328 TRP cc_start: 0.8571 (m-10) cc_final: 0.8224 (m-10) REVERT: C 336 ILE cc_start: 0.8503 (mm) cc_final: 0.8284 (mm) REVERT: C 338 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7530 (tpp-160) REVERT: C 345 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7998 (mm110) REVERT: C 359 ARG cc_start: 0.7757 (mmp-170) cc_final: 0.7334 (mmp80) REVERT: C 378 VAL cc_start: 0.8698 (t) cc_final: 0.8478 (p) REVERT: C 383 VAL cc_start: 0.8647 (t) cc_final: 0.8381 (p) REVERT: C 394 GLU cc_start: 0.7458 (tp30) cc_final: 0.6791 (tp30) REVERT: C 395 GLU cc_start: 0.7996 (pp20) cc_final: 0.7717 (pp20) REVERT: C 403 GLU cc_start: 0.7641 (pm20) cc_final: 0.7353 (pm20) REVERT: C 405 SER cc_start: 0.8412 (m) cc_final: 0.7702 (p) REVERT: C 406 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 407 LEU cc_start: 0.8819 (mt) cc_final: 0.8520 (mt) REVERT: C 410 GLN cc_start: 0.7355 (tm-30) cc_final: 0.6894 (tm-30) REVERT: C 411 GLU cc_start: 0.8142 (tt0) cc_final: 0.7877 (tm-30) REVERT: C 426 ASP cc_start: 0.8410 (t0) cc_final: 0.8072 (t0) REVERT: C 428 LEU cc_start: 0.8832 (tp) cc_final: 0.8470 (tp) REVERT: C 452 GLU cc_start: 0.7659 (mp0) cc_final: 0.7126 (mp0) REVERT: C 459 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6554 (mm-30) REVERT: C 470 GLU cc_start: 0.7845 (tt0) cc_final: 0.7475 (tt0) REVERT: C 504 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7363 (mm-30) REVERT: C 507 ILE cc_start: 0.8402 (mt) cc_final: 0.8165 (tp) REVERT: C 515 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: C 518 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7095 (tm-30) REVERT: C 539 ARG cc_start: 0.7972 (tpt-90) cc_final: 0.7591 (tpt-90) REVERT: C 541 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7801 (tp30) REVERT: C 550 ASP cc_start: 0.8016 (t70) cc_final: 0.7688 (t70) REVERT: C 552 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7744 (mmtm) REVERT: C 558 GLU cc_start: 0.6749 (tm-30) cc_final: 0.6031 (tm-30) REVERT: C 577 LEU cc_start: 0.8166 (mm) cc_final: 0.7544 (mm) REVERT: C 580 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7578 (mt-10) REVERT: C 581 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7143 (mt-10) REVERT: C 587 ILE cc_start: 0.8609 (mm) cc_final: 0.8274 (tp) REVERT: C 594 GLU cc_start: 0.7207 (mp0) cc_final: 0.6855 (mp0) REVERT: C 609 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7252 (mp0) REVERT: C 611 GLN cc_start: 0.8133 (mp10) cc_final: 0.7463 (mp10) REVERT: C 612 PHE cc_start: 0.8682 (m-80) cc_final: 0.8280 (m-10) REVERT: C 621 LEU cc_start: 0.8328 (mt) cc_final: 0.8109 (mt) REVERT: C 644 LYS cc_start: 0.8319 (tppt) cc_final: 0.7652 (tppt) REVERT: C 645 LYS cc_start: 0.8323 (mttt) cc_final: 0.7532 (mmtt) REVERT: C 660 GLN cc_start: 0.8609 (pp30) cc_final: 0.8241 (pp30) REVERT: C 677 MET cc_start: 0.5374 (mmm) cc_final: 0.5011 (mmm) REVERT: C 710 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.8101 (ptp-170) REVERT: C 711 LYS cc_start: 0.8840 (mppt) cc_final: 0.8555 (mppt) REVERT: C 712 GLU cc_start: 0.7858 (pm20) cc_final: 0.7491 (pm20) REVERT: C 713 PHE cc_start: 0.8624 (t80) cc_final: 0.8161 (t80) REVERT: C 735 ARG cc_start: 0.8192 (ttt-90) cc_final: 0.7884 (ttp80) REVERT: C 738 HIS cc_start: 0.7515 (t70) cc_final: 0.7232 (t70) REVERT: C 747 LYS cc_start: 0.8458 (mmmm) cc_final: 0.7929 (tppp) REVERT: C 757 LEU cc_start: 0.8602 (tp) cc_final: 0.8293 (tt) REVERT: C 764 ASN cc_start: 0.8200 (p0) cc_final: 0.7929 (p0) REVERT: C 766 ASP cc_start: 0.7264 (t0) cc_final: 0.6686 (t0) REVERT: C 768 GLN cc_start: 0.7967 (mp10) cc_final: 0.6860 (mp10) REVERT: C 772 GLU cc_start: 0.7735 (mp0) cc_final: 0.7199 (mp0) REVERT: C 792 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 802 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8088 (mtpp) REVERT: C 804 LEU cc_start: 0.8460 (mt) cc_final: 0.8110 (mt) REVERT: C 841 HIS cc_start: 0.7884 (t70) cc_final: 0.7205 (t70) REVERT: C 851 GLU cc_start: 0.6733 (pm20) cc_final: 0.6376 (mp0) REVERT: C 864 LYS cc_start: 0.8738 (tppt) cc_final: 0.8381 (ttmm) outliers start: 34 outliers final: 11 residues processed: 592 average time/residue: 0.3538 time to fit residues: 276.2700 Evaluate side-chains 566 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 552 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 A residue 826 ILE Chi-restraints excluded: chain A residue 863 LEU 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 515 GLN 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 95 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 100 optimal weight: 0.0060 chunk 141 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- 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 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103826 restraints weight = 26868.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.107446 restraints weight = 13066.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.109813 restraints weight = 7670.115| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13920 Z= 0.107 Angle : 0.557 9.076 18800 Z= 0.276 Chirality : 0.041 0.202 2058 Planarity : 0.003 0.047 2434 Dihedral : 3.578 16.491 1844 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.83 % Allowed : 27.30 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1648 helix: 0.63 (0.18), residues: 870 sheet: -1.13 (0.60), residues: 68 loop : 0.07 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 791 HIS 0.002 0.001 HIS D 31 PHE 0.020 0.001 PHE D 76 TYR 0.013 0.001 TYR C 659 ARG 0.005 0.000 ARG A 735 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 618) hydrogen bonds : angle 4.47710 ( 1752) metal coordination : bond 0.00353 ( 16) metal coordination : angle 2.86342 ( 24) covalent geometry : bond 0.00238 (13904) covalent geometry : angle 0.54826 (18776) *********************** 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 626 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 583 time to evaluate : 1.499 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 26 LEU cc_start: 0.8581 (mp) cc_final: 0.8271 (mp) REVERT: B 41 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7903 (mmtt) REVERT: B 44 LEU cc_start: 0.8702 (mp) cc_final: 0.8471 (mp) REVERT: B 76 PHE cc_start: 0.8333 (t80) cc_final: 0.8053 (t80) REVERT: B 77 TYR cc_start: 0.8118 (m-80) cc_final: 0.7672 (m-80) REVERT: B 85 HIS cc_start: 0.8731 (m90) cc_final: 0.8486 (m-70) REVERT: B 91 TYR cc_start: 0.8691 (m-10) cc_final: 0.8285 (m-10) REVERT: B 94 THR cc_start: 0.8454 (m) cc_final: 0.8175 (p) REVERT: B 96 GLU cc_start: 0.7750 (tp30) cc_final: 0.7398 (tp30) REVERT: B 131 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7900 (ttm110) REVERT: B 143 CYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7401 (p) REVERT: A 128 LEU cc_start: 0.8218 (mp) cc_final: 0.7934 (mp) REVERT: A 130 GLU cc_start: 0.7387 (pm20) cc_final: 0.7084 (pp20) REVERT: A 135 GLU cc_start: 0.7653 (pt0) cc_final: 0.7397 (pp20) REVERT: A 151 ARG cc_start: 0.7040 (ptm160) cc_final: 0.6791 (ptm160) REVERT: A 241 ARG cc_start: 0.7987 (mtm-85) cc_final: 0.7594 (mtm-85) REVERT: A 243 TYR cc_start: 0.7815 (m-80) cc_final: 0.7431 (m-80) REVERT: A 267 VAL cc_start: 0.8932 (t) cc_final: 0.8690 (p) REVERT: A 268 GLU cc_start: 0.8395 (tt0) cc_final: 0.7741 (tm-30) REVERT: A 276 VAL cc_start: 0.8547 (m) cc_final: 0.8220 (m) REVERT: A 306 LEU cc_start: 0.7944 (tp) cc_final: 0.7463 (tp) REVERT: A 310 CYS cc_start: 0.8254 (m) cc_final: 0.7748 (m) REVERT: A 315 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7994 (mmmm) REVERT: A 321 GLN cc_start: 0.8333 (mt0) cc_final: 0.8125 (mt0) REVERT: A 327 LEU cc_start: 0.8157 (mt) cc_final: 0.7856 (mt) REVERT: A 338 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7606 (mtp85) REVERT: A 340 MET cc_start: 0.7914 (tmm) cc_final: 0.7312 (tmm) REVERT: A 341 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7030 (pt0) REVERT: A 378 VAL cc_start: 0.8717 (t) cc_final: 0.8485 (p) REVERT: A 383 VAL cc_start: 0.8564 (t) cc_final: 0.8248 (p) REVERT: A 387 GLU cc_start: 0.6780 (pm20) cc_final: 0.5907 (mp0) REVERT: A 394 GLU cc_start: 0.7249 (tp30) cc_final: 0.6989 (tp30) REVERT: A 397 ASP cc_start: 0.6594 (p0) cc_final: 0.6051 (p0) REVERT: A 406 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 407 LEU cc_start: 0.8800 (mt) cc_final: 0.8433 (mt) REVERT: A 410 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7093 (tm-30) REVERT: A 411 GLU cc_start: 0.8136 (tt0) cc_final: 0.7622 (tm-30) REVERT: A 412 LEU cc_start: 0.8493 (mt) cc_final: 0.8101 (mt) REVERT: A 426 ASP cc_start: 0.8166 (t0) cc_final: 0.7908 (t0) REVERT: A 435 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7991 (tptp) REVERT: A 452 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7415 (mp0) REVERT: A 459 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6537 (mm-30) REVERT: A 462 LYS cc_start: 0.7918 (mttm) cc_final: 0.7625 (mtmm) REVERT: A 470 GLU cc_start: 0.7931 (tt0) cc_final: 0.7570 (tt0) REVERT: A 474 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8296 (mmmm) REVERT: A 490 ASN cc_start: 0.7823 (t0) cc_final: 0.7592 (t0) REVERT: A 515 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 533 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7194 (pt) REVERT: A 541 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7468 (tp30) REVERT: A 550 ASP cc_start: 0.7973 (m-30) cc_final: 0.7706 (m-30) REVERT: A 577 LEU cc_start: 0.8059 (mm) cc_final: 0.7453 (mm) REVERT: A 580 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 581 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 587 ILE cc_start: 0.8419 (mm) cc_final: 0.8199 (tp) REVERT: A 589 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6879 (ttp) REVERT: A 609 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7258 (mp0) REVERT: A 611 GLN cc_start: 0.7973 (mp10) cc_final: 0.7370 (mp10) REVERT: A 612 PHE cc_start: 0.8571 (m-80) cc_final: 0.8047 (m-10) REVERT: A 644 LYS cc_start: 0.8323 (tppt) cc_final: 0.7705 (tppt) REVERT: A 660 GLN cc_start: 0.8446 (pp30) cc_final: 0.8019 (pp30) REVERT: A 663 LYS cc_start: 0.8651 (pttp) cc_final: 0.8368 (pptt) REVERT: A 664 ASP cc_start: 0.8327 (m-30) cc_final: 0.7875 (m-30) REVERT: A 710 ARG cc_start: 0.8405 (ptm160) cc_final: 0.8152 (ptm160) REVERT: A 711 LYS cc_start: 0.8826 (mppt) cc_final: 0.8458 (mmtm) REVERT: A 713 PHE cc_start: 0.8489 (t80) cc_final: 0.8015 (t80) REVERT: A 717 TYR cc_start: 0.8123 (t80) cc_final: 0.7732 (t80) REVERT: A 738 HIS cc_start: 0.7257 (t70) cc_final: 0.6966 (t70) REVERT: A 747 LYS cc_start: 0.8493 (mmmm) cc_final: 0.7959 (tptt) REVERT: A 753 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 754 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7416 (mp0) REVERT: A 757 LEU cc_start: 0.8706 (tp) cc_final: 0.8420 (tt) REVERT: A 764 ASN cc_start: 0.8204 (p0) cc_final: 0.7950 (p0) REVERT: A 768 GLN cc_start: 0.7794 (mp10) cc_final: 0.7309 (mp10) REVERT: A 772 GLU cc_start: 0.7585 (mp0) cc_final: 0.7047 (mp0) REVERT: A 800 GLU cc_start: 0.7726 (tp30) cc_final: 0.6996 (tp30) REVERT: A 802 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8042 (mtpp) REVERT: A 804 LEU cc_start: 0.8300 (mt) cc_final: 0.7744 (mp) REVERT: A 841 HIS cc_start: 0.7904 (t70) cc_final: 0.7520 (t70) REVERT: A 863 LEU cc_start: 0.8430 (mp) cc_final: 0.8089 (pp) REVERT: A 864 LYS cc_start: 0.8682 (tppt) cc_final: 0.8244 (ttmm) REVERT: D 17 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6780 (mmt180) REVERT: D 22 LEU cc_start: 0.7804 (tp) cc_final: 0.7495 (tp) REVERT: D 25 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7855 (mp0) REVERT: D 26 LEU cc_start: 0.8494 (mp) cc_final: 0.8105 (mp) REVERT: D 41 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7925 (mmtt) REVERT: D 52 PHE cc_start: 0.8964 (t80) cc_final: 0.8640 (t80) REVERT: D 57 LEU cc_start: 0.8541 (mt) cc_final: 0.8326 (mp) REVERT: D 62 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7489 (tpp80) REVERT: D 76 PHE cc_start: 0.8054 (t80) cc_final: 0.7834 (t80) REVERT: D 77 TYR cc_start: 0.8008 (m-80) cc_final: 0.7724 (m-80) REVERT: D 84 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7849 (ttm170) REVERT: D 91 TYR cc_start: 0.8676 (m-10) cc_final: 0.8229 (m-10) REVERT: D 94 THR cc_start: 0.8404 (m) cc_final: 0.8154 (p) REVERT: D 95 LEU cc_start: 0.8960 (tp) cc_final: 0.8756 (tp) REVERT: D 96 GLU cc_start: 0.7815 (tp30) cc_final: 0.7581 (tp30) REVERT: D 101 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8430 (mttm) REVERT: D 121 GLU cc_start: 0.8224 (mp0) cc_final: 0.7743 (mp0) REVERT: D 124 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7868 (ttp80) REVERT: D 128 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8540 (mtpp) REVERT: D 131 ARG cc_start: 0.8259 (ttm110) cc_final: 0.7929 (ttm110) REVERT: C 128 LEU cc_start: 0.8221 (mp) cc_final: 0.7754 (mm) REVERT: C 135 GLU cc_start: 0.7780 (pt0) cc_final: 0.7543 (pp20) REVERT: C 144 GLU cc_start: 0.7295 (pm20) cc_final: 0.7039 (pm20) REVERT: C 149 LEU cc_start: 0.8418 (tp) cc_final: 0.8198 (mm) REVERT: C 151 ARG cc_start: 0.7044 (ptm160) cc_final: 0.6804 (mtm110) REVERT: C 239 ILE cc_start: 0.8824 (mm) cc_final: 0.8590 (mm) REVERT: C 243 TYR cc_start: 0.7992 (m-80) cc_final: 0.7513 (m-80) REVERT: C 245 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7477 (mmm-85) REVERT: C 247 LEU cc_start: 0.8012 (mp) cc_final: 0.7685 (mp) REVERT: C 268 GLU cc_start: 0.8254 (tt0) cc_final: 0.7670 (tm-30) REVERT: C 283 TYR cc_start: 0.7924 (t80) cc_final: 0.7564 (t80) REVERT: C 289 ILE cc_start: 0.8622 (mm) cc_final: 0.8309 (mm) REVERT: C 310 CYS cc_start: 0.8250 (m) cc_final: 0.7789 (m) REVERT: C 311 LYS cc_start: 0.8484 (mttt) cc_final: 0.8274 (mttm) REVERT: C 315 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8048 (mmmm) REVERT: C 323 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8050 (ttmt) REVERT: C 327 LEU cc_start: 0.8334 (mt) cc_final: 0.8090 (mt) REVERT: C 328 TRP cc_start: 0.8483 (m-10) cc_final: 0.8259 (m-10) REVERT: C 336 ILE cc_start: 0.8489 (mm) cc_final: 0.8239 (mm) REVERT: C 338 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7528 (mmm160) REVERT: C 341 GLU cc_start: 0.7773 (pt0) cc_final: 0.7505 (pt0) REVERT: C 359 ARG cc_start: 0.7713 (mmp-170) cc_final: 0.7317 (mmp80) REVERT: C 378 VAL cc_start: 0.8667 (t) cc_final: 0.8435 (p) REVERT: C 383 VAL cc_start: 0.8599 (t) cc_final: 0.8347 (p) REVERT: C 387 GLU cc_start: 0.6857 (pm20) cc_final: 0.6069 (mp0) REVERT: C 394 GLU cc_start: 0.7465 (tp30) cc_final: 0.6758 (tp30) REVERT: C 403 GLU cc_start: 0.7597 (pm20) cc_final: 0.7313 (pm20) REVERT: C 405 SER cc_start: 0.8301 (m) cc_final: 0.7712 (p) REVERT: C 406 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 407 LEU cc_start: 0.8836 (mt) cc_final: 0.8485 (mt) REVERT: C 410 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6759 (tm-30) REVERT: C 411 GLU cc_start: 0.8206 (tt0) cc_final: 0.7852 (tm-30) REVERT: C 426 ASP cc_start: 0.8421 (t0) cc_final: 0.8176 (t0) REVERT: C 428 LEU cc_start: 0.8815 (tp) cc_final: 0.8457 (tp) REVERT: C 448 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 452 GLU cc_start: 0.7728 (mp0) cc_final: 0.7251 (mp0) REVERT: C 459 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6541 (mm-30) REVERT: C 470 GLU cc_start: 0.7854 (tt0) cc_final: 0.7372 (tt0) REVERT: C 504 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7381 (mm-30) REVERT: C 507 ILE cc_start: 0.8353 (mt) cc_final: 0.8127 (tp) REVERT: C 518 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 539 ARG cc_start: 0.7940 (tpt-90) cc_final: 0.7547 (tpt-90) REVERT: C 541 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7853 (tp30) REVERT: C 550 ASP cc_start: 0.7911 (t70) cc_final: 0.7604 (t70) REVERT: C 552 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7716 (mmtm) REVERT: C 558 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6115 (tm-30) REVERT: C 577 LEU cc_start: 0.8055 (mm) cc_final: 0.7459 (mm) REVERT: C 580 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7468 (mt-10) REVERT: C 581 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 584 ASN cc_start: 0.8454 (t0) cc_final: 0.8056 (t0) REVERT: C 587 ILE cc_start: 0.8575 (mm) cc_final: 0.8334 (tp) REVERT: C 594 GLU cc_start: 0.7217 (mp0) cc_final: 0.6855 (mp0) REVERT: C 609 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7282 (mp0) REVERT: C 611 GLN cc_start: 0.8105 (mp10) cc_final: 0.7514 (mp10) REVERT: C 612 PHE cc_start: 0.8660 (m-80) cc_final: 0.8214 (m-10) REVERT: C 635 MET cc_start: 0.7295 (mmm) cc_final: 0.6360 (mmm) REVERT: C 644 LYS cc_start: 0.8283 (tppt) cc_final: 0.7631 (tppt) REVERT: C 645 LYS cc_start: 0.8250 (mttt) cc_final: 0.7489 (mmtt) REVERT: C 660 GLN cc_start: 0.8557 (pp30) cc_final: 0.8170 (pp30) REVERT: C 664 ASP cc_start: 0.8185 (m-30) cc_final: 0.7945 (m-30) REVERT: C 677 MET cc_start: 0.5341 (mmm) cc_final: 0.4996 (mmm) REVERT: C 712 GLU cc_start: 0.7847 (pm20) cc_final: 0.7442 (pm20) REVERT: C 713 PHE cc_start: 0.8590 (t80) cc_final: 0.8086 (t80) REVERT: C 735 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7819 (ttp80) REVERT: C 747 LYS cc_start: 0.8471 (mmmm) cc_final: 0.7897 (tppt) REVERT: C 753 GLU cc_start: 0.7937 (mp0) cc_final: 0.7690 (mm-30) REVERT: C 757 LEU cc_start: 0.8605 (tp) cc_final: 0.8292 (tt) REVERT: C 764 ASN cc_start: 0.8215 (p0) cc_final: 0.7938 (p0) REVERT: C 768 GLN cc_start: 0.7970 (mp10) cc_final: 0.6877 (mp10) REVERT: C 772 GLU cc_start: 0.7716 (mp0) cc_final: 0.7113 (mp0) REVERT: C 782 ARG cc_start: 0.7161 (tpt90) cc_final: 0.5823 (tpt90) REVERT: C 788 ARG cc_start: 0.6895 (mmm-85) cc_final: 0.6535 (tpp80) REVERT: C 802 LYS cc_start: 0.8388 (mtpp) cc_final: 0.8055 (mtpp) REVERT: C 804 LEU cc_start: 0.8446 (mt) cc_final: 0.8015 (mt) REVERT: C 836 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7472 (mtt90) REVERT: C 841 HIS cc_start: 0.7886 (t70) cc_final: 0.7438 (t70) REVERT: C 851 GLU cc_start: 0.6717 (pm20) cc_final: 0.6368 (mp0) REVERT: C 864 LYS cc_start: 0.8684 (tppt) cc_final: 0.8335 (ttmm) outliers start: 43 outliers final: 19 residues processed: 600 average time/residue: 0.3504 time to fit residues: 277.1219 Evaluate side-chains 573 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 551 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET 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 651 LEU 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 158 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** 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 = 0.3646 r_free = 0.3646 target = 0.113925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096945 restraints weight = 27088.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100454 restraints weight = 13244.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102751 restraints weight = 7812.299| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2856 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= 0.145 Angle : 0.571 9.252 18800 Z= 0.287 Chirality : 0.042 0.219 2058 Planarity : 0.003 0.034 2434 Dihedral : 3.658 16.162 1844 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.75 % Allowed : 27.43 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1648 helix: 0.64 (0.18), residues: 864 sheet: -1.19 (0.61), residues: 68 loop : 0.09 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 791 HIS 0.010 0.001 HIS C 738 PHE 0.019 0.002 PHE C 737 TYR 0.017 0.001 TYR A 273 ARG 0.006 0.000 ARG C 649 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 618) hydrogen bonds : angle 4.53580 ( 1752) metal coordination : bond 0.00605 ( 16) metal coordination : angle 3.23605 ( 24) covalent geometry : bond 0.00309 (13904) covalent geometry : angle 0.55978 (18776) *********************** 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 616 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 559 time to evaluate : 1.662 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 26 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8268 (mp) REVERT: B 41 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7999 (mmtt) REVERT: B 44 LEU cc_start: 0.8843 (mp) cc_final: 0.8625 (mp) REVERT: B 76 PHE cc_start: 0.8308 (t80) cc_final: 0.8088 (t80) REVERT: B 77 TYR cc_start: 0.8102 (m-80) cc_final: 0.7713 (m-80) REVERT: B 85 HIS cc_start: 0.8754 (m90) cc_final: 0.8514 (m-70) REVERT: B 91 TYR cc_start: 0.8728 (m-10) cc_final: 0.8097 (m-10) REVERT: B 94 THR cc_start: 0.8512 (m) cc_final: 0.8301 (p) REVERT: B 96 GLU cc_start: 0.7668 (tp30) cc_final: 0.7239 (tp30) REVERT: B 98 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 101 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8253 (mttm) REVERT: B 131 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7747 (ttm110) REVERT: B 143 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7473 (p) REVERT: A 128 LEU cc_start: 0.8247 (mp) cc_final: 0.7882 (mm) REVERT: A 130 GLU cc_start: 0.7352 (pm20) cc_final: 0.6962 (pm20) REVERT: A 135 GLU cc_start: 0.7566 (pt0) cc_final: 0.7334 (pp20) REVERT: A 167 PHE cc_start: 0.7423 (m-80) cc_final: 0.7222 (m-80) REVERT: A 241 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: A 243 TYR cc_start: 0.7801 (m-80) cc_final: 0.7189 (m-80) REVERT: A 247 LEU cc_start: 0.7992 (mp) cc_final: 0.7485 (tt) REVERT: A 264 SER cc_start: 0.8382 (m) cc_final: 0.8104 (p) REVERT: A 267 VAL cc_start: 0.8964 (t) cc_final: 0.8736 (p) REVERT: A 268 GLU cc_start: 0.8371 (tt0) cc_final: 0.7860 (tm-30) REVERT: A 273 TYR cc_start: 0.7935 (m-80) cc_final: 0.7725 (m-80) REVERT: A 306 LEU cc_start: 0.7922 (tp) cc_final: 0.7486 (tp) REVERT: A 310 CYS cc_start: 0.8200 (m) cc_final: 0.7672 (m) REVERT: A 311 LYS cc_start: 0.8505 (mttt) cc_final: 0.8272 (mptt) REVERT: A 315 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8135 (mmmm) REVERT: A 327 LEU cc_start: 0.8116 (mt) cc_final: 0.7822 (mt) REVERT: A 338 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7461 (tpt90) REVERT: A 340 MET cc_start: 0.7970 (tmm) cc_final: 0.7297 (tmm) REVERT: A 341 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6681 (mt-10) REVERT: A 345 GLN cc_start: 0.8243 (mm110) cc_final: 0.8029 (mm-40) REVERT: A 359 ARG cc_start: 0.7634 (mmp-170) cc_final: 0.7295 (mmp80) REVERT: A 387 GLU cc_start: 0.6819 (pm20) cc_final: 0.6063 (mp0) REVERT: A 394 GLU cc_start: 0.7276 (tp30) cc_final: 0.6353 (tp30) REVERT: A 397 ASP cc_start: 0.6618 (p0) cc_final: 0.6110 (p0) REVERT: A 406 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 407 LEU cc_start: 0.8775 (mt) cc_final: 0.8438 (mt) REVERT: A 410 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7024 (tm-30) REVERT: A 411 GLU cc_start: 0.8132 (tt0) cc_final: 0.7596 (tm-30) REVERT: A 426 ASP cc_start: 0.8112 (t0) cc_final: 0.7874 (t0) REVERT: A 435 LYS cc_start: 0.8317 (tmtt) cc_final: 0.8100 (tptp) REVERT: A 448 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 452 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7337 (mp0) REVERT: A 459 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6667 (mm-30) REVERT: A 470 GLU cc_start: 0.7844 (tt0) cc_final: 0.7370 (tt0) REVERT: A 490 ASN cc_start: 0.7828 (t0) cc_final: 0.7523 (t0) REVERT: A 515 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 533 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7031 (pt) REVERT: A 541 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7418 (tp30) REVERT: A 550 ASP cc_start: 0.7939 (m-30) cc_final: 0.7656 (m-30) REVERT: A 577 LEU cc_start: 0.8140 (mm) cc_final: 0.7565 (mm) REVERT: A 580 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 581 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7082 (mt-10) REVERT: A 609 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7252 (mp0) REVERT: A 611 GLN cc_start: 0.7943 (mp10) cc_final: 0.7333 (mp10) REVERT: A 644 LYS cc_start: 0.8430 (tppt) cc_final: 0.7746 (tppt) REVERT: A 645 LYS cc_start: 0.8175 (mttt) cc_final: 0.7418 (mmtt) REVERT: A 660 GLN cc_start: 0.8434 (pp30) cc_final: 0.7955 (pp30) REVERT: A 663 LYS cc_start: 0.8686 (pttp) cc_final: 0.8351 (pptt) REVERT: A 664 ASP cc_start: 0.8318 (m-30) cc_final: 0.7833 (m-30) REVERT: A 710 ARG cc_start: 0.8426 (ptm160) cc_final: 0.7573 (ptt180) REVERT: A 711 LYS cc_start: 0.8834 (mppt) cc_final: 0.8581 (mmtm) REVERT: A 713 PHE cc_start: 0.8501 (t80) cc_final: 0.8040 (t80) REVERT: A 717 TYR cc_start: 0.8222 (t80) cc_final: 0.7871 (t80) REVERT: A 738 HIS cc_start: 0.7191 (t70) cc_final: 0.6886 (t70) REVERT: A 747 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8042 (tppp) REVERT: A 757 LEU cc_start: 0.8684 (tp) cc_final: 0.8410 (tt) REVERT: A 764 ASN cc_start: 0.8205 (p0) cc_final: 0.7781 (p0) REVERT: A 768 GLN cc_start: 0.7801 (mp10) cc_final: 0.7285 (mp10) REVERT: A 772 GLU cc_start: 0.7641 (mp0) cc_final: 0.7108 (mp0) REVERT: A 800 GLU cc_start: 0.7782 (tp30) cc_final: 0.7222 (tp30) REVERT: A 802 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8054 (mtpp) REVERT: A 804 LEU cc_start: 0.8313 (mt) cc_final: 0.7858 (mt) REVERT: A 836 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7656 (mtt-85) REVERT: D 17 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6809 (mmt180) REVERT: D 22 LEU cc_start: 0.7807 (tp) cc_final: 0.7462 (tp) REVERT: D 26 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 39 TYR cc_start: 0.8051 (m-80) cc_final: 0.7725 (m-80) REVERT: D 41 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7994 (mmtt) REVERT: D 48 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7361 (mp0) REVERT: D 62 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7516 (tpp80) REVERT: D 77 TYR cc_start: 0.8066 (m-80) cc_final: 0.7662 (m-80) REVERT: D 84 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7873 (ttm170) REVERT: D 91 TYR cc_start: 0.8732 (m-10) cc_final: 0.8284 (m-10) REVERT: D 94 THR cc_start: 0.8477 (m) cc_final: 0.8259 (p) REVERT: D 96 GLU cc_start: 0.7691 (tp30) cc_final: 0.7423 (tp30) REVERT: D 101 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8463 (mttm) REVERT: D 121 GLU cc_start: 0.8145 (mp0) cc_final: 0.7749 (mp0) REVERT: D 124 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7854 (ttp80) REVERT: D 128 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8501 (mtpp) REVERT: D 131 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8013 (ttm110) REVERT: D 143 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7453 (p) REVERT: C 128 LEU cc_start: 0.8253 (mp) cc_final: 0.8001 (mp) REVERT: C 149 LEU cc_start: 0.8440 (tp) cc_final: 0.8225 (mm) REVERT: C 151 ARG cc_start: 0.7040 (ptm160) cc_final: 0.6808 (mtm110) REVERT: C 239 ILE cc_start: 0.8808 (mm) cc_final: 0.8554 (mm) REVERT: C 241 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7661 (mtm-85) REVERT: C 243 TYR cc_start: 0.7842 (m-80) cc_final: 0.7506 (m-80) REVERT: C 245 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7483 (mmm-85) REVERT: C 247 LEU cc_start: 0.8018 (mp) cc_final: 0.7673 (mm) REVERT: C 268 GLU cc_start: 0.8274 (tt0) cc_final: 0.7680 (tm-30) REVERT: C 283 TYR cc_start: 0.7884 (t80) cc_final: 0.7548 (t80) REVERT: C 289 ILE cc_start: 0.8622 (mm) cc_final: 0.8294 (mm) REVERT: C 310 CYS cc_start: 0.8264 (m) cc_final: 0.7757 (m) REVERT: C 311 LYS cc_start: 0.8533 (mttt) cc_final: 0.8260 (mttm) REVERT: C 315 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8158 (mmmm) REVERT: C 323 LYS cc_start: 0.8615 (ptmt) cc_final: 0.7956 (tttt) REVERT: C 336 ILE cc_start: 0.8477 (mm) cc_final: 0.8230 (mm) REVERT: C 338 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7681 (tpp-160) REVERT: C 340 MET cc_start: 0.7458 (tmm) cc_final: 0.7245 (tmm) REVERT: C 342 THR cc_start: 0.8656 (m) cc_final: 0.8401 (m) REVERT: C 359 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.7332 (mmp80) REVERT: C 366 ASP cc_start: 0.7737 (p0) cc_final: 0.7469 (p0) REVERT: C 401 ILE cc_start: 0.8698 (mm) cc_final: 0.8418 (pt) REVERT: C 403 GLU cc_start: 0.7603 (pm20) cc_final: 0.7283 (pm20) REVERT: C 406 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 407 LEU cc_start: 0.8856 (mt) cc_final: 0.8500 (mt) REVERT: C 410 GLN cc_start: 0.7496 (mm-40) cc_final: 0.6761 (tm-30) REVERT: C 411 GLU cc_start: 0.8167 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 426 ASP cc_start: 0.8375 (t0) cc_final: 0.8146 (t0) REVERT: C 428 LEU cc_start: 0.8803 (tp) cc_final: 0.8434 (tp) REVERT: C 452 GLU cc_start: 0.7695 (mp0) cc_final: 0.7234 (mp0) REVERT: C 470 GLU cc_start: 0.7824 (tt0) cc_final: 0.7452 (tt0) REVERT: C 504 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7290 (mm-30) REVERT: C 507 ILE cc_start: 0.8359 (mt) cc_final: 0.8152 (tp) REVERT: C 539 ARG cc_start: 0.7948 (tpt-90) cc_final: 0.7668 (tpt-90) REVERT: C 541 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7745 (tp30) REVERT: C 542 MET cc_start: 0.7340 (ptp) cc_final: 0.7123 (tpt) REVERT: C 546 GLU cc_start: 0.7494 (tp30) cc_final: 0.7137 (tp30) REVERT: C 552 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7679 (mmtm) REVERT: C 558 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6239 (tm-30) REVERT: C 577 LEU cc_start: 0.8113 (mm) cc_final: 0.7369 (mm) REVERT: C 580 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7512 (mt-10) REVERT: C 581 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7130 (mt-10) REVERT: C 584 ASN cc_start: 0.8579 (t0) cc_final: 0.8266 (t0) REVERT: C 594 GLU cc_start: 0.7267 (mp0) cc_final: 0.6937 (mp0) REVERT: C 609 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7206 (mp0) REVERT: C 611 GLN cc_start: 0.8052 (mp10) cc_final: 0.7487 (mp10) REVERT: C 635 MET cc_start: 0.7407 (mmm) cc_final: 0.7081 (tpp) REVERT: C 644 LYS cc_start: 0.8388 (tppt) cc_final: 0.7712 (tppt) REVERT: C 645 LYS cc_start: 0.8290 (mttt) cc_final: 0.7391 (mtpp) REVERT: C 660 GLN cc_start: 0.8552 (pp30) cc_final: 0.8269 (pp30) REVERT: C 665 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 712 GLU cc_start: 0.7867 (pm20) cc_final: 0.7439 (pm20) REVERT: C 713 PHE cc_start: 0.8564 (t80) cc_final: 0.8051 (t80) REVERT: C 735 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7794 (ttp80) REVERT: C 747 LYS cc_start: 0.8506 (mmmm) cc_final: 0.8069 (tppp) REVERT: C 754 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7308 (mt-10) REVERT: C 757 LEU cc_start: 0.8600 (tp) cc_final: 0.8276 (tt) REVERT: C 764 ASN cc_start: 0.8206 (p0) cc_final: 0.7896 (p0) REVERT: C 766 ASP cc_start: 0.7214 (t0) cc_final: 0.6668 (t0) REVERT: C 768 GLN cc_start: 0.7952 (mp10) cc_final: 0.6933 (mp10) REVERT: C 772 GLU cc_start: 0.7788 (mp0) cc_final: 0.7210 (mp0) REVERT: C 782 ARG cc_start: 0.7151 (tpt90) cc_final: 0.5808 (tpt90) REVERT: C 788 ARG cc_start: 0.6885 (mmm-85) cc_final: 0.6405 (tpp80) REVERT: C 800 GLU cc_start: 0.7629 (tp30) cc_final: 0.6843 (tp30) REVERT: C 802 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8121 (mtpp) REVERT: C 804 LEU cc_start: 0.8474 (mt) cc_final: 0.7567 (mp) REVERT: C 836 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7602 (mtt90) REVERT: C 841 HIS cc_start: 0.7896 (t70) cc_final: 0.7211 (t70) REVERT: C 864 LYS cc_start: 0.8739 (tppt) cc_final: 0.8530 (ttmm) outliers start: 57 outliers final: 31 residues processed: 579 average time/residue: 0.3412 time to fit residues: 262.3428 Evaluate side-chains 581 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 544 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain B residue 106 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 572 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS 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 368 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 615 ILE Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 665 LEU 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 101 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 801 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** 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 = 0.3645 r_free = 0.3645 target = 0.113876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096703 restraints weight = 27247.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100265 restraints weight = 13312.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102612 restraints weight = 7863.115| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13920 Z= 0.143 Angle : 0.588 9.215 18800 Z= 0.294 Chirality : 0.042 0.175 2058 Planarity : 0.004 0.036 2434 Dihedral : 3.722 17.208 1844 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.49 % Allowed : 27.89 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1648 helix: 0.69 (0.18), residues: 854 sheet: -1.39 (0.58), residues: 72 loop : 0.19 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 328 HIS 0.013 0.001 HIS C 738 PHE 0.022 0.002 PHE C 612 TYR 0.015 0.001 TYR C 277 ARG 0.008 0.001 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 618) hydrogen bonds : angle 4.49369 ( 1752) metal coordination : bond 0.00612 ( 16) metal coordination : angle 3.36715 ( 24) covalent geometry : bond 0.00308 (13904) covalent geometry : angle 0.57626 (18776) *********************** 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 606 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 553 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6866 (mmt180) REVERT: B 26 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8299 (mp) REVERT: B 41 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8038 (mmtt) REVERT: B 52 PHE cc_start: 0.8977 (t80) cc_final: 0.8754 (t80) REVERT: B 77 TYR cc_start: 0.8095 (m-80) cc_final: 0.7788 (m-80) REVERT: B 91 TYR cc_start: 0.8736 (m-10) cc_final: 0.8149 (m-10) REVERT: B 94 THR cc_start: 0.8450 (m) cc_final: 0.8232 (p) REVERT: B 96 GLU cc_start: 0.7694 (tp30) cc_final: 0.7368 (tp30) REVERT: B 98 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7962 (tm-30) REVERT: B 121 GLU cc_start: 0.8232 (mp0) cc_final: 0.8025 (mp0) REVERT: B 124 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7894 (ttp80) REVERT: B 131 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7720 (ttm110) REVERT: B 143 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7505 (p) REVERT: A 128 LEU cc_start: 0.8215 (mp) cc_final: 0.7886 (mm) REVERT: A 130 GLU cc_start: 0.7361 (pm20) cc_final: 0.6989 (pm20) REVERT: A 135 GLU cc_start: 0.7638 (pt0) cc_final: 0.7375 (pp20) REVERT: A 149 LEU cc_start: 0.8328 (tp) cc_final: 0.8116 (tp) REVERT: A 241 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7661 (mtm-85) REVERT: A 243 TYR cc_start: 0.7660 (m-80) cc_final: 0.7226 (m-80) REVERT: A 264 SER cc_start: 0.8454 (m) cc_final: 0.8185 (p) REVERT: A 267 VAL cc_start: 0.8937 (t) cc_final: 0.8703 (p) REVERT: A 268 GLU cc_start: 0.8391 (tt0) cc_final: 0.7900 (tm-30) REVERT: A 306 LEU cc_start: 0.7934 (tp) cc_final: 0.7400 (tp) REVERT: A 310 CYS cc_start: 0.8210 (m) cc_final: 0.7665 (m) REVERT: A 315 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8064 (mmmm) REVERT: A 327 LEU cc_start: 0.8113 (mt) cc_final: 0.7815 (mt) REVERT: A 338 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7291 (tpt90) REVERT: A 340 MET cc_start: 0.8025 (tmm) cc_final: 0.7307 (tmm) REVERT: A 341 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 359 ARG cc_start: 0.7618 (mmp-170) cc_final: 0.7276 (mmp80) REVERT: A 387 GLU cc_start: 0.6866 (pm20) cc_final: 0.6236 (mp0) REVERT: A 397 ASP cc_start: 0.6620 (p0) cc_final: 0.6091 (p0) REVERT: A 406 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 407 LEU cc_start: 0.8754 (mt) cc_final: 0.8403 (mt) REVERT: A 410 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7073 (tm-30) REVERT: A 411 GLU cc_start: 0.8142 (tt0) cc_final: 0.7540 (tm-30) REVERT: A 429 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 435 LYS cc_start: 0.8284 (tmtt) cc_final: 0.8072 (tptp) REVERT: A 447 GLU cc_start: 0.7546 (mp0) cc_final: 0.7175 (mp0) REVERT: A 448 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 452 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7313 (mp0) REVERT: A 459 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6543 (mm-30) REVERT: A 470 GLU cc_start: 0.7800 (tt0) cc_final: 0.7395 (tt0) REVERT: A 490 ASN cc_start: 0.7799 (t0) cc_final: 0.7492 (t0) REVERT: A 515 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 533 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7088 (pt) REVERT: A 541 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7422 (tp30) REVERT: A 550 ASP cc_start: 0.7996 (m-30) cc_final: 0.7659 (m-30) REVERT: A 558 GLU cc_start: 0.6531 (tm-30) cc_final: 0.6230 (tm-30) REVERT: A 577 LEU cc_start: 0.8171 (mm) cc_final: 0.7576 (mm) REVERT: A 580 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 581 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 598 LEU cc_start: 0.8632 (mt) cc_final: 0.8198 (mt) REVERT: A 609 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7218 (mp0) REVERT: A 611 GLN cc_start: 0.7928 (mp10) cc_final: 0.7667 (mp-120) REVERT: A 644 LYS cc_start: 0.8464 (tppt) cc_final: 0.7760 (tppt) REVERT: A 645 LYS cc_start: 0.8326 (mttt) cc_final: 0.7453 (mmtt) REVERT: A 660 GLN cc_start: 0.8378 (pp30) cc_final: 0.7990 (pp30) REVERT: A 663 LYS cc_start: 0.8777 (pttp) cc_final: 0.8344 (pptt) REVERT: A 664 ASP cc_start: 0.8305 (m-30) cc_final: 0.7902 (m-30) REVERT: A 676 MET cc_start: 0.5891 (pmm) cc_final: 0.5355 (pmm) REVERT: A 684 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: A 710 ARG cc_start: 0.8420 (ptm160) cc_final: 0.7526 (ptt180) REVERT: A 711 LYS cc_start: 0.8827 (mppt) cc_final: 0.8544 (mmtm) REVERT: A 713 PHE cc_start: 0.8490 (t80) cc_final: 0.8132 (t80) REVERT: A 717 TYR cc_start: 0.8230 (t80) cc_final: 0.7832 (t80) REVERT: A 727 GLU cc_start: 0.8141 (pp20) cc_final: 0.7925 (pp20) REVERT: A 738 HIS cc_start: 0.7155 (t70) cc_final: 0.6834 (t70) REVERT: A 747 LYS cc_start: 0.8501 (mmmm) cc_final: 0.8026 (tppp) REVERT: A 757 LEU cc_start: 0.8707 (tp) cc_final: 0.8439 (tt) REVERT: A 764 ASN cc_start: 0.8102 (p0) cc_final: 0.7821 (p0) REVERT: A 768 GLN cc_start: 0.7820 (mp10) cc_final: 0.7305 (mp10) REVERT: A 772 GLU cc_start: 0.7645 (mp0) cc_final: 0.7106 (mp0) REVERT: A 800 GLU cc_start: 0.7828 (tp30) cc_final: 0.7244 (tp30) REVERT: A 802 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8016 (mtpp) REVERT: A 804 LEU cc_start: 0.8334 (mt) cc_final: 0.7854 (mp) REVERT: A 836 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: A 841 HIS cc_start: 0.7919 (t70) cc_final: 0.7432 (t70) REVERT: A 851 GLU cc_start: 0.6753 (pm20) cc_final: 0.6496 (mp0) REVERT: D 15 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7294 (mtp85) REVERT: D 17 ARG cc_start: 0.7299 (mmt180) cc_final: 0.6836 (mmt180) REVERT: D 22 LEU cc_start: 0.7795 (tp) cc_final: 0.7444 (tp) REVERT: D 25 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8024 (mm-30) REVERT: D 26 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 41 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7982 (mmtt) REVERT: D 48 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7338 (mp0) REVERT: D 62 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7538 (tpp80) REVERT: D 77 TYR cc_start: 0.8042 (m-80) cc_final: 0.7742 (m-80) REVERT: D 84 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7876 (ttm170) REVERT: D 91 TYR cc_start: 0.8736 (m-10) cc_final: 0.8327 (m-10) REVERT: D 94 THR cc_start: 0.8501 (m) cc_final: 0.8283 (p) REVERT: D 101 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8438 (mttm) REVERT: D 121 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: D 124 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7868 (ttp80) REVERT: D 128 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8498 (mtpp) REVERT: D 131 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8017 (ttm110) REVERT: D 143 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7383 (p) REVERT: C 128 LEU cc_start: 0.8242 (mp) cc_final: 0.7980 (mp) REVERT: C 149 LEU cc_start: 0.8426 (tp) cc_final: 0.8175 (mm) REVERT: C 151 ARG cc_start: 0.7044 (ptm160) cc_final: 0.6793 (mtm110) REVERT: C 161 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7797 (pm20) REVERT: C 239 ILE cc_start: 0.8806 (mm) cc_final: 0.8583 (mm) REVERT: C 243 TYR cc_start: 0.7802 (m-80) cc_final: 0.7425 (m-80) REVERT: C 245 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7488 (mmm-85) REVERT: C 247 LEU cc_start: 0.7974 (mp) cc_final: 0.7665 (mm) REVERT: C 268 GLU cc_start: 0.8273 (tt0) cc_final: 0.7697 (tm-30) REVERT: C 283 TYR cc_start: 0.7914 (t80) cc_final: 0.7579 (t80) REVERT: C 289 ILE cc_start: 0.8611 (mm) cc_final: 0.8281 (mm) REVERT: C 310 CYS cc_start: 0.8296 (m) cc_final: 0.7690 (m) REVERT: C 311 LYS cc_start: 0.8535 (mttt) cc_final: 0.8260 (mttm) REVERT: C 315 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8133 (mmmm) REVERT: C 323 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8074 (tttt) REVERT: C 336 ILE cc_start: 0.8503 (mm) cc_final: 0.8249 (mm) REVERT: C 338 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.7703 (tpp-160) REVERT: C 340 MET cc_start: 0.7571 (tmm) cc_final: 0.7313 (tmm) REVERT: C 342 THR cc_start: 0.8593 (m) cc_final: 0.8372 (m) REVERT: C 359 ARG cc_start: 0.7677 (mmp-170) cc_final: 0.7345 (mmp80) REVERT: C 366 ASP cc_start: 0.7716 (p0) cc_final: 0.7485 (p0) REVERT: C 394 GLU cc_start: 0.7478 (tp30) cc_final: 0.6650 (tp30) REVERT: C 401 ILE cc_start: 0.8713 (mm) cc_final: 0.8390 (pt) REVERT: C 403 GLU cc_start: 0.7571 (pm20) cc_final: 0.7249 (pm20) REVERT: C 407 LEU cc_start: 0.8821 (mt) cc_final: 0.8528 (mt) REVERT: C 410 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6720 (tm-30) REVERT: C 411 GLU cc_start: 0.8166 (tt0) cc_final: 0.7874 (tm-30) REVERT: C 426 ASP cc_start: 0.8325 (t0) cc_final: 0.8112 (t0) REVERT: C 428 LEU cc_start: 0.8749 (tp) cc_final: 0.8369 (tp) REVERT: C 452 GLU cc_start: 0.7695 (mp0) cc_final: 0.7245 (mp0) REVERT: C 470 GLU cc_start: 0.7815 (tt0) cc_final: 0.7525 (tt0) REVERT: C 504 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 507 ILE cc_start: 0.8397 (mt) cc_final: 0.8168 (tp) REVERT: C 521 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7925 (tpt-90) cc_final: 0.7621 (tpt-90) REVERT: C 541 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7781 (tp30) REVERT: C 550 ASP cc_start: 0.8002 (m-30) cc_final: 0.7762 (m-30) REVERT: C 552 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7475 (mmtm) REVERT: C 577 LEU cc_start: 0.8206 (mm) cc_final: 0.7454 (mm) REVERT: C 580 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 581 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7213 (mt-10) REVERT: C 584 ASN cc_start: 0.8705 (t0) cc_final: 0.8374 (t0) REVERT: C 594 GLU cc_start: 0.7320 (mp0) cc_final: 0.6990 (mp0) REVERT: C 609 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7225 (mp0) REVERT: C 644 LYS cc_start: 0.8393 (tppt) cc_final: 0.7704 (tppt) REVERT: C 645 LYS cc_start: 0.8289 (mttt) cc_final: 0.7487 (mmtt) REVERT: C 660 GLN cc_start: 0.8546 (pp30) cc_final: 0.8266 (pp30) REVERT: C 712 GLU cc_start: 0.7858 (pm20) cc_final: 0.7396 (pm20) REVERT: C 713 PHE cc_start: 0.8534 (t80) cc_final: 0.8080 (t80) REVERT: C 735 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7755 (ttp80) REVERT: C 747 LYS cc_start: 0.8540 (mmmm) cc_final: 0.7901 (tppt) REVERT: C 754 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7340 (mt-10) REVERT: C 757 LEU cc_start: 0.8591 (tp) cc_final: 0.8228 (tt) REVERT: C 764 ASN cc_start: 0.8192 (p0) cc_final: 0.7877 (p0) REVERT: C 766 ASP cc_start: 0.7236 (t0) cc_final: 0.6668 (t0) REVERT: C 768 GLN cc_start: 0.7951 (mp10) cc_final: 0.6985 (mp10) REVERT: C 772 GLU cc_start: 0.7750 (mp0) cc_final: 0.7147 (mp0) REVERT: C 782 ARG cc_start: 0.7134 (tpt90) cc_final: 0.5661 (tpt90) REVERT: C 783 ASP cc_start: 0.6731 (p0) cc_final: 0.6509 (p0) REVERT: C 788 ARG cc_start: 0.6860 (mmm-85) cc_final: 0.6380 (tpp80) REVERT: C 800 GLU cc_start: 0.7679 (tp30) cc_final: 0.6894 (tp30) REVERT: C 802 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8030 (mtpp) REVERT: C 804 LEU cc_start: 0.8424 (mt) cc_final: 0.7520 (mp) REVERT: C 836 ARG cc_start: 0.7947 (mtt-85) cc_final: 0.7598 (mtt90) REVERT: C 841 HIS cc_start: 0.7908 (t70) cc_final: 0.7238 (t70) REVERT: C 864 LYS cc_start: 0.8722 (tppt) cc_final: 0.8459 (ttmm) outliers start: 53 outliers final: 35 residues processed: 570 average time/residue: 0.3378 time to fit residues: 256.5025 Evaluate side-chains 575 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 532 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE 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 106 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 288 ILE Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 368 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 615 ILE Chi-restraints excluded: chain C residue 682 ILE 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 38 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 801 GLN D 85 HIS ** C 455 ASN ** 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 = 0.3635 r_free = 0.3635 target = 0.113134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095736 restraints weight = 27540.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099328 restraints weight = 13542.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101729 restraints weight = 8034.011| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13920 Z= 0.142 Angle : 0.603 9.341 18800 Z= 0.299 Chirality : 0.042 0.250 2058 Planarity : 0.004 0.034 2434 Dihedral : 3.768 18.454 1844 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.49 % Allowed : 28.49 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1648 helix: 0.65 (0.18), residues: 850 sheet: -1.61 (0.55), residues: 72 loop : 0.26 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 791 HIS 0.009 0.001 HIS C 738 PHE 0.029 0.002 PHE B 76 TYR 0.018 0.001 TYR C 277 ARG 0.008 0.000 ARG A 649 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 618) hydrogen bonds : angle 4.45197 ( 1752) metal coordination : bond 0.00609 ( 16) metal coordination : angle 3.30506 ( 24) covalent geometry : bond 0.00306 (13904) covalent geometry : angle 0.59204 (18776) *********************** 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 599 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 546 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 26 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 41 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8033 (mmtt) REVERT: B 52 PHE cc_start: 0.8969 (t80) cc_final: 0.8736 (t80) REVERT: B 77 TYR cc_start: 0.8003 (m-80) cc_final: 0.7701 (m-80) REVERT: B 91 TYR cc_start: 0.8710 (m-10) cc_final: 0.8105 (m-10) REVERT: B 94 THR cc_start: 0.8544 (m) cc_final: 0.8300 (p) REVERT: B 96 GLU cc_start: 0.7705 (tp30) cc_final: 0.7413 (tp30) REVERT: B 98 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 124 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7851 (ttp80) REVERT: B 131 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7684 (ttm110) REVERT: B 143 CYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7388 (p) REVERT: A 128 LEU cc_start: 0.8283 (mp) cc_final: 0.7863 (mm) REVERT: A 130 GLU cc_start: 0.7311 (pm20) cc_final: 0.6934 (pm20) REVERT: A 135 GLU cc_start: 0.7734 (pt0) cc_final: 0.7396 (pp20) REVERT: A 241 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: A 243 TYR cc_start: 0.7670 (m-80) cc_final: 0.7286 (m-80) REVERT: A 264 SER cc_start: 0.8450 (m) cc_final: 0.8162 (p) REVERT: A 267 VAL cc_start: 0.8905 (t) cc_final: 0.8632 (p) REVERT: A 268 GLU cc_start: 0.8440 (tt0) cc_final: 0.7813 (tm-30) REVERT: A 283 TYR cc_start: 0.7897 (t80) cc_final: 0.7697 (t80) REVERT: A 291 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6821 (tmm) REVERT: A 306 LEU cc_start: 0.7882 (tp) cc_final: 0.7341 (tp) REVERT: A 310 CYS cc_start: 0.8230 (m) cc_final: 0.7621 (m) REVERT: A 313 MET cc_start: 0.8267 (ttm) cc_final: 0.8052 (mtp) REVERT: A 315 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8021 (mmmm) REVERT: A 327 LEU cc_start: 0.8124 (mt) cc_final: 0.7818 (mt) REVERT: A 338 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7296 (tpt90) REVERT: A 340 MET cc_start: 0.8057 (tmm) cc_final: 0.7476 (tmm) REVERT: A 341 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7257 (mt-10) REVERT: A 359 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.7301 (mmp80) REVERT: A 387 GLU cc_start: 0.6811 (pm20) cc_final: 0.6232 (mp0) REVERT: A 397 ASP cc_start: 0.6639 (p0) cc_final: 0.6149 (p0) REVERT: A 406 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 407 LEU cc_start: 0.8732 (mt) cc_final: 0.8381 (mt) REVERT: A 411 GLU cc_start: 0.8162 (tt0) cc_final: 0.7480 (tm-30) REVERT: A 429 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: A 435 LYS cc_start: 0.8270 (tmtt) cc_final: 0.8038 (tptp) REVERT: A 447 GLU cc_start: 0.7599 (mp0) cc_final: 0.7251 (mp0) REVERT: A 448 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 452 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7332 (mp0) REVERT: A 462 LYS cc_start: 0.7913 (mtmm) cc_final: 0.7622 (mtmm) REVERT: A 470 GLU cc_start: 0.7792 (tt0) cc_final: 0.7384 (tt0) REVERT: A 490 ASN cc_start: 0.7821 (t0) cc_final: 0.7490 (t0) REVERT: A 515 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 533 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.6973 (tt) REVERT: A 541 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7356 (tp30) REVERT: A 550 ASP cc_start: 0.8046 (m-30) cc_final: 0.7682 (m-30) REVERT: A 558 GLU cc_start: 0.6515 (tm-30) cc_final: 0.6232 (tm-30) REVERT: A 577 LEU cc_start: 0.8214 (mm) cc_final: 0.7755 (mm) REVERT: A 580 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 581 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7576 (pt0) REVERT: A 598 LEU cc_start: 0.8674 (mt) cc_final: 0.8273 (mt) REVERT: A 609 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7290 (mp0) REVERT: A 611 GLN cc_start: 0.7910 (mp10) cc_final: 0.7606 (mp-120) REVERT: A 645 LYS cc_start: 0.8319 (mttt) cc_final: 0.7452 (mmtt) REVERT: A 649 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7769 (mtm-85) REVERT: A 660 GLN cc_start: 0.8375 (pp30) cc_final: 0.7986 (pp30) REVERT: A 663 LYS cc_start: 0.8785 (pttp) cc_final: 0.8465 (pptt) REVERT: A 664 ASP cc_start: 0.8316 (m-30) cc_final: 0.7888 (m-30) REVERT: A 710 ARG cc_start: 0.8556 (ptm160) cc_final: 0.7321 (ptt180) REVERT: A 711 LYS cc_start: 0.8814 (mppt) cc_final: 0.8501 (mmtt) REVERT: A 712 GLU cc_start: 0.7951 (pm20) cc_final: 0.7555 (pm20) REVERT: A 713 PHE cc_start: 0.8511 (t80) cc_final: 0.8159 (t80) REVERT: A 721 ILE cc_start: 0.8789 (tp) cc_final: 0.8548 (tt) REVERT: A 724 LYS cc_start: 0.8317 (ptpp) cc_final: 0.8042 (ptpp) REVERT: A 727 GLU cc_start: 0.8147 (pp20) cc_final: 0.7919 (pp20) REVERT: A 738 HIS cc_start: 0.7199 (t70) cc_final: 0.6882 (t70) REVERT: A 739 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7430 (tpp) REVERT: A 747 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8023 (tptt) REVERT: A 757 LEU cc_start: 0.8676 (tp) cc_final: 0.8360 (tt) REVERT: A 764 ASN cc_start: 0.8081 (p0) cc_final: 0.7855 (p0) REVERT: A 768 GLN cc_start: 0.7845 (mp10) cc_final: 0.7386 (mp10) REVERT: A 772 GLU cc_start: 0.7684 (mp0) cc_final: 0.7145 (mp0) REVERT: A 800 GLU cc_start: 0.7860 (tp30) cc_final: 0.7555 (tp30) REVERT: A 802 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7978 (mtpt) REVERT: A 804 LEU cc_start: 0.8346 (mt) cc_final: 0.8021 (mt) REVERT: A 829 LYS cc_start: 0.8417 (tttt) cc_final: 0.8090 (ttpp) REVERT: A 836 ARG cc_start: 0.7967 (mtt-85) cc_final: 0.7630 (mtt-85) REVERT: A 841 HIS cc_start: 0.7870 (t70) cc_final: 0.7329 (t70) REVERT: D 17 ARG cc_start: 0.7306 (mmt180) cc_final: 0.6843 (mmt180) REVERT: D 22 LEU cc_start: 0.7817 (tp) cc_final: 0.7472 (tp) REVERT: D 25 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 26 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8191 (mp) REVERT: D 41 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8011 (mmtt) REVERT: D 48 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: D 62 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7518 (tpp80) REVERT: D 77 TYR cc_start: 0.7981 (m-80) cc_final: 0.7715 (m-80) REVERT: D 91 TYR cc_start: 0.8721 (m-10) cc_final: 0.8256 (m-10) REVERT: D 94 THR cc_start: 0.8531 (m) cc_final: 0.8319 (p) REVERT: D 121 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 124 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7845 (ttp80) REVERT: D 128 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8510 (mtpp) REVERT: D 131 ARG cc_start: 0.8301 (ttm110) cc_final: 0.7985 (ttm110) REVERT: D 143 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7343 (p) REVERT: C 128 LEU cc_start: 0.8271 (mp) cc_final: 0.8008 (mp) REVERT: C 149 LEU cc_start: 0.8407 (tp) cc_final: 0.8144 (mm) REVERT: C 151 ARG cc_start: 0.7083 (ptm160) cc_final: 0.6785 (mtm110) REVERT: C 161 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7895 (pm20) REVERT: C 167 PHE cc_start: 0.8017 (m-80) cc_final: 0.7816 (m-80) REVERT: C 239 ILE cc_start: 0.8870 (mm) cc_final: 0.8663 (mm) REVERT: C 241 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7746 (mtm-85) REVERT: C 243 TYR cc_start: 0.7826 (m-80) cc_final: 0.7549 (m-80) REVERT: C 268 GLU cc_start: 0.8307 (tt0) cc_final: 0.7718 (tm-30) REVERT: C 283 TYR cc_start: 0.7946 (t80) cc_final: 0.7587 (t80) REVERT: C 289 ILE cc_start: 0.8624 (mm) cc_final: 0.8339 (mm) REVERT: C 310 CYS cc_start: 0.8353 (m) cc_final: 0.7898 (m) REVERT: C 311 LYS cc_start: 0.8522 (mttt) cc_final: 0.8254 (mttm) REVERT: C 315 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8111 (mmmm) REVERT: C 323 LYS cc_start: 0.8685 (ptmt) cc_final: 0.8175 (tttt) REVERT: C 336 ILE cc_start: 0.8545 (mm) cc_final: 0.8285 (mm) REVERT: C 338 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7467 (tpp-160) REVERT: C 340 MET cc_start: 0.7631 (tmm) cc_final: 0.7287 (tmm) REVERT: C 341 GLU cc_start: 0.7797 (pt0) cc_final: 0.6833 (pp20) REVERT: C 345 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7837 (mm110) REVERT: C 359 ARG cc_start: 0.7762 (mmp-170) cc_final: 0.7391 (mmp80) REVERT: C 366 ASP cc_start: 0.7751 (p0) cc_final: 0.7544 (p0) REVERT: C 394 GLU cc_start: 0.7540 (tp30) cc_final: 0.6692 (tp30) REVERT: C 401 ILE cc_start: 0.8718 (mm) cc_final: 0.8402 (pt) REVERT: C 403 GLU cc_start: 0.7554 (pm20) cc_final: 0.7189 (pm20) REVERT: C 407 LEU cc_start: 0.8820 (mt) cc_final: 0.8513 (mt) REVERT: C 410 GLN cc_start: 0.7430 (mm-40) cc_final: 0.6696 (tm-30) REVERT: C 411 GLU cc_start: 0.8202 (tt0) cc_final: 0.7827 (tm-30) REVERT: C 426 ASP cc_start: 0.8329 (t0) cc_final: 0.8110 (t0) REVERT: C 428 LEU cc_start: 0.8777 (tp) cc_final: 0.8380 (tp) REVERT: C 447 GLU cc_start: 0.7631 (mp0) cc_final: 0.7090 (mp0) REVERT: C 452 GLU cc_start: 0.7755 (mp0) cc_final: 0.7238 (mp0) REVERT: C 470 GLU cc_start: 0.7836 (tt0) cc_final: 0.7598 (tt0) REVERT: C 504 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7394 (mm-30) REVERT: C 521 PRO cc_start: 0.8522 (Cg_endo) cc_final: 0.8268 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7544 (tpt-90) REVERT: C 541 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7519 (tp30) REVERT: C 546 GLU cc_start: 0.7432 (tp30) cc_final: 0.7137 (tp30) REVERT: C 550 ASP cc_start: 0.8045 (m-30) cc_final: 0.7766 (m-30) REVERT: C 552 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7428 (mmtm) REVERT: C 558 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6349 (tm-30) REVERT: C 577 LEU cc_start: 0.8216 (mm) cc_final: 0.7390 (mm) REVERT: C 580 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 581 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7245 (mt-10) REVERT: C 584 ASN cc_start: 0.8754 (t0) cc_final: 0.8243 (t0) REVERT: C 594 GLU cc_start: 0.7362 (mp0) cc_final: 0.7011 (mp0) REVERT: C 609 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7246 (mp0) REVERT: C 612 PHE cc_start: 0.8610 (m-80) cc_final: 0.8247 (m-10) REVERT: C 644 LYS cc_start: 0.8391 (tppt) cc_final: 0.7689 (tppt) REVERT: C 645 LYS cc_start: 0.8289 (mttt) cc_final: 0.7430 (mmtt) REVERT: C 649 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: C 660 GLN cc_start: 0.8578 (pp30) cc_final: 0.8330 (pp30) REVERT: C 712 GLU cc_start: 0.7890 (pm20) cc_final: 0.7408 (pm20) REVERT: C 713 PHE cc_start: 0.8560 (t80) cc_final: 0.8137 (t80) REVERT: C 735 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7747 (ttp80) REVERT: C 747 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8028 (tppp) REVERT: C 754 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7348 (mp0) REVERT: C 757 LEU cc_start: 0.8556 (tp) cc_final: 0.8218 (tt) REVERT: C 763 ARG cc_start: 0.7346 (ptp-110) cc_final: 0.7122 (ptp-110) REVERT: C 764 ASN cc_start: 0.8155 (p0) cc_final: 0.7843 (p0) REVERT: C 766 ASP cc_start: 0.7253 (t0) cc_final: 0.6781 (t0) REVERT: C 768 GLN cc_start: 0.7960 (mp10) cc_final: 0.7013 (mp10) REVERT: C 772 GLU cc_start: 0.7778 (mp0) cc_final: 0.7157 (mp0) REVERT: C 800 GLU cc_start: 0.7686 (tp30) cc_final: 0.7120 (tp30) REVERT: C 802 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8008 (mtpp) REVERT: C 804 LEU cc_start: 0.8479 (mt) cc_final: 0.7853 (mp) REVERT: C 836 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7627 (mtt90) REVERT: C 841 HIS cc_start: 0.7838 (t70) cc_final: 0.7091 (t70) REVERT: C 864 LYS cc_start: 0.8737 (tppt) cc_final: 0.8468 (ttmm) outliers start: 53 outliers final: 33 residues processed: 566 average time/residue: 0.3451 time to fit residues: 260.8748 Evaluate side-chains 580 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 537 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 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 613 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE 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 294 ARG 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 572 LYS Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 615 ILE 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 132 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.0270 chunk 157 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** C 738 HIS ** 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 = 0.3675 r_free = 0.3675 target = 0.118402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100959 restraints weight = 27221.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104559 restraints weight = 13353.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106889 restraints weight = 7850.886| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3542 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= 0.128 Angle : 0.624 10.433 18800 Z= 0.303 Chirality : 0.042 0.250 2058 Planarity : 0.003 0.033 2434 Dihedral : 3.758 17.055 1844 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.62 % Allowed : 29.54 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1648 helix: 0.63 (0.18), residues: 846 sheet: -1.93 (0.54), residues: 72 loop : 0.27 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 328 HIS 0.016 0.001 HIS C 738 PHE 0.022 0.002 PHE B 76 TYR 0.015 0.001 TYR A 659 ARG 0.008 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 618) hydrogen bonds : angle 4.40931 ( 1752) metal coordination : bond 0.00511 ( 16) metal coordination : angle 3.23516 ( 24) covalent geometry : bond 0.00283 (13904) covalent geometry : angle 0.61318 (18776) *********************** 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 601 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 546 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8098 (mm-30) REVERT: B 26 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 41 LYS cc_start: 0.8350 (mmtt) cc_final: 0.8004 (mmtt) REVERT: B 77 TYR cc_start: 0.7886 (m-80) cc_final: 0.7620 (m-80) REVERT: B 91 TYR cc_start: 0.8749 (m-10) cc_final: 0.8155 (m-10) REVERT: B 94 THR cc_start: 0.8575 (m) cc_final: 0.8316 (p) REVERT: B 96 GLU cc_start: 0.7773 (tp30) cc_final: 0.7485 (tp30) REVERT: B 121 GLU cc_start: 0.8447 (mp0) cc_final: 0.7913 (pm20) REVERT: B 124 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7792 (ttp80) REVERT: B 131 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7670 (ttm110) REVERT: B 143 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7388 (p) REVERT: A 128 LEU cc_start: 0.8287 (mp) cc_final: 0.7866 (mm) REVERT: A 130 GLU cc_start: 0.7345 (pm20) cc_final: 0.6955 (pm20) REVERT: A 135 GLU cc_start: 0.7786 (pt0) cc_final: 0.7345 (pp20) REVERT: A 149 LEU cc_start: 0.8339 (tp) cc_final: 0.8100 (mm) REVERT: A 241 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: A 243 TYR cc_start: 0.7689 (m-80) cc_final: 0.7308 (m-80) REVERT: A 264 SER cc_start: 0.8457 (m) cc_final: 0.8160 (p) REVERT: A 267 VAL cc_start: 0.8857 (t) cc_final: 0.8572 (p) REVERT: A 268 GLU cc_start: 0.8454 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 283 TYR cc_start: 0.7917 (t80) cc_final: 0.7696 (t80) REVERT: A 291 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6828 (tmm) REVERT: A 306 LEU cc_start: 0.7879 (tp) cc_final: 0.7321 (tp) REVERT: A 310 CYS cc_start: 0.8294 (m) cc_final: 0.7661 (m) REVERT: A 313 MET cc_start: 0.8262 (ttm) cc_final: 0.8046 (mtp) REVERT: A 315 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7947 (mmmm) REVERT: A 327 LEU cc_start: 0.8119 (mt) cc_final: 0.7807 (mt) REVERT: A 336 ILE cc_start: 0.8441 (mm) cc_final: 0.8177 (mm) REVERT: A 338 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7326 (tpt90) REVERT: A 340 MET cc_start: 0.8095 (tmm) cc_final: 0.7498 (tmm) REVERT: A 341 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 359 ARG cc_start: 0.7674 (mmp-170) cc_final: 0.7282 (mmp80) REVERT: A 387 GLU cc_start: 0.6833 (pm20) cc_final: 0.6135 (mp0) REVERT: A 392 HIS cc_start: 0.7525 (m-70) cc_final: 0.6731 (m-70) REVERT: A 397 ASP cc_start: 0.6592 (p0) cc_final: 0.6062 (p0) REVERT: A 406 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 407 LEU cc_start: 0.8726 (mt) cc_final: 0.8374 (mt) REVERT: A 411 GLU cc_start: 0.8172 (tt0) cc_final: 0.7465 (tm-30) REVERT: A 429 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: A 435 LYS cc_start: 0.8295 (tmtt) cc_final: 0.8053 (tptp) REVERT: A 447 GLU cc_start: 0.7564 (mp0) cc_final: 0.7272 (mp0) REVERT: A 448 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 452 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7336 (mp0) REVERT: A 462 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7539 (mtmm) REVERT: A 470 GLU cc_start: 0.7783 (tt0) cc_final: 0.7381 (tt0) REVERT: A 490 ASN cc_start: 0.7796 (t0) cc_final: 0.7512 (t0) REVERT: A 515 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 533 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.6988 (tt) REVERT: A 541 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7337 (tp30) REVERT: A 550 ASP cc_start: 0.8060 (m-30) cc_final: 0.7705 (m-30) REVERT: A 558 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6221 (tm-30) REVERT: A 577 LEU cc_start: 0.8168 (mm) cc_final: 0.7680 (mm) REVERT: A 580 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 581 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7517 (pt0) REVERT: A 598 LEU cc_start: 0.8687 (mt) cc_final: 0.8306 (mt) REVERT: A 609 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7307 (mp0) REVERT: A 611 GLN cc_start: 0.7981 (mp10) cc_final: 0.7598 (mp-120) REVERT: A 644 LYS cc_start: 0.8460 (tppt) cc_final: 0.7743 (tppp) REVERT: A 645 LYS cc_start: 0.8244 (mttt) cc_final: 0.7126 (mmtm) REVERT: A 649 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7754 (mtm-85) REVERT: A 660 GLN cc_start: 0.8347 (pp30) cc_final: 0.7952 (pp30) REVERT: A 663 LYS cc_start: 0.8832 (pttp) cc_final: 0.8423 (pptt) REVERT: A 664 ASP cc_start: 0.8311 (m-30) cc_final: 0.7862 (m-30) REVERT: A 692 MET cc_start: 0.6951 (pmm) cc_final: 0.6549 (pmm) REVERT: A 710 ARG cc_start: 0.8551 (ptm160) cc_final: 0.8154 (ptp-170) REVERT: A 711 LYS cc_start: 0.8789 (mppt) cc_final: 0.8403 (mmtm) REVERT: A 712 GLU cc_start: 0.7911 (pm20) cc_final: 0.7662 (pm20) REVERT: A 713 PHE cc_start: 0.8518 (t80) cc_final: 0.8174 (t80) REVERT: A 721 ILE cc_start: 0.8802 (tp) cc_final: 0.8567 (tt) REVERT: A 724 LYS cc_start: 0.8319 (ptpp) cc_final: 0.8059 (ptpp) REVERT: A 735 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8152 (ttt-90) REVERT: A 738 HIS cc_start: 0.7191 (t70) cc_final: 0.6882 (t70) REVERT: A 739 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7420 (tpp) REVERT: A 747 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8088 (tptt) REVERT: A 757 LEU cc_start: 0.8642 (tp) cc_final: 0.8165 (tt) REVERT: A 764 ASN cc_start: 0.8107 (p0) cc_final: 0.7881 (p0) REVERT: A 768 GLN cc_start: 0.7852 (mp10) cc_final: 0.7390 (mp10) REVERT: A 772 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7158 (mp0) REVERT: A 788 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6695 (tpp-160) REVERT: A 800 GLU cc_start: 0.7890 (tp30) cc_final: 0.7286 (tp30) REVERT: A 802 LYS cc_start: 0.8438 (mtpp) cc_final: 0.7983 (mtpt) REVERT: A 804 LEU cc_start: 0.8318 (mt) cc_final: 0.7823 (mp) REVERT: A 829 LYS cc_start: 0.8408 (tttt) cc_final: 0.8122 (ttpt) REVERT: A 836 ARG cc_start: 0.7962 (mtt-85) cc_final: 0.7543 (mtt90) REVERT: A 841 HIS cc_start: 0.7850 (t70) cc_final: 0.7292 (t70) REVERT: D 15 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7319 (mtp85) REVERT: D 17 ARG cc_start: 0.7310 (mmt180) cc_final: 0.6821 (mmt180) REVERT: D 22 LEU cc_start: 0.7816 (tp) cc_final: 0.7469 (tp) REVERT: D 25 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 26 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8187 (mp) REVERT: D 39 TYR cc_start: 0.8150 (m-80) cc_final: 0.7538 (m-80) REVERT: D 41 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7995 (mmtt) REVERT: D 48 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: D 62 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7520 (tpp80) REVERT: D 76 PHE cc_start: 0.8137 (t80) cc_final: 0.7870 (t80) REVERT: D 77 TYR cc_start: 0.7938 (m-80) cc_final: 0.7482 (m-80) REVERT: D 91 TYR cc_start: 0.8701 (m-10) cc_final: 0.8130 (m-10) REVERT: D 94 THR cc_start: 0.8460 (m) cc_final: 0.8247 (p) REVERT: D 101 LYS cc_start: 0.8807 (mtmm) cc_final: 0.8578 (mttm) REVERT: D 121 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 124 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7803 (ttp80) REVERT: D 128 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8500 (mtpp) REVERT: D 131 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7958 (ttm110) REVERT: D 143 CYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7280 (p) REVERT: C 128 LEU cc_start: 0.8220 (mp) cc_final: 0.7954 (mp) REVERT: C 149 LEU cc_start: 0.8449 (tp) cc_final: 0.8166 (mm) REVERT: C 161 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7907 (pm20) REVERT: C 239 ILE cc_start: 0.8854 (mm) cc_final: 0.8648 (mm) REVERT: C 241 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: C 243 TYR cc_start: 0.7846 (m-80) cc_final: 0.7489 (m-80) REVERT: C 268 GLU cc_start: 0.8342 (tt0) cc_final: 0.7720 (tm-30) REVERT: C 283 TYR cc_start: 0.7976 (t80) cc_final: 0.7584 (t80) REVERT: C 289 ILE cc_start: 0.8631 (mm) cc_final: 0.8339 (mm) REVERT: C 310 CYS cc_start: 0.8354 (m) cc_final: 0.7829 (m) REVERT: C 311 LYS cc_start: 0.8504 (mttt) cc_final: 0.8242 (mttm) REVERT: C 315 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8046 (mmmm) REVERT: C 323 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8232 (tttt) REVERT: C 336 ILE cc_start: 0.8547 (mm) cc_final: 0.8289 (mm) REVERT: C 338 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7802 (tpp-160) REVERT: C 340 MET cc_start: 0.7669 (tmm) cc_final: 0.7316 (tmm) REVERT: C 345 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7872 (mm110) REVERT: C 359 ARG cc_start: 0.7738 (mmp-170) cc_final: 0.7361 (mmp80) REVERT: C 366 ASP cc_start: 0.7757 (p0) cc_final: 0.7550 (p0) REVERT: C 394 GLU cc_start: 0.7547 (tp30) cc_final: 0.6704 (tp30) REVERT: C 401 ILE cc_start: 0.8721 (mm) cc_final: 0.8426 (pt) REVERT: C 403 GLU cc_start: 0.7529 (pm20) cc_final: 0.7182 (pm20) REVERT: C 407 LEU cc_start: 0.8798 (mt) cc_final: 0.8486 (mt) REVERT: C 410 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6677 (tm-30) REVERT: C 411 GLU cc_start: 0.8230 (tt0) cc_final: 0.7814 (tm-30) REVERT: C 426 ASP cc_start: 0.8333 (t0) cc_final: 0.8107 (t0) REVERT: C 428 LEU cc_start: 0.8778 (tp) cc_final: 0.8388 (tp) REVERT: C 447 GLU cc_start: 0.7653 (mp0) cc_final: 0.7093 (mp0) REVERT: C 452 GLU cc_start: 0.7768 (mp0) cc_final: 0.7290 (mp0) REVERT: C 470 GLU cc_start: 0.7822 (tt0) cc_final: 0.7567 (tt0) REVERT: C 504 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7421 (mm-30) REVERT: C 521 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8235 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7595 (tpt-90) REVERT: C 541 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7525 (tp30) REVERT: C 546 GLU cc_start: 0.7431 (tp30) cc_final: 0.6816 (tp30) REVERT: C 547 ASN cc_start: 0.7735 (m-40) cc_final: 0.7171 (m-40) REVERT: C 550 ASP cc_start: 0.7966 (m-30) cc_final: 0.7687 (m-30) REVERT: C 552 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7410 (mmtm) REVERT: C 558 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6320 (tm-30) REVERT: C 577 LEU cc_start: 0.8232 (mm) cc_final: 0.7391 (mm) REVERT: C 580 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7552 (mt-10) REVERT: C 581 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7258 (mt-10) REVERT: C 584 ASN cc_start: 0.8772 (t0) cc_final: 0.8308 (t0) REVERT: C 594 GLU cc_start: 0.7386 (mp0) cc_final: 0.7012 (mp0) REVERT: C 609 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7197 (mp0) REVERT: C 612 PHE cc_start: 0.8565 (m-80) cc_final: 0.8191 (m-10) REVERT: C 644 LYS cc_start: 0.8324 (tppt) cc_final: 0.7653 (tppt) REVERT: C 645 LYS cc_start: 0.8281 (mttt) cc_final: 0.7422 (mmtt) REVERT: C 660 GLN cc_start: 0.8610 (pp30) cc_final: 0.8286 (pp30) REVERT: C 663 LYS cc_start: 0.8919 (pttp) cc_final: 0.8620 (pptt) REVERT: C 712 GLU cc_start: 0.7887 (pm20) cc_final: 0.7404 (pm20) REVERT: C 713 PHE cc_start: 0.8563 (t80) cc_final: 0.8133 (t80) REVERT: C 735 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.7742 (ttp80) REVERT: C 743 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7028 (mt-10) REVERT: C 747 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8044 (tppp) REVERT: C 754 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7334 (mp0) REVERT: C 757 LEU cc_start: 0.8539 (tp) cc_final: 0.8231 (tt) REVERT: C 763 ARG cc_start: 0.7388 (ptp-110) cc_final: 0.7179 (ptp-110) REVERT: C 764 ASN cc_start: 0.8139 (p0) cc_final: 0.7842 (p0) REVERT: C 766 ASP cc_start: 0.7263 (t0) cc_final: 0.6788 (t0) REVERT: C 768 GLN cc_start: 0.7978 (mp10) cc_final: 0.7208 (mp10) REVERT: C 772 GLU cc_start: 0.7802 (mp0) cc_final: 0.7386 (mp0) REVERT: C 800 GLU cc_start: 0.7688 (tp30) cc_final: 0.7318 (tp30) REVERT: C 802 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8153 (mtpp) REVERT: C 804 LEU cc_start: 0.8400 (mt) cc_final: 0.7954 (mt) REVERT: C 836 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7610 (mtt90) REVERT: C 841 HIS cc_start: 0.7778 (t70) cc_final: 0.7137 (t70) REVERT: C 864 LYS cc_start: 0.8730 (tppt) cc_final: 0.8469 (ttmm) outliers start: 55 outliers final: 36 residues processed: 567 average time/residue: 0.3649 time to fit residues: 277.2379 Evaluate side-chains 579 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 533 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 458 LEU 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 613 THR Chi-restraints excluded: chain A residue 642 MET 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 294 ARG 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 615 ILE Chi-restraints excluded: chain C residue 642 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 125 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS A 801 GLN ** C 455 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.113346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096393 restraints weight = 27312.