Starting phenix.real_space_refine on Sun Jul 21 07:38:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_36601_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_36601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_36601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_36601_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrp_36601/07_2024/8jrp_36601_neut.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 Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 771": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.63, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 5.22 Conformation dependent library (CDL) restraints added in 2.5 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: 1.33 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: 3.88 Time building geometry restraints manager: 5.72 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: 99.80 - 106.65: 334 106.65 - 113.49: 7355 113.49 - 120.34: 5427 120.34 - 127.19: 5554 127.19 - 134.03: 106 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 2.440 nonbonded pdb=" O LEU C 770 " pdb=" OG1 THR C 774 " model vdw 2.212 2.440 nonbonded pdb=" O ASN A 295 " pdb=" OG SER A 298 " model vdw 2.219 2.440 nonbonded pdb=" O ASN C 295 " pdb=" OG SER C 298 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR A 464 " pdb=" OD1 ASP A 496 " model vdw 2.220 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 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: 0.090 Set scattering table: 0.120 Process input model: 38.750 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- 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 13904 Z= 0.176 Angle : 0.542 11.754 18776 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 598 time to evaluate : 1.550 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: 0.3562 time to fit residues: 280.6237 Evaluate side-chains 554 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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: 0.5980 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 490 ASN C 517 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13904 Z= 0.398 Angle : 0.667 10.497 18776 Z= 0.357 Chirality : 0.045 0.176 2058 Planarity : 0.005 0.064 2434 Dihedral : 4.255 15.771 1844 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.08 % Allowed : 25.26 % Favored : 70.66 % 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: 0.11 (0.20), residues: 1648 helix: 0.40 (0.17), residues: 876 sheet: -1.17 (0.61), residues: 68 loop : -0.02 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 328 HIS 0.004 0.001 HIS C 841 PHE 0.026 0.002 PHE C 733 TYR 0.020 0.002 TYR A 494 ARG 0.006 0.001 ARG A 294 *********************** 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 651 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 589 time to evaluate : 1.547 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 22 LEU cc_start: 0.7725 (tp) cc_final: 0.7444 (tp) REVERT: B 25 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 26 LEU cc_start: 0.8505 (mp) cc_final: 0.8194 (mp) REVERT: B 41 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8035 (mmtt) REVERT: B 44 LEU cc_start: 0.8947 (mp) cc_final: 0.8727 (mp) REVERT: B 48 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: B 60 VAL cc_start: 0.8363 (p) cc_final: 0.7710 (p) REVERT: B 77 TYR cc_start: 0.8363 (m-80) cc_final: 0.8096 (m-80) REVERT: B 91 TYR cc_start: 0.8742 (m-10) cc_final: 0.8265 (m-10) REVERT: B 94 THR cc_start: 0.8468 (m) cc_final: 0.8199 (p) REVERT: B 96 GLU cc_start: 0.7555 (tp30) cc_final: 0.7341 (tp30) REVERT: B 97 GLN cc_start: 0.8018 (tp40) cc_final: 0.7543 (tp40) REVERT: B 118 SER cc_start: 0.8784 (m) cc_final: 0.8175 (t) REVERT: B 123 GLN cc_start: 0.8013 (tp40) cc_final: 0.6919 (tp40) REVERT: B 131 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7974 (ttm110) REVERT: B 143 CYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6984 (p) REVERT: A 128 LEU cc_start: 0.8291 (mp) cc_final: 0.7800 (mm) REVERT: A 135 GLU cc_start: 0.8169 (pt0) cc_final: 0.7685 (pp20) REVERT: A 167 PHE cc_start: 0.7883 (m-80) cc_final: 0.7533 (m-80) REVERT: A 236 ILE cc_start: 0.8387 (mt) cc_final: 0.8150 (mt) REVERT: A 239 ILE cc_start: 0.8778 (mm) cc_final: 0.8517 (mm) REVERT: A 243 TYR cc_start: 0.8103 (m-80) cc_final: 0.7396 (m-80) REVERT: A 245 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7875 (mmm-85) REVERT: A 247 LEU cc_start: 0.8427 (mp) cc_final: 0.7868 (mt) REVERT: A 264 SER cc_start: 0.8337 (m) cc_final: 0.8122 (p) REVERT: A 267 VAL cc_start: 0.8978 (t) cc_final: 0.8749 (p) REVERT: A 268 GLU cc_start: 0.8362 (tt0) cc_final: 0.7813 (tm-30) REVERT: A 276 VAL cc_start: 0.8697 (m) cc_final: 0.8428 (m) REVERT: A 295 ASN cc_start: 0.8465 (m-40) cc_final: 0.8254 (m110) REVERT: A 310 CYS cc_start: 0.8025 (m) cc_final: 0.7529 (m) REVERT: A 311 LYS cc_start: 0.8411 (mttm) cc_final: 0.8162 (mttt) REVERT: A 315 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8340 (mmmm) REVERT: A 321 GLN cc_start: 0.8319 (mt0) cc_final: 0.8098 (mt0) REVERT: A 327 LEU cc_start: 0.8169 (mt) cc_final: 0.7922 (mt) REVERT: A 338 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.7440 (mtp85) REVERT: A 340 MET cc_start: 0.7621 (tmm) cc_final: 0.6956 (tmm) REVERT: A 341 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 397 ASP cc_start: 0.6819 (p0) cc_final: 0.6281 (p0) REVERT: A 403 GLU cc_start: 0.7544 (pm20) cc_final: 0.7271 (pm20) REVERT: A 405 SER cc_start: 0.8279 (m) cc_final: 0.7855 (p) REVERT: A 406 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 407 LEU cc_start: 0.8855 (mt) cc_final: 0.8535 (mt) REVERT: A 410 GLN cc_start: 0.7176 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 411 GLU cc_start: 0.8017 (tt0) cc_final: 0.7689 (tt0) REVERT: A 435 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8113 (tptp) REVERT: A 459 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 462 LYS cc_start: 0.7956 (mttm) cc_final: 0.7753 (mtmm) REVERT: A 470 GLU cc_start: 0.7786 (tt0) cc_final: 0.7509 (tt0) REVERT: A 507 ILE cc_start: 0.8330 (mt) cc_final: 0.8102 (tp) REVERT: A 541 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7387 (tp30) REVERT: A 577 LEU cc_start: 0.8257 (mm) cc_final: 0.7739 (mm) REVERT: A 580 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 581 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7270 (mt-10) REVERT: A 609 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7240 (mp0) REVERT: A 611 GLN cc_start: 0.7940 (mp10) cc_final: 0.7340 (mp10) REVERT: A 621 LEU cc_start: 0.8796 (mt) cc_final: 0.8576 (mt) REVERT: A 644 LYS cc_start: 0.8374 (tppt) cc_final: 0.7888 (tppt) REVERT: A 645 LYS cc_start: 0.8375 (mttt) cc_final: 0.7560 (mmtt) REVERT: A 668 TYR cc_start: 0.7945 (t80) cc_final: 0.7623 (t80) REVERT: A 677 MET cc_start: 0.5790 (mmm) cc_final: 0.5382 (mmm) REVERT: A 713 PHE cc_start: 0.8626 (t80) cc_final: 0.8103 (t80) REVERT: A 717 TYR cc_start: 0.8280 (t80) cc_final: 0.7952 (t80) REVERT: A 728 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8450 (ttpp) REVERT: A 738 HIS cc_start: 0.7031 (t-90) cc_final: 0.6669 (t-90) REVERT: A 747 LYS cc_start: 0.8373 (mmmm) cc_final: 0.7943 (tppp) REVERT: A 751 ARG cc_start: 0.7904 (mtm110) cc_final: 0.6966 (mtm110) REVERT: A 757 LEU cc_start: 0.8800 (tp) cc_final: 0.8532 (tt) REVERT: A 764 ASN cc_start: 0.8169 (p0) cc_final: 0.7716 (p0) REVERT: A 768 GLN cc_start: 0.7830 (mp10) cc_final: 0.7251 (mp10) REVERT: A 772 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7164 (mp0) REVERT: A 800 GLU cc_start: 0.7820 (tp30) cc_final: 0.7367 (tp30) REVERT: A 802 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7955 (mtpp) REVERT: A 804 LEU cc_start: 0.8389 (mt) cc_final: 0.8041 (mt) REVERT: A 829 LYS cc_start: 0.8478 (tttt) cc_final: 0.8231 (ttpt) REVERT: A 858 LEU cc_start: 0.8758 (tp) cc_final: 0.8507 (tt) REVERT: D 17 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6805 (mmt180) REVERT: D 22 LEU cc_start: 0.7675 (tp) cc_final: 0.7433 (tp) REVERT: D 25 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7867 (mp0) REVERT: D 26 LEU cc_start: 0.8443 (mp) cc_final: 0.8126 (mp) REVERT: D 41 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8080 (mmtt) REVERT: D 62 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7528 (tpp80) REVERT: D 77 TYR cc_start: 0.8315 (m-80) cc_final: 0.8016 (m-80) REVERT: D 91 TYR cc_start: 0.8722 (m-10) cc_final: 0.8470 (m-10) REVERT: D 94 THR cc_start: 0.8475 (m) cc_final: 0.8189 (t) REVERT: D 95 LEU cc_start: 0.8772 (tp) cc_final: 0.8569 (tt) REVERT: D 104 SER cc_start: 0.8483 (m) cc_final: 0.8270 (p) REVERT: D 124 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7851 (ttp80) REVERT: D 131 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8064 (ttm110) REVERT: D 143 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 128 LEU cc_start: 0.8166 (mp) cc_final: 0.7641 (mm) REVERT: C 135 GLU cc_start: 0.8208 (pt0) cc_final: 0.7848 (pp20) REVERT: C 151 ARG cc_start: 0.7133 (ptm160) cc_final: 0.6762 (mtm110) REVERT: C 167 PHE cc_start: 0.7919 (m-80) cc_final: 0.7503 (m-80) REVERT: C 243 TYR cc_start: 0.8084 (m-80) cc_final: 0.7313 (m-80) REVERT: C 247 LEU cc_start: 0.8212 (mp) cc_final: 0.7765 (tp) REVERT: C 268 GLU cc_start: 0.8255 (tt0) cc_final: 0.7443 (tm-30) REVERT: C 283 TYR cc_start: 0.7853 (t80) cc_final: 0.7482 (t80) REVERT: C 289 ILE cc_start: 0.8686 (mm) cc_final: 0.8450 (mm) REVERT: C 311 LYS cc_start: 0.8396 (mttt) cc_final: 0.8156 (mttm) REVERT: C 315 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8390 (mmmm) REVERT: C 327 LEU cc_start: 0.8271 (mt) cc_final: 0.8008 (mt) REVERT: C 328 TRP cc_start: 0.8598 (m-10) cc_final: 0.8288 (m-10) REVERT: C 336 ILE cc_start: 0.8538 (mm) cc_final: 0.8301 (mm) REVERT: C 338 ARG cc_start: 0.7863 (tpp-160) cc_final: 0.7447 (tpt170) REVERT: C 348 THR cc_start: 0.8819 (m) cc_final: 0.8574 (p) REVERT: C 359 ARG cc_start: 0.7859 (mmp-170) cc_final: 0.7519 (mmp80) REVERT: C 366 ASP cc_start: 0.7742 (p0) cc_final: 0.7540 (p0) REVERT: C 394 GLU cc_start: 0.7344 (tp30) cc_final: 0.7018 (tp30) REVERT: C 395 GLU cc_start: 0.7980 (pp20) cc_final: 0.7727 (pp20) REVERT: C 403 GLU cc_start: 0.7562 (pm20) cc_final: 0.7298 (pm20) REVERT: C 405 SER cc_start: 0.8489 (m) cc_final: 0.7857 (p) REVERT: C 406 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7751 (tm-30) REVERT: C 407 LEU cc_start: 0.8918 (mt) cc_final: 0.8604 (mt) REVERT: C 426 ASP cc_start: 0.8163 (t0) cc_final: 0.7861 (t0) REVERT: C 428 LEU cc_start: 0.8751 (tp) cc_final: 0.8370 (tp) REVERT: C 452 GLU cc_start: 0.7599 (mp0) cc_final: 0.7152 (mp0) REVERT: C 520 ASN cc_start: 0.8413 (t0) cc_final: 0.8113 (t0) REVERT: C 521 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8251 (Cg_exo) REVERT: C 541 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7747 (tp30) REVERT: C 546 GLU cc_start: 0.7381 (tp30) cc_final: 0.7014 (tp30) REVERT: C 566 ASP cc_start: 0.6541 (t0) cc_final: 0.6223 (t0) REVERT: C 572 LYS cc_start: 0.8043 (ptpt) cc_final: 0.7507 (mtmm) REVERT: C 577 LEU cc_start: 0.8261 (mm) cc_final: 0.7773 (mm) REVERT: C 580 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7613 (mt-10) REVERT: C 581 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 587 ILE cc_start: 0.8533 (mm) cc_final: 0.8299 (tp) REVERT: C 594 GLU cc_start: 0.7221 (mp0) cc_final: 0.6916 (mp0) REVERT: C 609 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7268 (mp0) REVERT: C 611 GLN cc_start: 0.8174 (mp10) cc_final: 0.7466 (mp10) REVERT: C 612 PHE cc_start: 0.8598 (m-80) cc_final: 0.8302 (m-10) REVERT: C 619 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 644 LYS cc_start: 0.8392 (tppt) cc_final: 0.7815 (tppt) REVERT: C 645 LYS cc_start: 0.8429 (mttt) cc_final: 0.7847 (mmtt) REVERT: C 660 GLN cc_start: 0.8615 (pp30) cc_final: 0.8347 (pp30) REVERT: C 677 MET cc_start: 0.5618 (mmm) cc_final: 0.5181 (mmm) REVERT: C 712 GLU cc_start: 0.7828 (pm20) cc_final: 0.7540 (pm20) REVERT: C 713 PHE cc_start: 0.8657 (t80) cc_final: 0.8216 (t80) REVERT: C 746 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8594 (tp) REVERT: C 757 LEU cc_start: 0.8669 (tp) cc_final: 0.8408 (tt) REVERT: C 764 ASN cc_start: 0.8097 (p0) cc_final: 0.7691 (p0) REVERT: C 766 ASP cc_start: 0.7394 (t0) cc_final: 0.6817 (t0) REVERT: C 768 GLN cc_start: 0.7900 (mp10) cc_final: 0.6908 (mp10) REVERT: C 772 GLU cc_start: 0.7737 (mp0) cc_final: 0.7262 (mp0) REVERT: C 788 ARG cc_start: 0.6818 (mmm-85) cc_final: 0.6557 (tpp80) REVERT: C 792 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 800 GLU cc_start: 0.7896 (pm20) cc_final: 0.7343 (tp30) REVERT: C 802 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7991 (mtpp) REVERT: C 804 LEU cc_start: 0.8531 (mt) cc_final: 0.7320 (mp) REVERT: C 836 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7454 (mtt90) outliers start: 62 outliers final: 24 residues processed: 615 average time/residue: 0.3357 time to fit residues: 273.1377 Evaluate side-chains 582 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 553 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 619 LEU Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 744 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 82 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 123 optimal weight: 0.0060 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13904 Z= 0.209 Angle : 0.566 9.337 18776 Z= 0.291 Chirality : 0.042 0.212 2058 Planarity : 0.004 0.052 2434 Dihedral : 3.902 14.372 1844 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.88 % Allowed : 28.03 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1648 helix: 0.76 (0.18), residues: 854 sheet: -1.24 (0.58), residues: 72 loop : 0.03 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 791 HIS 0.012 0.001 HIS C 738 PHE 0.022 0.002 PHE B 76 TYR 0.016 0.001 TYR C 277 ARG 0.005 0.000 ARG A 735 *********************** 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 624 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 565 time to evaluate : 1.443 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 22 LEU cc_start: 0.7717 (tp) cc_final: 0.7417 (tp) REVERT: B 25 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 26 LEU cc_start: 0.8527 (mp) cc_final: 0.8223 (mp) REVERT: B 41 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8029 (mmtt) REVERT: B 60 VAL cc_start: 0.8332 (p) cc_final: 0.7659 (p) REVERT: B 77 TYR cc_start: 0.8209 (m-80) cc_final: 0.7907 (m-80) REVERT: B 96 GLU cc_start: 0.7511 (tp30) cc_final: 0.7157 (tp30) REVERT: B 98 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 131 ARG cc_start: 0.8316 (ttm110) cc_final: 0.8038 (mtt90) REVERT: B 143 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6970 (p) REVERT: B 144 MET cc_start: 0.7225 (mmm) cc_final: 0.6882 (mmm) REVERT: A 128 LEU cc_start: 0.8272 (mp) cc_final: 0.7831 (mt) REVERT: A 135 GLU cc_start: 0.8123 (pt0) cc_final: 0.7621 (pp20) REVERT: A 167 PHE cc_start: 0.7792 (m-80) cc_final: 0.7502 (m-80) REVERT: A 236 ILE cc_start: 0.8360 (mt) cc_final: 0.8121 (mt) REVERT: A 239 ILE cc_start: 0.8760 (mm) cc_final: 0.8528 (mm) REVERT: A 243 TYR cc_start: 0.7950 (m-80) cc_final: 0.7257 (m-80) REVERT: A 247 LEU cc_start: 0.8437 (mp) cc_final: 0.7784 (mt) REVERT: A 264 SER cc_start: 0.8320 (m) cc_final: 0.8043 (p) REVERT: A 267 VAL cc_start: 0.8965 (t) cc_final: 0.8715 (p) REVERT: A 268 GLU cc_start: 0.8328 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 282 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7285 (p0) REVERT: A 295 ASN cc_start: 0.8423 (m-40) cc_final: 0.8134 (m110) REVERT: A 310 CYS cc_start: 0.8064 (m) cc_final: 0.7508 (m) REVERT: A 311 LYS cc_start: 0.8375 (mttm) cc_final: 0.8133 (mttt) REVERT: A 315 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8261 (mmmm) REVERT: A 316 LEU cc_start: 0.9019 (tp) cc_final: 0.8697 (tp) REVERT: A 321 GLN cc_start: 0.8246 (mt0) cc_final: 0.8021 (mt0) REVERT: A 327 LEU cc_start: 0.8093 (mt) cc_final: 0.7820 (mt) REVERT: A 338 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7125 (tpt90) REVERT: A 340 MET cc_start: 0.7599 (tmm) cc_final: 0.6993 (tmm) REVERT: A 341 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6581 (mt-10) REVERT: A 359 ARG cc_start: 0.7758 (mmp-170) cc_final: 0.7410 (mmp80) REVERT: A 397 ASP cc_start: 0.6735 (p0) cc_final: 0.6258 (p0) REVERT: A 406 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 407 LEU cc_start: 0.8812 (mt) cc_final: 0.8503 (mt) REVERT: A 410 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6852 (tm-30) REVERT: A 411 GLU cc_start: 0.7975 (tt0) cc_final: 0.7633 (tt0) REVERT: A 435 LYS cc_start: 0.8290 (tmtt) cc_final: 0.8061 (tptp) REVERT: A 462 LYS cc_start: 0.7823 (mttm) cc_final: 0.7459 (mtmm) REVERT: A 463 ASP cc_start: 0.7858 (t70) cc_final: 0.7640 (t0) REVERT: A 520 ASN cc_start: 0.8349 (t0) cc_final: 0.8008 (t0) REVERT: A 541 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7369 (tp30) REVERT: A 546 GLU cc_start: 0.7407 (tp30) cc_final: 0.6807 (tp30) REVERT: A 547 ASN cc_start: 0.7737 (m-40) cc_final: 0.7188 (m-40) REVERT: A 552 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7478 (mmtm) REVERT: A 566 ASP cc_start: 0.6563 (t0) cc_final: 0.6160 (t0) REVERT: A 577 LEU cc_start: 0.8173 (mm) cc_final: 0.7703 (mm) REVERT: A 580 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 587 ILE cc_start: 0.8315 (mm) cc_final: 0.8086 (tp) REVERT: A 611 GLN cc_start: 0.7866 (mp10) cc_final: 0.7330 (mp10) REVERT: A 621 LEU cc_start: 0.8766 (mt) cc_final: 0.8558 (mt) REVERT: A 644 LYS cc_start: 0.8376 (tppt) cc_final: 0.7816 (tppt) REVERT: A 645 LYS cc_start: 0.8333 (mttt) cc_final: 0.7496 (mmtt) REVERT: A 668 TYR cc_start: 0.7709 (t80) cc_final: 0.7283 (t80) REVERT: A 677 MET cc_start: 0.5688 (mmm) cc_final: 0.5290 (mmm) REVERT: A 710 ARG cc_start: 0.8466 (ptm160) cc_final: 0.7346 (ptp-170) REVERT: A 711 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8530 (mmtt) REVERT: A 713 PHE cc_start: 0.8579 (t80) cc_final: 0.8072 (t80) REVERT: A 717 TYR cc_start: 0.8267 (t80) cc_final: 0.7929 (t80) REVERT: A 728 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8333 (ttpp) REVERT: A 738 HIS cc_start: 0.6936 (t-90) cc_final: 0.6524 (t-90) REVERT: A 747 LYS cc_start: 0.8392 (mmmm) cc_final: 0.8045 (tppp) REVERT: A 757 LEU cc_start: 0.8755 (tp) cc_final: 0.8466 (tt) REVERT: A 762 SER cc_start: 0.8169 (m) cc_final: 0.7830 (p) REVERT: A 764 ASN cc_start: 0.8085 (p0) cc_final: 0.7605 (p0) REVERT: A 768 GLN cc_start: 0.7796 (mp10) cc_final: 0.6887 (mp10) REVERT: A 772 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7102 (mp0) REVERT: A 800 GLU cc_start: 0.7764 (tp30) cc_final: 0.7338 (tp30) REVERT: A 802 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7997 (mtpp) REVERT: A 804 LEU cc_start: 0.8443 (mt) cc_final: 0.8087 (mt) REVERT: A 829 LYS cc_start: 0.8465 (tttt) cc_final: 0.8176 (ttpp) REVERT: A 836 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7436 (mtt-85) REVERT: A 841 HIS cc_start: 0.8047 (t70) cc_final: 0.7815 (t-90) REVERT: A 858 LEU cc_start: 0.8705 (tp) cc_final: 0.8452 (tt) REVERT: D 17 ARG cc_start: 0.7249 (mmt180) cc_final: 0.6918 (mmt180) REVERT: D 22 LEU cc_start: 0.7671 (tp) cc_final: 0.7439 (tp) REVERT: D 25 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7821 (mp0) REVERT: D 26 LEU cc_start: 0.8496 (mp) cc_final: 0.8179 (mp) REVERT: D 62 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7403 (tpp80) REVERT: D 77 TYR cc_start: 0.8250 (m-80) cc_final: 0.7956 (m-80) REVERT: D 84 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7875 (ttm170) REVERT: D 98 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7923 (tm-30) REVERT: D 121 GLU cc_start: 0.8049 (mp0) cc_final: 0.7586 (mp0) REVERT: D 124 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7618 (ttp80) REVERT: D 131 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7979 (ttm110) REVERT: D 143 CYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7025 (p) REVERT: D 144 MET cc_start: 0.7298 (mmm) cc_final: 0.6948 (mmm) REVERT: C 128 LEU cc_start: 0.8119 (mp) cc_final: 0.7569 (mm) REVERT: C 135 GLU cc_start: 0.8056 (pt0) cc_final: 0.7697 (pp20) REVERT: C 143 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8185 (mmm160) REVERT: C 151 ARG cc_start: 0.7019 (ptm160) cc_final: 0.6563 (mtm110) REVERT: C 161 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7990 (pm20) REVERT: C 167 PHE cc_start: 0.7935 (m-80) cc_final: 0.7623 (m-80) REVERT: C 241 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8228 (mtm180) REVERT: C 243 TYR cc_start: 0.7967 (m-80) cc_final: 0.7154 (m-80) REVERT: C 247 LEU cc_start: 0.8193 (mp) cc_final: 0.7790 (tp) REVERT: C 268 GLU cc_start: 0.8225 (tt0) cc_final: 0.7647 (tm-30) REVERT: C 283 TYR cc_start: 0.7866 (t80) cc_final: 0.7503 (t80) REVERT: C 289 ILE cc_start: 0.8523 (mm) cc_final: 0.8268 (mm) REVERT: C 310 CYS cc_start: 0.8040 (m) cc_final: 0.7523 (m) REVERT: C 315 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8291 (mmmm) REVERT: C 323 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8001 (tttt) REVERT: C 327 LEU cc_start: 0.8231 (mt) cc_final: 0.8014 (mt) REVERT: C 336 ILE cc_start: 0.8421 (mm) cc_final: 0.8204 (mm) REVERT: C 338 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7427 (tpt170) REVERT: C 366 ASP cc_start: 0.7719 (p0) cc_final: 0.7497 (p0) REVERT: C 406 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7530 (tm-30) REVERT: C 407 LEU cc_start: 0.8870 (mt) cc_final: 0.8526 (mt) REVERT: C 411 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7085 (pp20) REVERT: C 426 ASP cc_start: 0.8177 (t0) cc_final: 0.7884 (t0) REVERT: C 428 LEU cc_start: 0.8701 (tp) cc_final: 0.8311 (tp) REVERT: C 451 ASN cc_start: 0.7912 (t0) cc_final: 0.7606 (t0) REVERT: C 452 GLU cc_start: 0.7612 (mp0) cc_final: 0.7154 (mp0) REVERT: C 458 LEU cc_start: 0.8460 (tt) cc_final: 0.8238 (tp) REVERT: C 487 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8295 (t) REVERT: C 507 ILE cc_start: 0.8409 (mt) cc_final: 0.8095 (tp) REVERT: C 520 ASN cc_start: 0.8385 (t0) cc_final: 0.8083 (t0) REVERT: C 521 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8225 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7858 (tpt-90) cc_final: 0.7502 (tpt-90) REVERT: C 546 GLU cc_start: 0.7309 (tp30) cc_final: 0.7057 (tp30) REVERT: C 566 ASP cc_start: 0.6480 (t0) cc_final: 0.6200 (t0) REVERT: C 572 LYS cc_start: 0.7944 (ptpt) cc_final: 0.7386 (mtmm) REVERT: C 577 LEU cc_start: 0.8174 (mm) cc_final: 0.7505 (mm) REVERT: C 580 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 581 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 584 ASN cc_start: 0.8685 (t0) cc_final: 0.8348 (t0) REVERT: C 594 GLU cc_start: 0.7210 (mp0) cc_final: 0.6930 (mp0) REVERT: C 609 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7222 (mp0) REVERT: C 611 GLN cc_start: 0.8016 (mp10) cc_final: 0.7473 (mp10) REVERT: C 612 PHE cc_start: 0.8555 (m-80) cc_final: 0.8185 (m-10) REVERT: C 635 MET cc_start: 0.7325 (mmm) cc_final: 0.6496 (mmm) REVERT: C 644 LYS cc_start: 0.8411 (tppt) cc_final: 0.7795 (tppt) REVERT: C 645 LYS cc_start: 0.8361 (mttt) cc_final: 0.7560 (mtpp) REVERT: C 677 MET cc_start: 0.5567 (mmm) cc_final: 0.5174 (mmm) REVERT: C 694 TYR cc_start: 0.8052 (t80) cc_final: 0.7831 (t80) REVERT: C 710 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8086 (ptp-170) REVERT: C 712 GLU cc_start: 0.7799 (pm20) cc_final: 0.7489 (pm20) REVERT: C 713 PHE cc_start: 0.8611 (t80) cc_final: 0.8160 (t80) REVERT: C 747 LYS cc_start: 0.8307 (mmmm) cc_final: 0.8098 (mmmm) REVERT: C 753 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7107 (mm-30) REVERT: C 757 LEU cc_start: 0.8644 (tp) cc_final: 0.8236 (tt) REVERT: C 758 LEU cc_start: 0.8453 (tp) cc_final: 0.8213 (tt) REVERT: C 764 ASN cc_start: 0.8119 (p0) cc_final: 0.7759 (p0) REVERT: C 766 ASP cc_start: 0.7261 (t0) cc_final: 0.6669 (t0) REVERT: C 768 GLN cc_start: 0.7865 (mp10) cc_final: 0.6847 (mp10) REVERT: C 772 GLU cc_start: 0.7595 (mp0) cc_final: 0.7141 (mp0) REVERT: C 788 ARG cc_start: 0.6660 (mmm-85) cc_final: 0.6283 (tpp80) REVERT: C 792 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7384 (mt-10) REVERT: C 802 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8010 (mtpp) REVERT: C 804 LEU cc_start: 0.8518 (mt) cc_final: 0.8146 (mt) REVERT: C 836 ARG cc_start: 0.7682 (mtt-85) cc_final: 0.7250 (mtt90) outliers start: 59 outliers final: 32 residues processed: 587 average time/residue: 0.3297 time to fit residues: 258.3878 Evaluate side-chains 597 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 561 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 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 258 ASN Chi-restraints excluded: chain A residue 282 ASN 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 480 CYS Chi-restraints excluded: chain A residue 499 ILE 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 629 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13904 Z= 0.219 Angle : 0.568 9.105 18776 Z= 0.292 Chirality : 0.041 0.149 2058 Planarity : 0.004 0.036 2434 Dihedral : 3.862 14.242 1844 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.61 % Allowed : 28.36 % Favored : 67.04 % 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: 0.23 (0.21), residues: 1648 helix: 0.65 (0.18), residues: 874 sheet: -1.37 (0.57), residues: 72 loop : -0.16 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 791 HIS 0.012 0.001 HIS C 738 PHE 0.022 0.002 PHE B 76 TYR 0.013 0.001 TYR A 494 ARG 0.004 0.000 ARG C 424 *********************** 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 653 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 583 time to evaluate : 1.596 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 26 LEU cc_start: 0.8592 (mp) cc_final: 0.8329 (mp) REVERT: B 41 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8127 (mmtt) REVERT: B 77 TYR cc_start: 0.8197 (m-80) cc_final: 0.7925 (m-80) REVERT: B 131 ARG cc_start: 0.8301 (ttm110) cc_final: 0.8026 (ttm110) REVERT: B 143 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6965 (p) REVERT: B 144 MET cc_start: 0.7217 (mmm) cc_final: 0.6844 (mmm) REVERT: A 128 LEU cc_start: 0.8328 (mp) cc_final: 0.7836 (mm) REVERT: A 135 GLU cc_start: 0.8111 (pt0) cc_final: 0.7636 (pp20) REVERT: A 143 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8162 (mmm160) REVERT: A 236 ILE cc_start: 0.8367 (mt) cc_final: 0.8128 (mt) REVERT: A 243 TYR cc_start: 0.7911 (m-80) cc_final: 0.7354 (m-80) REVERT: A 245 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7693 (mmp80) REVERT: A 264 SER cc_start: 0.8318 (m) cc_final: 0.8045 (p) REVERT: A 267 VAL cc_start: 0.8965 (t) cc_final: 0.8706 (p) REVERT: A 268 GLU cc_start: 0.8316 (tt0) cc_final: 0.7852 (tm-30) REVERT: A 273 TYR cc_start: 0.8082 (m-80) cc_final: 0.7677 (m-80) REVERT: A 282 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7260 (p0) REVERT: A 310 CYS cc_start: 0.8119 (m) cc_final: 0.7647 (m) REVERT: A 311 LYS cc_start: 0.8380 (mttm) cc_final: 0.8123 (mttt) REVERT: A 315 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8281 (mmmm) REVERT: A 321 GLN cc_start: 