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099943 restraints weight = 13426.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102271 restraints weight = 7899.555| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13920 Z= 0.138 Angle : 0.627 9.607 18800 Z= 0.308 Chirality : 0.043 0.266 2058 Planarity : 0.004 0.033 2434 Dihedral : 3.778 17.634 1844 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.42 % Allowed : 30.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1648 helix: 0.60 (0.18), residues: 848 sheet: -1.91 (0.55), residues: 72 loop : 0.26 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 328 HIS 0.012 0.001 HIS C 738 PHE 0.028 0.002 PHE B 76 TYR 0.017 0.001 TYR A 659 ARG 0.009 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 618) hydrogen bonds : angle 4.44958 ( 1752) metal coordination : bond 0.00567 ( 16) metal coordination : angle 3.31504 ( 24) covalent geometry : bond 0.00300 (13904) covalent geometry : angle 0.61631 (18776) *********************** 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 601 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 549 time to evaluate : 1.544 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: 0.7555 (mtp85) cc_final: 0.7142 (mmt180) REVERT: B 21 GLN cc_start: 0.8020 (tt0) cc_final: 0.7737 (tt0) REVERT: B 25 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 26 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 41 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8039 (mmtt) REVERT: B 77 TYR cc_start: 0.7944 (m-80) cc_final: 0.7697 (m-80) REVERT: B 91 TYR cc_start: 0.8723 (m-10) cc_final: 0.8095 (m-10) REVERT: B 94 THR cc_start: 0.8583 (m) cc_final: 0.8340 (p) REVERT: B 96 GLU cc_start: 0.7630 (tp30) cc_final: 0.7291 (tp30) REVERT: B 121 GLU cc_start: 0.8418 (mp0) cc_final: 0.8184 (pm20) REVERT: B 123 GLN cc_start: 0.8018 (tp40) cc_final: 0.7390 (tp40) REVERT: B 131 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7703 (ttm110) REVERT: B 143 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7354 (p) REVERT: B 144 MET cc_start: 0.7317 (mmm) cc_final: 0.6955 (mmm) REVERT: A 128 LEU cc_start: 0.8303 (mp) cc_final: 0.7880 (mm) REVERT: A 130 GLU cc_start: 0.7318 (pm20) cc_final: 0.6944 (pm20) REVERT: A 135 GLU cc_start: 0.7679 (pt0) cc_final: 0.7339 (pp20) REVERT: A 149 LEU cc_start: 0.8303 (tp) cc_final: 0.8083 (mm) REVERT: A 241 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7807 (mtm-85) REVERT: A 243 TYR cc_start: 0.7670 (m-80) cc_final: 0.7324 (m-80) REVERT: A 264 SER cc_start: 0.8468 (m) cc_final: 0.8188 (p) REVERT: A 267 VAL cc_start: 0.8865 (t) cc_final: 0.8579 (p) REVERT: A 268 GLU cc_start: 0.8434 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 283 TYR cc_start: 0.7928 (t80) cc_final: 0.7699 (t80) REVERT: A 291 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6827 (tmm) REVERT: A 310 CYS cc_start: 0.8307 (m) cc_final: 0.7750 (m) REVERT: A 313 MET cc_start: 0.8229 (ttm) cc_final: 0.8018 (mtp) REVERT: A 315 LYS cc_start: 0.8524 (mmtt) cc_final: 0.7942 (mmmm) REVERT: A 327 LEU cc_start: 0.8073 (mt) cc_final: 0.7762 (mt) REVERT: A 336 ILE cc_start: 0.8447 (mm) cc_final: 0.8234 (mm) REVERT: A 338 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7291 (tpt90) REVERT: A 340 MET cc_start: 0.8075 (tmm) cc_final: 0.7437 (tmm) REVERT: A 341 GLU cc_start: 0.7951 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 342 THR cc_start: 0.8801 (p) cc_final: 0.8267 (p) REVERT: A 387 GLU cc_start: 0.6828 (pm20) cc_final: 0.6222 (mp0) REVERT: A 392 HIS cc_start: 0.7498 (m-70) cc_final: 0.6699 (m-70) REVERT: A 397 ASP cc_start: 0.6536 (p0) cc_final: 0.6150 (p0) REVERT: A 406 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 407 LEU cc_start: 0.8735 (mt) cc_final: 0.8391 (mt) REVERT: A 411 GLU cc_start: 0.8157 (tt0) cc_final: 0.7472 (tm-30) REVERT: A 429 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: A 435 LYS cc_start: 0.8323 (tmtt) cc_final: 0.8090 (tptp) REVERT: A 447 GLU cc_start: 0.7605 (mp0) cc_final: 0.7370 (mp0) REVERT: A 452 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7311 (mp0) REVERT: A 470 GLU cc_start: 0.7787 (tt0) cc_final: 0.7369 (tt0) REVERT: A 490 ASN cc_start: 0.7779 (t0) cc_final: 0.7494 (t0) REVERT: A 515 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 533 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7020 (tt) REVERT: A 550 ASP cc_start: 0.8031 (m-30) cc_final: 0.7699 (m-30) REVERT: A 558 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 577 LEU cc_start: 0.8194 (mm) cc_final: 0.7707 (mm) REVERT: A 580 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 581 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7531 (pt0) REVERT: A 598 LEU cc_start: 0.8697 (mt) cc_final: 0.8374 (mt) REVERT: A 611 GLN cc_start: 0.7777 (mp10) cc_final: 0.7166 (mp10) REVERT: A 627 CYS cc_start: 0.8188 (m) cc_final: 0.7975 (m) REVERT: A 644 LYS cc_start: 0.8466 (tppt) cc_final: 0.7736 (tppp) REVERT: A 645 LYS cc_start: 0.8187 (mttt) cc_final: 0.7076 (mmmm) REVERT: A 649 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: A 660 GLN cc_start: 0.8328 (pp30) cc_final: 0.7911 (pp30) REVERT: A 663 LYS cc_start: 0.8784 (pttp) cc_final: 0.8430 (pptt) REVERT: A 664 ASP cc_start: 0.8302 (m-30) cc_final: 0.7879 (m-30) REVERT: A 710 ARG cc_start: 0.8550 (ptm160) cc_final: 0.8321 (ptp-170) REVERT: A 712 GLU cc_start: 0.7908 (pm20) cc_final: 0.7667 (pm20) REVERT: A 713 PHE cc_start: 0.8496 (t80) cc_final: 0.8155 (t80) REVERT: A 721 ILE cc_start: 0.8840 (tp) cc_final: 0.8599 (tt) REVERT: A 724 LYS cc_start: 0.8334 (ptpp) cc_final: 0.8075 (ptpp) REVERT: A 738 HIS cc_start: 0.7157 (t-90) cc_final: 0.6810 (t-90) REVERT: A 739 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7481 (tpp) REVERT: A 747 LYS cc_start: 0.8557 (mmmm) cc_final: 0.8042 (tppp) REVERT: A 757 LEU cc_start: 0.8538 (tp) cc_final: 0.8225 (tt) REVERT: A 768 GLN cc_start: 0.7818 (mp10) cc_final: 0.7374 (mp10) REVERT: A 772 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7141 (mp0) REVERT: A 788 ARG cc_start: 0.7045 (mmm-85) cc_final: 0.6706 (tpp-160) REVERT: A 800 GLU cc_start: 0.7923 (tp30) cc_final: 0.7336 (tp30) REVERT: A 802 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7995 (mtpt) REVERT: A 804 LEU cc_start: 0.8325 (mt) cc_final: 0.7834 (mp) REVERT: A 829 LYS cc_start: 0.8418 (tttt) cc_final: 0.8071 (ttpt) REVERT: A 836 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7584 (mtt90) REVERT: A 841 HIS cc_start: 0.7883 (t70) cc_final: 0.7268 (t70) REVERT: D 17 ARG cc_start: 0.7332 (mmt180) cc_final: 0.6889 (mmt180) REVERT: D 22 LEU cc_start: 0.7860 (tp) cc_final: 0.7504 (tp) REVERT: D 25 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8196 (mm-30) REVERT: D 26 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 39 TYR cc_start: 0.8185 (m-80) cc_final: 0.7553 (m-80) REVERT: D 41 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7990 (mmtt) REVERT: D 48 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 77 TYR cc_start: 0.7949 (m-80) cc_final: 0.7476 (m-80) REVERT: D 89 SER cc_start: 0.8406 (p) cc_final: 0.8116 (t) REVERT: D 91 TYR cc_start: 0.8746 (m-10) cc_final: 0.8290 (m-10) REVERT: D 115 LYS cc_start: 0.8660 (tttm) cc_final: 0.8174 (ptmm) REVERT: D 121 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: D 124 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7807 (ttp80) REVERT: D 131 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7775 (ttm110) REVERT: D 143 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7263 (p) REVERT: C 123 LYS cc_start: 0.7988 (tptp) cc_final: 0.7515 (tppt) REVERT: C 128 LEU cc_start: 0.8195 (mp) cc_final: 0.7701 (mm) REVERT: C 151 ARG cc_start: 0.7204 (ptp-110) cc_final: 0.6915 (mtm110) REVERT: C 161 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7919 (pm20) REVERT: C 243 TYR cc_start: 0.7737 (m-80) cc_final: 0.7533 (m-80) REVERT: C 245 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7785 (mmp80) REVERT: C 268 GLU cc_start: 0.8317 (tt0) cc_final: 0.7738 (tm-30) REVERT: C 283 TYR cc_start: 0.7975 (t80) cc_final: 0.7626 (t80) REVERT: C 287 PHE cc_start: 0.8220 (m-10) cc_final: 0.8011 (m-80) REVERT: C 289 ILE cc_start: 0.8640 (mm) cc_final: 0.8375 (mm) REVERT: C 310 CYS cc_start: 0.8350 (m) cc_final: 0.7860 (m) REVERT: C 311 LYS cc_start: 0.8520 (mttt) cc_final: 0.8252 (mttm) REVERT: C 315 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8002 (mmmm) REVERT: C 323 LYS cc_start: 0.8685 (ptmt) cc_final: 0.8243 (tttt) REVERT: C 336 ILE cc_start: 0.8552 (mm) cc_final: 0.8305 (mm) REVERT: C 338 ARG cc_start: 0.7998 (tpp-160) cc_final: 0.7722 (tpp-160) REVERT: C 340 MET cc_start: 0.7634 (tmm) cc_final: 0.7218 (tmm) REVERT: C 345 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7845 (mm110) REVERT: C 394 GLU cc_start: 0.7523 (tp30) cc_final: 0.6957 (tp30) REVERT: C 395 GLU cc_start: 0.8294 (pp20) cc_final: 0.7818 (pp20) REVERT: C 397 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6643 (p0) REVERT: C 401 ILE cc_start: 0.8725 (mm) cc_final: 0.8449 (pt) REVERT: C 403 GLU cc_start: 0.7521 (pm20) cc_final: 0.7155 (pm20) REVERT: C 407 LEU cc_start: 0.8829 (mt) cc_final: 0.8527 (mt) REVERT: C 410 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6681 (tm-30) REVERT: C 411 GLU cc_start: 0.8192 (tt0) cc_final: 0.7787 (tm-30) REVERT: C 426 ASP cc_start: 0.8327 (t0) cc_final: 0.7983 (t0) REVERT: C 428 LEU cc_start: 0.8772 (tp) cc_final: 0.8384 (tp) REVERT: C 447 GLU cc_start: 0.7639 (mp0) cc_final: 0.7078 (mp0) REVERT: C 452 GLU cc_start: 0.7763 (mp0) cc_final: 0.7293 (mp0) REVERT: C 504 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7474 (mm-30) REVERT: C 539 ARG cc_start: 0.7938 (tpt-90) cc_final: 0.7581 (tpt-90) REVERT: C 541 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7827 (tp30) REVERT: C 546 GLU cc_start: 0.7391 (tp30) cc_final: 0.6763 (tp30) REVERT: C 547 ASN cc_start: 0.7765 (m-40) cc_final: 0.7163 (m-40) REVERT: C 550 ASP cc_start: 0.8017 (m-30) cc_final: 0.7714 (m-30) REVERT: C 552 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7549 (mmtm) REVERT: C 558 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6307 (tm-30) REVERT: C 577 LEU cc_start: 0.8249 (mm) cc_final: 0.7664 (mm) REVERT: C 580 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 584 ASN cc_start: 0.8756 (t0) cc_final: 0.8354 (t0) REVERT: C 594 GLU cc_start: 0.7351 (mp0) cc_final: 0.6979 (mp0) REVERT: C 609 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7053 (mp0) REVERT: C 644 LYS cc_start: 0.8321 (tppt) cc_final: 0.7806 (tppt) REVERT: C 645 LYS cc_start: 0.8325 (mttt) cc_final: 0.7288 (mmmm) REVERT: C 660 GLN cc_start: 0.8578 (pp30) cc_final: 0.8276 (pp30) REVERT: C 663 LYS cc_start: 0.8927 (pttp) cc_final: 0.8643 (pptt) REVERT: C 712 GLU cc_start: 0.7857 (pm20) cc_final: 0.7392 (pm20) REVERT: C 713 PHE cc_start: 0.8495 (t80) cc_final: 0.8060 (t80) REVERT: C 735 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7703 (ttp80) REVERT: C 743 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6932 (mt-10) REVERT: C 747 LYS cc_start: 0.8560 (mmmm) cc_final: 0.8072 (tppp) REVERT: C 754 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7354 (mp0) REVERT: C 757 LEU cc_start: 0.8541 (tp) cc_final: 0.8303 (tt) REVERT: C 763 ARG cc_start: 0.7393 (ptp-110) cc_final: 0.7189 (ptp-110) REVERT: C 764 ASN cc_start: 0.8107 (p0) cc_final: 0.7822 (p0) REVERT: C 766 ASP cc_start: 0.7254 (t0) cc_final: 0.6672 (t0) REVERT: C 768 GLN cc_start: 0.7961 (mp10) cc_final: 0.7180 (mp10) REVERT: C 772 GLU cc_start: 0.7781 (mp0) cc_final: 0.7374 (mp0) REVERT: C 800 GLU cc_start: 0.7696 (tp30) cc_final: 0.7336 (tp30) REVERT: C 802 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8144 (mtpp) REVERT: C 804 LEU cc_start: 0.8415 (mt) cc_final: 0.7967 (mt) REVERT: C 836 ARG cc_start: 0.8000 (mtt-85) cc_final: 0.7565 (mtt90) REVERT: C 841 HIS cc_start: 0.7799 (t70) cc_final: 0.7161 (t70) REVERT: C 864 LYS cc_start: 0.8742 (tppt) cc_final: 0.8482 (ttmm) outliers start: 52 outliers final: 31 residues processed: 570 average time/residue: 0.3442 time to fit residues: 260.1202 Evaluate side-chains 576 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 534 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 458 LEU 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 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE 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 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 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 642 MET Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.2980 chunk 24 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 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 C 738 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098872 restraints weight = 27136.