0.8264 (mt0) cc_final: 0.8055 (mt0) REVERT: A 327 LEU cc_start: 0.8060 (mt) cc_final: 0.7805 (mt) REVERT: A 338 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.7396 (tpt90) REVERT: A 340 MET cc_start: 0.7684 (tmm) cc_final: 0.7022 (tmm) REVERT: A 341 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6546 (mt-10) REVERT: A 359 ARG cc_start: 0.7681 (mmp-170) cc_final: 0.7394 (mmp80) REVERT: A 397 ASP cc_start: 0.6702 (p0) cc_final: 0.6360 (p0) REVERT: A 406 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 407 LEU cc_start: 0.8826 (mt) cc_final: 0.8494 (mt) REVERT: A 411 GLU cc_start: 0.7977 (tt0) cc_final: 0.7711 (tt0) REVERT: A 435 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7776 (ttmm) REVERT: A 452 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7192 (mp0) REVERT: A 520 ASN cc_start: 0.8341 (t0) cc_final: 0.8139 (t0) REVERT: A 541 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7305 (tp30) REVERT: A 546 GLU cc_start: 0.7308 (tp30) cc_final: 0.6691 (tp30) REVERT: A 547 ASN cc_start: 0.7521 (m-40) cc_final: 0.7288 (m-40) REVERT: A 558 GLU cc_start: 0.6450 (tm-30) cc_final: 0.6214 (tm-30) REVERT: A 566 ASP cc_start: 0.6534 (t0) cc_final: 0.6105 (t0) REVERT: A 577 LEU cc_start: 0.8253 (mm) cc_final: 0.7938 (mm) REVERT: A 580 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 644 LYS cc_start: 0.8439 (tppt) cc_final: 0.7999 (tppt) REVERT: A 645 LYS cc_start: 0.8335 (mttt) cc_final: 0.7551 (mmtt) REVERT: A 665 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 711 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8419 (mmtm) REVERT: A 713 PHE cc_start: 0.8548 (t80) cc_final: 0.8075 (t80) REVERT: A 717 TYR cc_start: 0.8275 (t80) cc_final: 0.8003 (t80) REVERT: A 724 LYS cc_start: 0.8392 (ptpp) cc_final: 0.8161 (ptpp) REVERT: A 735 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7901 (ttt-90) REVERT: A 738 HIS cc_start: 0.6869 (t-90) cc_final: 0.6510 (t-90) REVERT: A 747 LYS cc_start: 0.8411 (mmmm) cc_final: 0.8066 (tptt) REVERT: A 757 LEU cc_start: 0.8740 (tp) cc_final: 0.8477 (tt) REVERT: A 762 SER cc_start: 0.8092 (m) cc_final: 0.7718 (p) REVERT: A 764 ASN cc_start: 0.7920 (p0) cc_final: 0.7597 (p0) REVERT: A 768 GLN cc_start: 0.7801 (mp10) cc_final: 0.7292 (mp10) REVERT: A 772 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7106 (mp0) REVERT: A 788 ARG cc_start: 0.6718 (mmm-85) cc_final: 0.6419 (tpp-160) REVERT: A 800 GLU cc_start: 0.7825 (tp30) cc_final: 0.7125 (tp30) REVERT: A 802 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7970 (mtpp) REVERT: A 804 LEU cc_start: 0.8432 (mt) cc_final: 0.7381 (mp) REVERT: A 829 LYS cc_start: 0.8494 (tttt) cc_final: 0.8173 (ttpp) REVERT: A 836 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7467 (mtt-85) REVERT: A 841 HIS cc_start: 0.8013 (t70) cc_final: 0.7575 (t70) REVERT: A 842 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8858 (m) REVERT: A 858 LEU cc_start: 0.8697 (tp) cc_final: 0.8428 (tt) REVERT: D 17 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6924 (mmt180) REVERT: D 22 LEU cc_start: 0.7683 (tp) cc_final: 0.7443 (tp) REVERT: D 25 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7837 (mp0) REVERT: D 26 LEU cc_start: 0.8538 (mp) cc_final: 0.8216 (mp) REVERT: D 39 TYR cc_start: 0.8195 (m-80) cc_final: 0.7839 (m-80) REVERT: D 55 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8353 (mtt180) REVERT: D 62 ARG cc_start: 0.7727 (tpp80) cc_final: 0.7418 (tpp80) REVERT: D 77 TYR cc_start: 0.8243 (m-80) cc_final: 0.7854 (m-80) REVERT: D 98 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 101 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8385 (ttmm) REVERT: D 121 GLU cc_start: 0.8020 (mp0) cc_final: 0.7595 (mp0) REVERT: D 124 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7749 (ttp80) REVERT: D 128 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8498 (mtmm) REVERT: D 131 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7975 (ttm110) REVERT: D 143 CYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7000 (p) REVERT: D 144 MET cc_start: 0.7294 (mmm) cc_final: 0.6911 (mmm) REVERT: C 128 LEU cc_start: 0.8171 (mp) cc_final: 0.7725 (mm) REVERT: C 135 GLU cc_start: 0.8004 (pt0) cc_final: 0.7640 (pp20) REVERT: C 151 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6602 (mtm110) REVERT: C 161 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8041 (pm20) REVERT: C 241 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: C 243 TYR cc_start: 0.7883 (m-80) cc_final: 0.7189 (m-80) REVERT: C 245 ARG cc_start: 0.8102 (mmp80) cc_final: 0.7686 (mmm-85) REVERT: C 247 LEU cc_start: 0.8230 (mp) cc_final: 0.7881 (tp) REVERT: C 268 GLU cc_start: 0.8245 (tt0) cc_final: 0.7694 (tm-30) REVERT: C 283 TYR cc_start: 0.7894 (t80) cc_final: 0.7499 (t80) REVERT: C 289 ILE cc_start: 0.8498 (mm) cc_final: 0.8281 (mm) REVERT: C 310 CYS cc_start: 0.8050 (m) cc_final: 0.7506 (m) REVERT: C 315 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8275 (mmmm) REVERT: C 321 GLN cc_start: 0.8267 (mt0) cc_final: 0.8046 (mt0) REVERT: C 323 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8062 (tttt) REVERT: C 327 LEU cc_start: 0.8226 (mt) cc_final: 0.7998 (mt) REVERT: C 338 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7179 (tpt170) REVERT: C 341 GLU cc_start: 0.7535 (pt0) cc_final: 0.6870 (pp20) REVERT: C 406 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 407 LEU cc_start: 0.8841 (mt) cc_final: 0.8468 (mt) REVERT: C 411 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7197 (pp20) REVERT: C 426 ASP cc_start: 0.8198 (t0) cc_final: 0.7888 (t0) REVERT: C 428 LEU cc_start: 0.8687 (tp) cc_final: 0.8306 (tp) REVERT: C 440 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6663 (ttt90) REVERT: C 451 ASN cc_start: 0.7968 (t0) cc_final: 0.7645 (t0) REVERT: C 452 GLU cc_start: 0.7497 (mp0) cc_final: 0.7043 (mp0) REVERT: C 470 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: C 487 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8217 (t) REVERT: C 507 ILE cc_start: 0.8406 (mt) cc_final: 0.8073 (tp) REVERT: C 518 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6981 (pp30) REVERT: C 520 ASN cc_start: 0.8375 (t0) cc_final: 0.7911 (t0) REVERT: C 521 PRO cc_start: 0.8502 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7544 (tpt-90) REVERT: C 546 GLU cc_start: 0.7278 (tp30) cc_final: 0.6912 (tp30) REVERT: C 558 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6287 (tm-30) REVERT: C 566 ASP cc_start: 0.6497 (t0) cc_final: 0.6194 (t0) REVERT: C 572 LYS cc_start: 0.7949 (ptpt) cc_final: 0.7400 (mtmm) REVERT: C 577 LEU cc_start: 0.8169 (mm) cc_final: 0.7461 (mm) REVERT: C 580 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7537 (mt-10) REVERT: C 581 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7170 (mt-10) REVERT: C 584 ASN cc_start: 0.8803 (t0) cc_final: 0.8316 (t0) REVERT: C 594 GLU cc_start: 0.7231 (mp0) cc_final: 0.6925 (mp0) REVERT: C 609 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7237 (mp0) REVERT: C 635 MET cc_start: 0.7357 (mmm) cc_final: 0.7094 (tpp) REVERT: C 644 LYS cc_start: 0.8382 (tppt) cc_final: 0.7749 (tppt) REVERT: C 645 LYS cc_start: 0.8403 (mttt) cc_final: 0.7721 (mmtt) REVERT: C 677 MET cc_start: 0.5561 (mmm) cc_final: 0.5348 (mmm) REVERT: C 712 GLU cc_start: 0.7787 (pm20) cc_final: 0.7492 (pm20) REVERT: C 713 PHE cc_start: 0.8588 (t80) cc_final: 0.8162 (t80) REVERT: C 747 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7961 (tppp) REVERT: C 757 LEU cc_start: 0.8639 (tp) cc_final: 0.8368 (tt) REVERT: C 758 LEU cc_start: 0.8487 (tp) cc_final: 0.8256 (tt) REVERT: C 762 SER cc_start: 0.8112 (m) cc_final: 0.7747 (p) REVERT: C 764 ASN cc_start: 0.8091 (p0) cc_final: 0.7758 (p0) REVERT: C 766 ASP cc_start: 0.7299 (t0) cc_final: 0.6995 (t0) REVERT: C 768 GLN cc_start: 0.7891 (mp10) cc_final: 0.6964 (mp10) REVERT: C 772 GLU cc_start: 0.7650 (mp0) cc_final: 0.7240 (mp0) REVERT: C 788 ARG cc_start: 0.6702 (mmm-85) cc_final: 0.6308 (tpp80) REVERT: C 802 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7902 (mtpp) REVERT: C 804 LEU cc_start: 0.8520 (mt) cc_final: 0.8015 (mt) REVERT: C 836 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7332 (mtt90) outliers start: 70 outliers final: 38 residues processed: 613 average time/residue: 0.3253 time to fit residues: 267.0102 Evaluate side-chains 601 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 556 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 118 SER 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 258 ASN Chi-restraints excluded: chain A residue 282 ASN 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 591 THR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG 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 842 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 591 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.6980 chunk 89 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 801 GLN ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 345 GLN C 455 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13904 Z= 0.161 Angle : 0.561 9.064 18776 Z= 0.282 Chirality : 0.040 0.138 2058 Planarity : 0.003 0.037 2434 Dihedral : 3.724 13.410 1844 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.01 % Allowed : 29.54 % Favored : 66.45 % 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: 0.62 (0.21), residues: 1648 helix: 0.87 (0.18), residues: 856 sheet: -2.38 (0.65), residues: 48 loop : 0.23 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 791 HIS 0.010 0.001 HIS C 738 PHE 0.027 0.001 PHE D 76 TYR 0.018 0.001 TYR C 694 ARG 0.006 0.000 ARG A 639 *********************** 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 631 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 570 time to evaluate : 1.611 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 26 LEU cc_start: 0.8594 (mp) cc_final: 0.8328 (mp) REVERT: B 41 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8105 (mmtt) REVERT: B 77 TYR cc_start: 0.8085 (m-80) cc_final: 0.7845 (m-80) REVERT: B 121 GLU cc_start: 0.8345 (mp0) cc_final: 0.8014 (mp0) REVERT: B 124 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7517 (ttp80) REVERT: B 131 ARG cc_start: 0.8237 (ttm110) cc_final: 0.8034 (mtt90) REVERT: B 143 CYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7141 (p) REVERT: B 144 MET cc_start: 0.7125 (mmm) cc_final: 0.6785 (mmm) REVERT: A 128 LEU cc_start: 0.8356 (mp) cc_final: 0.7980 (mt) REVERT: A 135 GLU cc_start: 0.8027 (pt0) cc_final: 0.7515 (pp20) REVERT: A 143 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8134 (mmm160) REVERT: A 153 ILE cc_start: 0.8917 (mt) cc_final: 0.8626 (tt) REVERT: A 236 ILE cc_start: 0.8364 (mt) cc_final: 0.8059 (mp) REVERT: A 241 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.8094 (mtm-85) REVERT: A 243 TYR cc_start: 0.7826 (m-80) cc_final: 0.7244 (m-80) REVERT: A 264 SER cc_start: 0.8334 (m) cc_final: 0.8042 (p) REVERT: A 267 VAL cc_start: 0.8914 (t) cc_final: 0.8671 (p) REVERT: A 268 GLU cc_start: 0.8443 (tt0) cc_final: 0.7901 (tm-30) REVERT: A 273 TYR cc_start: 0.7973 (m-80) cc_final: 0.7683 (m-80) REVERT: A 282 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7195 (p0) REVERT: A 291 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6712 (tmm) REVERT: A 295 ASN cc_start: 0.7759 (p0) cc_final: 0.7253 (p0) REVERT: A 310 CYS cc_start: 0.8069 (m) cc_final: 0.7593 (m) REVERT: A 315 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8128 (mmmm) REVERT: A 321 GLN cc_start: 0.8282 (mt0) cc_final: 0.8012 (mt0) REVERT: A 327 LEU cc_start: 0.8014 (mt) cc_final: 0.7727 (mt) REVERT: A 338 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7216 (tpt90) REVERT: A 340 MET cc_start: 0.7683 (tmm) cc_final: 0.7010 (tmm) REVERT: A 341 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6836 (pt0) REVERT: A 397 ASP cc_start: 0.6656 (p0) cc_final: 0.6056 (p0) REVERT: A 406 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 407 LEU cc_start: 0.8824 (mt) cc_final: 0.8495 (mt) REVERT: A 408 THR cc_start: 0.8509 (m) cc_final: 0.8267 (p) REVERT: A 411 GLU cc_start: 0.7943 (tt0) cc_final: 0.7688 (tt0) REVERT: A 429 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: A 435 LYS cc_start: 0.8293 (tmtt) cc_final: 0.8015 (tptp) REVERT: A 452 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 474 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8096 (mmmm) REVERT: A 504 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 515 GLN cc_start: 0.7319 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 518 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 520 ASN cc_start: 0.8308 (t0) cc_final: 0.7890 (t0) REVERT: A 541 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7303 (tp30) REVERT: A 547 ASN cc_start: 0.7697 (m-40) cc_final: 0.7458 (m-40) REVERT: A 552 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7465 (mmtm) REVERT: A 558 GLU cc_start: 0.6429 (tm-30) cc_final: 0.6172 (tm-30) REVERT: A 566 ASP cc_start: 0.6551 (t0) cc_final: 0.6155 (t0) REVERT: A 577 LEU cc_start: 0.8277 (mm) cc_final: 0.7891 (mm) REVERT: A 580 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 592 TYR cc_start: 0.7055 (t80) cc_final: 0.6847 (t80) REVERT: A 611 GLN cc_start: 0.7932 (mp-120) cc_final: 0.7404 (mp10) REVERT: A 613 THR cc_start: 0.8561 (m) cc_final: 0.8306 (p) REVERT: A 645 LYS cc_start: 0.8309 (mttt) cc_final: 0.6933 (mmtt) REVERT: A 649 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7759 (mtp85) REVERT: A 665 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 