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102413 restraints weight = 13249.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104715 restraints weight = 7798.723| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13920 Z= 0.123 Angle : 0.650 9.948 18800 Z= 0.316 Chirality : 0.042 0.269 2058 Planarity : 0.004 0.033 2434 Dihedral : 3.772 17.576 1844 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.96 % Allowed : 30.92 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1648 helix: 0.60 (0.18), residues: 844 sheet: -2.10 (0.54), residues: 72 loop : 0.27 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 328 HIS 0.012 0.001 HIS C 738 PHE 0.025 0.002 PHE D 76 TYR 0.017 0.001 TYR A 659 ARG 0.011 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 618) hydrogen bonds : angle 4.42650 ( 1752) metal coordination : bond 0.00400 ( 16) metal coordination : angle 3.17727 ( 24) covalent geometry : bond 0.00275 (13904) covalent geometry : angle 0.64023 (18776) *********************** 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 592 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 547 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 GLN cc_start: 0.8010 (tt0) cc_final: 0.7723 (tt0) REVERT: B 25 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 26 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 41 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8108 (mmtt) REVERT: B 77 TYR cc_start: 0.7867 (m-80) cc_final: 0.7609 (m-80) REVERT: B 91 TYR cc_start: 0.8693 (m-10) cc_final: 0.8145 (m-10) REVERT: B 94 THR cc_start: 0.8534 (m) cc_final: 0.8299 (p) REVERT: B 96 GLU cc_start: 0.7692 (tp30) cc_final: 0.7373 (tp30) REVERT: B 131 ARG cc_start: 0.8334 (ttm110) cc_final: 0.7730 (ttm110) REVERT: A 123 LYS cc_start: 0.7970 (tptp) cc_final: 0.7547 (tppt) REVERT: A 128 LEU cc_start: 0.8275 (mp) cc_final: 0.7853 (mm) REVERT: A 130 GLU cc_start: 0.7266 (pm20) cc_final: 0.6886 (pm20) REVERT: A 135 GLU cc_start: 0.7632 (pt0) cc_final: 0.7316 (pp20) REVERT: A 149 LEU cc_start: 0.8264 (tp) cc_final: 0.8028 (mm) REVERT: A 241 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: A 243 TYR cc_start: 0.7637 (m-80) cc_final: 0.7296 (m-80) REVERT: A 264 SER cc_start: 0.8476 (m) cc_final: 0.8217 (p) REVERT: A 267 VAL cc_start: 0.8833 (t) cc_final: 0.8563 (p) REVERT: A 268 GLU cc_start: 0.8437 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 283 TYR cc_start: 0.7936 (t80) cc_final: 0.7681 (t80) REVERT: A 291 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6937 (tmm) REVERT: A 297 HIS cc_start: 0.7152 (t-170) cc_final: 0.6090 (t-170) REVERT: A 310 CYS cc_start: 0.8271 (m) cc_final: 0.7656 (m) REVERT: A 315 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7926 (mmmm) REVERT: A 327 LEU cc_start: 0.7976 (mt) cc_final: 0.7685 (mt) REVERT: A 336 ILE cc_start: 0.8412 (mm) cc_final: 0.8209 (mm) REVERT: A 338 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7359 (tpt90) REVERT: A 340 MET cc_start: 0.8039 (tmm) cc_final: 0.7418 (tmm) REVERT: A 341 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 387 GLU cc_start: 0.6801 (pm20) cc_final: 0.6575 (pm20) REVERT: A 392 HIS cc_start: 0.7471 (m-70) cc_final: 0.6692 (m-70) REVERT: A 397 ASP cc_start: 0.6495 (p0) cc_final: 0.6207 (p0) REVERT: A 406 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 407 LEU cc_start: 0.8719 (mt) cc_final: 0.8379 (mt) REVERT: A 411 GLU cc_start: 0.8152 (tt0) cc_final: 0.7461 (tm-30) REVERT: A 429 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: A 435 LYS cc_start: 0.8309 (tmtt) cc_final: 0.8055 (tptp) REVERT: A 447 GLU cc_start: 0.7604 (mp0) cc_final: 0.7332 (mp0) REVERT: A 452 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7296 (mp0) REVERT: A 470 GLU cc_start: 0.7777 (tt0) cc_final: 0.7382 (tt0) REVERT: A 490 ASN cc_start: 0.7741 (t0) cc_final: 0.7431 (t0) REVERT: A 515 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 518 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 542 MET cc_start: 0.7408 (ptp) cc_final: 0.7003 (ptp) REVERT: A 550 ASP cc_start: 0.8076 (m-30) cc_final: 0.7745 (m-30) REVERT: A 558 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6188 (tm-30) REVERT: A 577 LEU cc_start: 0.8170 (mm) cc_final: 0.7682 (mm) REVERT: A 580 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 581 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7499 (pt0) REVERT: A 598 LEU cc_start: 0.8693 (mt) cc_final: 0.8369 (mt) REVERT: A 611 GLN cc_start: 0.7591 (mp10) cc_final: 0.7075 (mp10) REVERT: A 627 CYS cc_start: 0.8202 (m) cc_final: 0.7985 (m) REVERT: A 644 LYS cc_start: 0.8472 (tppt) cc_final: 0.7744 (tppp) REVERT: A 645 LYS cc_start: 0.8130 (mttt) cc_final: 0.7068 (mmmm) REVERT: A 660 GLN cc_start: 0.8301 (pp30) cc_final: 0.7836 (pp30) REVERT: A 663 LYS cc_start: 0.8809 (pttp) cc_final: 0.8438 (pptt) REVERT: A 664 ASP cc_start: 0.8245 (m-30) cc_final: 0.7817 (m-30) REVERT: A 710 ARG cc_start: 0.8520 (ptm160) cc_final: 0.7798 (ptt180) REVERT: A 712 GLU cc_start: 0.7873 (pm20) cc_final: 0.7628 (pm20) REVERT: A 713 PHE cc_start: 0.8464 (t80) cc_final: 0.8122 (t80) REVERT: A 721 ILE cc_start: 0.8852 (tp) cc_final: 0.8618 (tt) REVERT: A 724 LYS cc_start: 0.8303 (ptpp) cc_final: 0.8039 (ptpp) REVERT: A 738 HIS cc_start: 0.7110 (t-90) cc_final: 0.6800 (t-90) REVERT: A 739 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7676 (tpp) REVERT: A 747 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8088 (tptt) REVERT: A 757 LEU cc_start: 0.8532 (tp) cc_final: 0.8240 (tt) REVERT: A 768 GLN cc_start: 0.7824 (mp10) cc_final: 0.7380 (mp10) REVERT: A 772 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7125 (mp0) REVERT: A 800 GLU cc_start: 0.7906 (tp30) cc_final: 0.7319 (tp30) REVERT: A 802 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7968 (mtpt) REVERT: A 804 LEU cc_start: 0.8333 (mt) cc_final: 0.7839 (mp) REVERT: A 829 LYS cc_start: 0.8404 (tttt) cc_final: 0.7975 (ttpt) REVERT: A 836 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7579 (mtt90) REVERT: A 841 HIS cc_start: 0.7879 (t70) cc_final: 0.7269 (t70) REVERT: A 855 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7763 (tttt) REVERT: D 17 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6860 (mmt180) REVERT: D 22 LEU cc_start: 0.7825 (tp) cc_final: 0.7468 (tp) REVERT: D 25 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8193 (mm-30) REVERT: D 26 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8148 (mp) REVERT: D 39 TYR cc_start: 0.8196 (m-80) cc_final: 0.7495 (m-80) REVERT: D 41 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8090 (mmtt) REVERT: D 48 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: D 77 TYR cc_start: 0.7924 (m-80) cc_final: 0.7408 (m-80) REVERT: D 89 SER cc_start: 0.8391 (p) cc_final: 0.7982 (t) REVERT: D 91 TYR cc_start: 0.8675 (m-10) cc_final: 0.8406 (m-10) REVERT: D 101 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8539 (mttm) REVERT: D 115 LYS cc_start: 0.8667 (tttm) cc_final: 0.8188 (ptmm) REVERT: D 121 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: D 124 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7761 (ttp80) REVERT: D 128 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8489 (mtpp) REVERT: D 131 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7476 (ttm110) REVERT: D 143 CYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7243 (p) REVERT: C 123 LYS cc_start: 0.7972 (tptp) cc_final: 0.7498 (tppt) REVERT: C 128 LEU cc_start: 0.8144 (mp) cc_final: 0.7667 (mm) REVERT: C 149 LEU cc_start: 0.8360 (tp) cc_final: 0.8114 (mm) REVERT: C 161 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7910 (pm20) REVERT: C 241 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: C 243 TYR cc_start: 0.7782 (m-80) cc_final: 0.7398 (m-80) REVERT: C 245 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7471 (mmm-85) REVERT: C 251 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7805 (mtmm) REVERT: C 268 GLU cc_start: 0.8312 (tt0) cc_final: 0.7738 (tm-30) REVERT: C 283 TYR cc_start: 0.7966 (t80) cc_final: 0.7608 (t80) REVERT: C 289 ILE cc_start: 0.8592 (mm) cc_final: 0.8336 (mm) REVERT: C 310 CYS cc_start: 0.8359 (m) cc_final: 0.7866 (m) REVERT: C 315 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7958 (mmmm) REVERT: C 323 LYS cc_start: 0.8619 (ptmt) cc_final: 0.8104 (tttt) REVERT: C 336 ILE cc_start: 0.8526 (mm) cc_final: 0.8274 (mm) REVERT: C 338 ARG cc_start: 0.8012 (tpp-160) cc_final: 0.7734 (tpp-160) REVERT: C 340 MET cc_start: 0.7591 (tmm) cc_final: 0.7019 (tmm) REVERT: C 394 GLU cc_start: 0.7509 (tp30) cc_final: 0.6638 (tp30) REVERT: C 395 GLU cc_start: 0.8319 (pp20) cc_final: 0.7762 (pp20) REVERT: C 397 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6832 (p0) REVERT: C 401 ILE cc_start: 0.8744 (mm) cc_final: 0.8465 (pt) REVERT: C 403 GLU cc_start: 0.7494 (pm20) cc_final: 0.7169 (pm20) REVERT: C 407 LEU cc_start: 0.8827 (mt) cc_final: 0.8527 (mt) REVERT: C 410 GLN cc_start: 0.7494 (mm-40) cc_final: 0.6686 (tm-30) REVERT: C 411 GLU cc_start: 0.8185 (tt0) cc_final: 0.7787 (tm-30) REVERT: C 426 ASP cc_start: 0.8349 (t0) cc_final: 0.8075 (t0) REVERT: C 428 LEU cc_start: 0.8758 (tp) cc_final: 0.8378 (tp) REVERT: C 447 GLU cc_start: 0.7601 (mp0) cc_final: 0.7045 (mp0) REVERT: C 452 GLU cc_start: 0.7725 (mp0) cc_final: 0.7259 (mp0) REVERT: C 470 GLU cc_start: 0.7807 (tt0) cc_final: 0.7250 (tt0) REVERT: C 539 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7624 (tpt-90) REVERT: C 541 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 546 GLU cc_start: 0.7374 (tp30) cc_final: 0.6733 (tp30) REVERT: C 547 ASN cc_start: 0.7756 (m-40) cc_final: 0.7152 (m-40) REVERT: C 550 ASP cc_start: 0.7977 (m-30) cc_final: 0.7657 (m-30) REVERT: C 552 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7567 (mmtm) REVERT: C 558 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6287 (tm-30) REVERT: C 577 LEU cc_start: 0.8187 (mm) cc_final: 0.7603 (mm) REVERT: C 580 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 584 ASN cc_start: 0.8749 (t0) cc_final: 0.8361 (t0) REVERT: C 594 GLU cc_start: 0.7329 (mp0) cc_final: 0.6956 (mp0) REVERT: C 609 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7086 (mp0) REVERT: C 644 LYS cc_start: 0.8283 (tppt) cc_final: 0.7793 (tppt) REVERT: C 645 LYS cc_start: 0.8292 (mttt) cc_final: 0.7437 (mmtm) REVERT: C 660 GLN cc_start: 0.8593 (pp30) cc_final: 0.8284 (pp30) REVERT: C 663 LYS cc_start: 0.8911 (pttp) cc_final: 0.8612 (pptt) REVERT: C 712 GLU cc_start: 0.7832 (pm20) cc_final: 0.7509 (pm20) REVERT: C 713 PHE cc_start: 0.8467 (t80) cc_final: 0.8014 (t80) REVERT: C 735 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7709 (ttp80) REVERT: C 743 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6905 (mt-10) REVERT: C 747 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8077 (tppp) REVERT: C 754 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7332 (mp0) REVERT: C 757 LEU cc_start: 0.8527 (tp) cc_final: 0.8211 (tt) REVERT: C 762 SER cc_start: 0.8052 (m) cc_final: 0.7542 (p) REVERT: C 763 ARG cc_start: 0.7370 (ptp-110) cc_final: 0.7163 (ptp-110) REVERT: C 764 ASN cc_start: 0.8116 (p0) cc_final: 0.7810 (p0) REVERT: C 766 ASP cc_start: 0.7226 (t0) cc_final: 0.6642 (t0) REVERT: C 768 GLN cc_start: 0.7940 (mp10) cc_final: 0.7183 (mp10) REVERT: C 772 GLU cc_start: 0.7763 (mp0) cc_final: 0.7354 (mp0) REVERT: C 800 GLU cc_start: 0.7686 (tp30) cc_final: 0.7327 (tp30) REVERT: C 802 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8164 (mtpp) REVERT: C 804 LEU cc_start: 0.8408 (mt) cc_final: 0.7954 (mt) REVERT: C 836 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7558 (mtt90) REVERT: C 841 HIS cc_start: 0.7795 (t70) cc_final: 0.7083 (t70) REVERT: C 864 LYS cc_start: 0.8724 (tppt) cc_final: 0.8475 (ttmm) outliers start: 45 outliers final: 33 residues processed: 564 average time/residue: 0.3441 time to fit residues: 258.1214 Evaluate side-chains 580 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 538 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 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 595 SER Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 806 LEU 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 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 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 615 ILE Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 806 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 151 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 138 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 335 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 455 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.116015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098832 restraints weight = 27098.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102402 restraints weight = 13198.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104730 restraints weight = 7769.194| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13920 Z= 0.125 Angle : 0.664 10.402 18800 Z= 0.324 Chirality : 0.043 0.277 2058 Planarity : 0.004 0.032 2434 Dihedral : 3.782 17.802 1844 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.89 % Allowed : 31.25 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1648 helix: 0.60 (0.18), residues: 844 sheet: -2.22 (0.53), residues: 72 loop : 0.28 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 328 HIS 0.005 0.001 HIS C 738 PHE 0.026 0.002 PHE C 343 TYR 0.022 0.001 TYR B 99 ARG 0.009 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 618) hydrogen bonds : angle 4.44331 ( 1752) metal coordination : bond 0.00391 ( 16) metal coordination : angle 3.11423 ( 24) covalent geometry : bond 0.00284 (13904) covalent geometry : angle 0.65494 (18776) ********************** 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 590 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 546 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 GLN cc_start: 0.8000 (tt0) cc_final: 0.7717 (tt0) REVERT: B 25 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 26 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 41 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8103 (mmtt) REVERT: B 77 TYR cc_start: 0.7868 (m-80) cc_final: 0.7610 (m-80) REVERT: B 91 TYR cc_start: 0.8723 (m-10) cc_final: 0.8136 (m-10) REVERT: B 94 THR cc_start: 0.8516 (m) cc_final: 0.8258 (p) REVERT: B 96 GLU cc_start: 0.7585 (tp30) cc_final: 0.7241 (tp30) REVERT: B 131 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7695 (ttm110) REVERT: A 123 LYS cc_start: 0.7998 (tptp) cc_final: 0.7542 (tppt) REVERT: A 128 LEU cc_start: 0.8282 (mp) cc_final: 0.7984 (mm) REVERT: A 130 GLU cc_start: 0.7286 (pm20) cc_final: 0.6853 (pm20) REVERT: A 135 GLU cc_start: 0.7645 (pt0) cc_final: 0.7331 (pp20) REVERT: A 149 LEU cc_start: 0.8276 (tp) cc_final: 0.8059 (mm) REVERT: A 153 ILE cc_start: 0.8819 (mt) cc_final: 0.8513 (tt) REVERT: A 241 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: A 243 TYR cc_start: 0.7647 (m-80) cc_final: 0.7325 (m-80) REVERT: A 264 SER cc_start: 0.8490 (m) cc_final: 0.8124 (p) REVERT: A 267 VAL cc_start: 0.8868 (t) cc_final: 0.8569 (p) REVERT: A 268 GLU cc_start: 0.8431 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 283 TYR cc_start: 0.7925 (t80) cc_final: 0.7677 (t80) REVERT: A 291 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6926 (tmm) REVERT: A 297 HIS cc_start: 0.7198 (t-170) cc_final: 0.6110 (t-170) REVERT: A 310 CYS cc_start: 0.8315 (m) cc_final: 0.7667 (m) REVERT: A 315 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7803 (mmmm) REVERT: A 336 ILE cc_start: 0.8427 (mm) cc_final: 0.8209 (mm) REVERT: A 338 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.7391 (tpt90) REVERT: A 340 MET cc_start: 0.8028 (tmm) cc_final: 0.7396 (tmm) REVERT: A 341 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 387 GLU cc_start: 0.6808 (pm20) cc_final: 0.6195 (mp0) REVERT: A 392 HIS cc_start: 0.7463 (m-70) cc_final: 0.6599 (m-70) REVERT: A 394 GLU cc_start: 0.7420 (tp30) cc_final: 0.5952 (tp30) REVERT: A 397 ASP cc_start: 0.6531 (p0) cc_final: 0.6204 (p0) REVERT: A 406 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 407 LEU cc_start: 0.8719 (mt) cc_final: 0.8376 (mt) REVERT: A 411 GLU cc_start: 0.8156 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 429 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: A 435 LYS cc_start: 0.8312 (tmtt) cc_final: 0.8051 (tptp) REVERT: A 447 GLU cc_start: 0.7612 (mp0) cc_final: 0.7379 (mp0) REVERT: A 452 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7376 (mp0) REVERT: A 463 ASP cc_start: 0.8100 (t0) cc_final: 0.7893 (t0) REVERT: A 470 GLU cc_start: 0.7775 (tt0) cc_final: 0.7364 (tt0) REVERT: A 490 ASN cc_start: 0.7732 (t0) cc_final: 0.7427 (t0) REVERT: A 515 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 518 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 542 MET cc_start: 0.7395 (ptp) cc_final: 0.7002 (ptp) REVERT: A 550 ASP cc_start: 0.8007 (m-30) cc_final: 0.7659 (m-30) REVERT: A 558 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6167 (tm-30) REVERT: A 577 LEU cc_start: 0.8161 (mm) cc_final: 0.7675 (mm) REVERT: A 580 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 581 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7492 (pt0) REVERT: A 587 ILE cc_start: 0.8527 (tp) cc_final: 0.8291 (tp) REVERT: A 598 LEU cc_start: 0.8684 (mt) cc_final: 0.8364 (mt) REVERT: A 611 GLN cc_start: 0.7636 (mp10) cc_final: 0.7074 (mp10) REVERT: A 627 CYS cc_start: 0.8226 (m) cc_final: 0.7977 (m) REVERT: A 632 HIS cc_start: 0.8285 (m90) cc_final: 0.8063 (m-70) REVERT: A 644 LYS cc_start: 0.8457 (tppt) cc_final: 0.7794 (tppp) REVERT: A 645 LYS cc_start: 0.8205 (mttt) cc_final: 0.7261 (mmtm) REVERT: A 649 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: A 660 GLN cc_start: 0.8309 (pp30) cc_final: 0.7810 (pp30) REVERT: A 663 LYS cc_start: 0.8804 (pttp) cc_final: 0.8438 (pptt) REVERT: A 664 ASP cc_start: 0.8236 (m-30) cc_final: 0.7797 (m-30) REVERT: A 710 ARG cc_start: 0.8522 (ptm160) cc_final: 0.7801 (ptt180) REVERT: A 712 GLU cc_start: 0.7870 (pm20) cc_final: 0.7621 (pm20) REVERT: A 713 PHE cc_start: 0.8481 (t80) cc_final: 0.8102 (t80) REVERT: A 721 ILE cc_start: 0.8847 (tp) cc_final: 0.8603 (tt) REVERT: A 724 LYS cc_start: 0.8303 (ptpp) cc_final: 0.8035 (ptpp) REVERT: A 728 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8475 (ttpp) REVERT: A 738 HIS cc_start: 0.7127 (t-90) cc_final: 0.6791 (t-90) REVERT: A 739 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7374 (tpp) REVERT: A 747 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8086 (tptt) REVERT: A 757 LEU cc_start: 0.8544 (tp) cc_final: 0.8223 (tt) REVERT: A 768 GLN cc_start: 0.7801 (mp10) cc_final: 0.7380 (mp10) REVERT: A 772 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7079 (mp0) REVERT: A 800 GLU cc_start: 0.7914 (tp30) cc_final: 0.7325 (tp30) REVERT: A 802 LYS cc_start: 0.8378 (mtpp) cc_final: 0.7963 (mtpt) REVERT: A 804 LEU cc_start: 0.8322 (mt) cc_final: 0.7820 (mp) REVERT: A 829 LYS cc_start: 0.8414 (tttt) cc_final: 0.8013 (ttpp) REVERT: A 836 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7660 (mtt90) REVERT: A 841 HIS cc_start: 0.7896 (t70) cc_final: 0.7294 (t70) REVERT: A 855 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7756 (ttpp) REVERT: D 17 ARG cc_start: 0.7294 (mmt180) cc_final: 0.6866 (mmt180) REVERT: D 22 LEU cc_start: 0.7819 (tp) cc_final: 0.7470 (tp) REVERT: D 25 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 26 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8149 (mp) REVERT: D 39 TYR cc_start: 0.8196 (m-80) cc_final: 0.7537 (m-80) REVERT: D 41 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8084 (mmtt) REVERT: D 48 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: D 77 TYR cc_start: 0.7937 (m-80) cc_final: 0.7387 (m-80) REVERT: D 89 SER cc_start: 0.8384 (p) cc_final: 0.8123 (t) REVERT: D 91 TYR cc_start: 0.8688 (m-10) cc_final: 0.8362 (m-10) REVERT: D 101 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8478 (mttm) REVERT: D 115 LYS cc_start: 0.8662 (tttm) cc_final: 0.8151 (ptmm) REVERT: D 121 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: D 124 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7791 (ttp80) REVERT: D 128 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8521 (mtpp) REVERT: D 131 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7772 (ttm110) REVERT: C 123 LYS cc_start: 0.7981 (tptp) cc_final: 0.7511 (tppt) REVERT: C 128 LEU cc_start: 0.8148 (mp) cc_final: 0.7642 (mm) REVERT: C 161 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7926 (pm20) REVERT: C 241 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7848 (mtm110) REVERT: C 243 TYR cc_start: 0.7818 (m-80) cc_final: 0.7411 (m-80) REVERT: C 245 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7490 (mmm-85) REVERT: C 251 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7812 (mtmm) REVERT: C 268 GLU cc_start: 0.8318 (tt0) cc_final: 0.7744 (tm-30) REVERT: C 283 TYR cc_start: 0.7970 (t80) cc_final: 0.7600 (t80) REVERT: C 289 ILE cc_start: 0.8611 (mm) cc_final: 0.8371 (mm) REVERT: C 291 MET cc_start: 0.7999 (tpp) cc_final: 0.7054 (tmm) REVERT: C 310 CYS cc_start: 0.8167 (m) cc_final: 0.7600 (m) REVERT: C 315 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7959 (mmmm) REVERT: C 323 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8149 (tttt) REVERT: C 336 ILE cc_start: 0.8522 (mm) cc_final: 0.8285 (mm) REVERT: C 338 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7568 (tpt-90) REVERT: C 340 MET cc_start: 0.7590 (tmm) cc_final: 0.7048 (tmm) REVERT: C 341 GLU cc_start: 0.7672 (pt0) cc_final: 0.7054 (pt0) REVERT: C 394 GLU cc_start: 0.7535 (tp30) cc_final: 0.6574 (tp30) REVERT: C 397 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6733 (p0) REVERT: C 401 ILE cc_start: 0.8776 (mm) cc_final: 0.8515 (pt) REVERT: C 403 GLU cc_start: 0.7521 (pm20) cc_final: 0.7185 (pm20) REVERT: C 407 LEU cc_start: 0.8830 (mt) cc_final: 0.8531 (mt) REVERT: C 410 GLN cc_start: 0.7489 (mm-40) cc_final: 0.6686 (tm-30) REVERT: C 411 GLU cc_start: 0.8185 (tt0) cc_final: 0.7790 (tm-30) REVERT: C 426 ASP cc_start: 0.8351 (t0) cc_final: 0.8075 (t0) REVERT: C 428 LEU cc_start: 0.8757 (tp) cc_final: 0.8392 (tp) REVERT: C 447 GLU cc_start: 0.7609 (mp0) cc_final: 0.7049 (mp0) REVERT: C 452 GLU cc_start: 0.7700 (mp0) cc_final: 0.7224 (mp0) REVERT: C 470 GLU cc_start: 0.7804 (tt0) cc_final: 0.7092 (tt0) REVERT: C 539 ARG cc_start: 0.7957 (tpt-90) cc_final: 0.7624 (tpt-90) REVERT: C 541 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7542 (tp30) REVERT: C 546 GLU cc_start: 0.7380 (tp30) cc_final: 0.6742 (tp30) REVERT: C 547 ASN cc_start: 0.7749 (m-40) cc_final: 0.7125 (m-40) REVERT: C 550 ASP cc_start: 0.7978 (m-30) cc_final: 0.7678 (m-30) REVERT: C 552 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7671 (mmtm) REVERT: C 558 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6273 (tm-30) REVERT: C 560 GLU cc_start: 0.7506 (tt0) cc_final: 0.7143 (pp20) REVERT: C 577 LEU cc_start: 0.8170 (mm) cc_final: 0.7664 (mm) REVERT: C 580 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7581 (mt-10) REVERT: C 584 ASN cc_start: 0.8747 (t0) cc_final: 0.8363 (t0) REVERT: C 594 GLU cc_start: 0.7319 (mp0) cc_final: 0.6935 (mp0) REVERT: C 609 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7022 (mp0) REVERT: C 644 LYS cc_start: 0.8272 (tppt) cc_final: 0.7789 (tppt) REVERT: C 645 LYS cc_start: 0.8269 (mttt) cc_final: 0.7408 (mmtm) REVERT: C 660 GLN cc_start: 0.8583 (pp30) cc_final: 0.8305 (pp30) REVERT: C 663 LYS cc_start: 0.8907 (pttp) cc_final: 0.8635 (pptt) REVERT: C 712 GLU cc_start: 0.7846 (pm20) cc_final: 0.7391 (pm20) REVERT: C 713 PHE cc_start: 0.8460 (t80) cc_final: 0.8010 (t80) REVERT: C 735 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7716 (ttp80) REVERT: C 743 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6950 (mt-10) REVERT: C 747 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8179 (mmmm) REVERT: C 754 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7301 (mp0) REVERT: C 757 LEU cc_start: 0.8528 (tp) cc_final: 0.8258 (tt) REVERT: C 762 SER cc_start: 0.8074 (m) cc_final: 0.7570 (p) REVERT: C 763 ARG cc_start: 0.7386 (ptp-110) cc_final: 0.7179 (ptp-110) REVERT: C 764 ASN cc_start: 0.8154 (p0) cc_final: 0.7843 (p0) REVERT: C 766 ASP cc_start: 0.7223 (t0) cc_final: 0.6629 (t0) REVERT: C 768 GLN cc_start: 0.7944 (mp10) cc_final: 0.7184 (mp10) REVERT: C 772 GLU cc_start: 0.7766 (mp0) cc_final: 0.7352 (mp0) REVERT: C 800 GLU cc_start: 0.7695 (tp30) cc_final: 0.7340 (tp30) REVERT: C 802 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8177 (mtpp) REVERT: C 804 LEU cc_start: 0.8394 (mt) cc_final: 0.7942 (mt) REVERT: C 836 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7491 (mtt90) REVERT: C 841 HIS cc_start: 0.7822 (t70) cc_final: 0.7156 (t70) REVERT: C 864 LYS cc_start: 0.8725 (tppt) cc_final: 0.8476 (ttmm) outliers start: 44 outliers final: 34 residues processed: 563 average time/residue: 0.3350 time to fit residues: 250.0708 Evaluate side-chains 581 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 539 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 100 ASN 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 350 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 458 LEU 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 595 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 806 LEU 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 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 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 615 ILE Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 806 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 160 optimal weight: 0.0870 chunk 156 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** C 455 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.115998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098793 restraints weight = 27279.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102352 restraints weight = 13290.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104715 restraints weight = 7815.230| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 13920 Z= 0.159 Angle : 0.868 59.196 18800 Z= 0.473 Chirality : 0.044 0.689 2058 Planarity : 0.004 0.067 2434 Dihedral : 3.793 17.725 1844 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 3.03 % Allowed : 30.66 % Favored : 66.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1648 helix: 0.60 (0.18), residues: 844 sheet: -2.22 (0.54), residues: 72 loop : 0.27 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 328 HIS 0.005 0.001 HIS C 738 PHE 0.024 0.001 PHE C 343 TYR 0.016 0.001 TYR B 99 ARG 0.009 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 618) hydrogen bonds : angle 4.43760 ( 1752) metal coordination : bond 0.00384 ( 16) metal coordination : angle 3.11468 ( 24) covalent geometry : bond 0.00350 (13904) covalent geometry : angle 0.86113 (18776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5999.57 seconds wall clock time: 103 minutes 47.80 seconds (6227.80 seconds total)