710 ARG cc_start: 0.8402 (ptp-170) cc_final: 0.7992 (ptm160) REVERT: A 713 PHE cc_start: 0.8478 (t80) cc_final: 0.8025 (t80) REVERT: A 717 TYR cc_start: 0.8272 (t80) cc_final: 0.7916 (t80) REVERT: A 721 ILE cc_start: 0.8747 (tp) cc_final: 0.8519 (tt) REVERT: A 734 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7897 (ptm-80) REVERT: A 738 HIS cc_start: 0.6727 (t-90) cc_final: 0.6327 (t-90) REVERT: A 739 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7264 (tpp) REVERT: A 747 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8041 (tppp) REVERT: A 757 LEU cc_start: 0.8698 (tp) cc_final: 0.8409 (tt) REVERT: A 762 SER cc_start: 0.8060 (m) cc_final: 0.7754 (p) REVERT: A 764 ASN cc_start: 0.7946 (p0) cc_final: 0.7678 (p0) REVERT: A 768 GLN cc_start: 0.7748 (mp10) cc_final: 0.7323 (mp10) REVERT: A 772 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7037 (mp0) REVERT: A 800 GLU cc_start: 0.7807 (tp30) cc_final: 0.7421 (tp30) REVERT: A 802 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7915 (mtpt) REVERT: A 804 LEU cc_start: 0.8415 (mt) cc_final: 0.8083 (mt) REVERT: A 807 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 829 LYS cc_start: 0.8453 (tttt) cc_final: 0.8107 (ttpp) REVERT: A 836 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7512 (mtt-85) REVERT: A 841 HIS cc_start: 0.7996 (t70) cc_final: 0.7673 (t-90) REVERT: A 842 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8817 (m) REVERT: A 855 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7806 (ttpp) REVERT: D 17 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6912 (mmt180) REVERT: D 22 LEU cc_start: 0.7670 (tp) cc_final: 0.7355 (tp) REVERT: D 25 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8046 (mm-30) REVERT: D 26 LEU cc_start: 0.8551 (mp) cc_final: 0.8206 (mp) REVERT: D 39 TYR cc_start: 0.8119 (m-80) cc_final: 0.7623 (m-80) REVERT: D 55 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8264 (mtt180) REVERT: D 62 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7406 (tpp80) REVERT: D 77 TYR cc_start: 0.8160 (m-80) cc_final: 0.7666 (m-80) REVERT: D 89 SER cc_start: 0.8429 (p) cc_final: 0.8067 (t) REVERT: D 121 GLU cc_start: 0.7936 (mp0) cc_final: 0.7478 (mp0) REVERT: D 124 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7558 (ttp80) REVERT: D 131 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7856 (ttm110) REVERT: D 143 CYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7098 (p) REVERT: D 144 MET cc_start: 0.7262 (mmm) cc_final: 0.6869 (mmm) REVERT: C 128 LEU cc_start: 0.8151 (mp) cc_final: 0.7681 (mm) REVERT: C 135 GLU cc_start: 0.7959 (pt0) cc_final: 0.7682 (pp20) REVERT: C 143 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8195 (mmm160) REVERT: C 151 ARG cc_start: 0.7020 (ptm160) cc_final: 0.6591 (mtm110) REVERT: C 161 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8009 (pm20) REVERT: C 241 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: C 243 TYR cc_start: 0.7897 (m-80) cc_final: 0.7105 (m-80) REVERT: C 245 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7688 (mmm-85) REVERT: C 247 LEU cc_start: 0.8200 (mp) cc_final: 0.7871 (tp) REVERT: C 268 GLU cc_start: 0.8207 (tt0) cc_final: 0.7673 (tm-30) REVERT: C 283 TYR cc_start: 0.7902 (t80) cc_final: 0.7475 (t80) REVERT: C 289 ILE cc_start: 0.8460 (mm) cc_final: 0.8253 (mm) REVERT: C 291 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7602 (ttm) REVERT: C 310 CYS cc_start: 0.8022 (m) cc_final: 0.7449 (m) REVERT: C 315 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8219 (mmmm) REVERT: C 323 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8025 (tttt) REVERT: C 327 LEU cc_start: 0.8125 (mt) cc_final: 0.7863 (mt) REVERT: C 338 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7434 (mmm160) REVERT: C 401 ILE cc_start: 0.8700 (mm) cc_final: 0.8412 (pt) REVERT: C 406 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 407 LEU cc_start: 0.8762 (mt) cc_final: 0.8333 (mt) REVERT: C 426 ASP cc_start: 0.8203 (t0) cc_final: 0.7887 (t0) REVERT: C 428 LEU cc_start: 0.8670 (tp) cc_final: 0.8345 (tp) REVERT: C 451 ASN cc_start: 0.7915 (t0) cc_final: 0.7693 (t0) REVERT: C 452 GLU cc_start: 0.7470 (mp0) cc_final: 0.7074 (mp0) REVERT: C 507 ILE cc_start: 0.8329 (mt) cc_final: 0.8071 (tp) REVERT: C 520 ASN cc_start: 0.8333 (t0) cc_final: 0.8062 (t0) REVERT: C 521 PRO cc_start: 0.8489 (Cg_endo) cc_final: 0.8219 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7529 (tpt-90) REVERT: C 546 GLU cc_start: 0.7179 (tp30) cc_final: 0.6717 (tp30) REVERT: C 558 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6253 (tm-30) REVERT: C 566 ASP cc_start: 0.6525 (t0) cc_final: 0.6192 (t0) REVERT: C 572 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7270 (mtmm) REVERT: C 577 LEU cc_start: 0.8125 (mm) cc_final: 0.7419 (mm) REVERT: C 580 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 581 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7099 (mt-10) REVERT: C 584 ASN cc_start: 0.8790 (t0) cc_final: 0.8316 (t0) REVERT: C 594 GLU cc_start: 0.7187 (mp0) cc_final: 0.6883 (mp0) REVERT: C 609 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7211 (mp0) REVERT: C 644 LYS cc_start: 0.8339 (tppt) cc_final: 0.7745 (tppt) REVERT: C 645 LYS cc_start: 0.8328 (mttt) cc_final: 0.7497 (mtpp) REVERT: C 677 MET cc_start: 0.5729 (mmm) cc_final: 0.5462 (mmm) REVERT: C 710 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.7998 (ptp-170) REVERT: C 711 LYS cc_start: 0.8696 (mppt) cc_final: 0.8384 (mppt) REVERT: C 713 PHE cc_start: 0.8569 (t80) cc_final: 0.8125 (t80) REVERT: C 747 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8090 (mmmm) REVERT: C 757 LEU cc_start: 0.8621 (tp) cc_final: 0.8230 (tt) REVERT: C 762 SER cc_start: 0.8134 (m) cc_final: 0.7752 (p) REVERT: C 764 ASN cc_start: 0.8109 (p0) cc_final: 0.7780 (p0) REVERT: C 766 ASP cc_start: 0.7272 (t0) cc_final: 0.6679 (t0) REVERT: C 768 GLN cc_start: 0.7871 (mp10) cc_final: 0.7155 (mp10) REVERT: C 772 GLU cc_start: 0.7539 (mp0) cc_final: 0.7196 (mp0) REVERT: C 788 ARG cc_start: 0.6554 (mmm-85) cc_final: 0.6203 (tpp80) REVERT: C 800 GLU cc_start: 0.7622 (tp30) cc_final: 0.7325 (tp30) REVERT: C 802 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7946 (mtpt) REVERT: C 804 LEU cc_start: 0.8511 (mt) cc_final: 0.8126 (mt) REVERT: C 836 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7397 (mtt90) REVERT: C 855 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7608 (ttpp) outliers start: 61 outliers final: 31 residues processed: 598 average time/residue: 0.3229 time to fit residues: 258.1277 Evaluate side-chains 586 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 545 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 SER 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 258 ASN Chi-restraints excluded: chain A residue 282 ASN 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 533 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 325 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 591 THR Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 666 LEU Chi-restraints excluded: chain C residue 795 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 93 optimal weight: 0.1980 chunk 39 optimal weight: 0.0270 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 285 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 801 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13904 Z= 0.158 Angle : 0.579 9.389 18776 Z= 0.286 Chirality : 0.040 0.143 2058 Planarity : 0.003 0.038 2434 Dihedral : 3.682 22.224 1844 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.03 % Allowed : 30.59 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1648 helix: 0.79 (0.18), residues: 870 sheet: -2.44 (0.65), residues: 48 loop : 0.08 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 791 HIS 0.009 0.001 HIS C 738 PHE 0.023 0.001 PHE B 52 TYR 0.015 0.001 TYR C 349 ARG 0.008 0.000 ARG A 639 *********************** 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 607 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 561 time to evaluate : 1.591 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 26 LEU cc_start: 0.8588 (mp) cc_final: 0.8320 (mp) REVERT: B 41 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8084 (mmtt) REVERT: B 55 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8299 (mtt180) REVERT: B 77 TYR cc_start: 0.8066 (m-80) cc_final: 0.7786 (m-80) REVERT: B 96 GLU cc_start: 0.7408 (tp30) cc_final: 0.7206 (tp30) REVERT: B 121 GLU cc_start: 0.8325 (mp0) cc_final: 0.7160 (mp0) REVERT: B 143 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7096 (p) REVERT: B 144 MET cc_start: 0.7077 (mmm) cc_final: 0.6700 (mmm) REVERT: A 128 LEU cc_start: 0.8306 (mp) cc_final: 0.7929 (mt) REVERT: A 135 GLU cc_start: 0.7974 (pt0) cc_final: 0.7512 (pp20) REVERT: A 153 ILE cc_start: 0.8909 (mt) cc_final: 0.8646 (tt) REVERT: A 241 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8089 (mtm-85) REVERT: A 243 TYR cc_start: 0.7855 (m-80) cc_final: 0.7253 (m-80) REVERT: A 264 SER cc_start: 0.8340 (m) cc_final: 0.8070 (p) REVERT: A 267 VAL cc_start: 0.8851 (t) cc_final: 0.8599 (p) REVERT: A 268 GLU cc_start: 0.8434 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 273 TYR cc_start: 0.7986 (m-80) cc_final: 0.7696 (m-80) REVERT: A 282 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7177 (p0) REVERT: A 291 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6770 (tmm) REVERT: A 295 ASN cc_start: 0.7827 (p0) cc_final: 0.7416 (p0) REVERT: A 306 LEU cc_start: 0.7949 (tp) cc_final: 0.7422 (tp) REVERT: A 310 CYS cc_start: 0.8042 (m) cc_final: 0.7580 (m) REVERT: A 315 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8107 (mmmm) REVERT: A 321 GLN cc_start: 0.8241 (mt0) cc_final: 0.7988 (mt0) REVERT: A 327 LEU cc_start: 0.7956 (mt) cc_final: 0.7696 (mt) REVERT: A 340 MET cc_start: 0.7739 (tmm) cc_final: 0.7024 (tmm) REVERT: A 341 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6851 (pt0) REVERT: A 392 HIS cc_start: 0.7341 (m-70) cc_final: 0.6989 (m-70) REVERT: A 397 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.5977 (p0) REVERT: A 406 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 407 LEU cc_start: 0.8831 (mt) cc_final: 0.8515 (mt) REVERT: A 408 THR cc_start: 0.8502 (m) cc_final: 0.8246 (p) REVERT: A 411 GLU cc_start: 0.7933 (tt0) cc_final: 0.7676 (tt0) REVERT: A 429 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: A 435 LYS cc_start: 0.8250 (tmtt) cc_final: 0.7986 (tptp) REVERT: A 450 ILE cc_start: 0.8717 (mt) cc_final: 0.8237 (tt) REVERT: A 452 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7216 (mp0) REVERT: A 474 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8130 (mmmm) REVERT: A 504 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 515 GLN cc_start: 0.7397 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 518 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 520 ASN cc_start: 0.8281 (t0) cc_final: 0.7842 (t0) REVERT: A 537 LEU cc_start: 0.8452 (tp) cc_final: 0.8053 (tt) REVERT: A 541 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 558 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6177 (tm-30) REVERT: A 566 ASP cc_start: 0.6580 (t0) cc_final: 0.6170 (t0) REVERT: A 577 LEU cc_start: 0.8266 (mm) cc_final: 0.7884 (mm) REVERT: A 580 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 592 TYR cc_start: 0.7034 (t80) cc_final: 0.6830 (t80) REVERT: A 611 GLN cc_start: 0.7917 (mp-120) cc_final: 0.7456 (mp10) REVERT: A 645 LYS cc_start: 0.8265 (mttt) cc_final: 0.7388 (mmtm) REVERT: A 649 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7790 (mtp85) REVERT: A 665 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 710 ARG cc_start: 0.8352 (ptp-170) cc_final: 0.7883 (ptm160) REVERT: A 713 PHE cc_start: 0.8447 (t80) cc_final: 0.7997 (t80) REVERT: A 717 TYR cc_start: 0.8271 (t80) cc_final: 0.7850 (t80) REVERT: A 721 ILE cc_start: 0.8774 (tp) cc_final: 0.8563 (tt) REVERT: A 734 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7884 (ptm-80) REVERT: A 738 HIS cc_start: 0.6727 (t-90) cc_final: 0.6271 (t-90) REVERT: A 739 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7278 (tpp) REVERT: A 747 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8058 (tppp) REVERT: A 757 LEU cc_start: 0.8587 (tp) cc_final: 0.8348 (tt) REVERT: A 762 SER cc_start: 0.8014 (m) cc_final: 0.7732 (p) REVERT: A 764 ASN cc_start: 0.7976 (p0) cc_final: 0.7742 (p0) REVERT: A 768 GLN cc_start: 0.7746 (mp10) cc_final: 0.7288 (mp10) REVERT: A 772 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6967 (mp0) REVERT: A 788 ARG cc_start: 0.6640 (mmm-85) cc_final: 0.6429 (tpp-160) REVERT: A 800 GLU cc_start: 0.7812 (tp30) cc_final: 0.7294 (tp30) REVERT: A 802 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7895 (mtpt) REVERT: A 804 LEU cc_start: 0.8403 (mt) cc_final: 0.7921 (mp) REVERT: A 807 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 829 LYS cc_start: 0.8427 (tttt) cc_final: 0.8211 (ttpp) REVERT: A 836 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7495 (mtt-85) REVERT: A 841 HIS cc_start: 0.7982 (t70) cc_final: 0.7493 (t70) REVERT: A 855 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7725 (ttpp) REVERT: D 17 ARG cc_start: 0.7254 (mmt180) cc_final: 0.6904 (mmt180) REVERT: D 22 LEU cc_start: 0.7656 (tp) cc_final: 0.7341 (tp) REVERT: D 25 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8026 (mm-30) REVERT: D 26 LEU cc_start: 0.8595 (mp) cc_final: 0.8242 (mp) REVERT: D 39 TYR cc_start: 0.8125 (m-80) cc_final: 0.7692 (m-80) REVERT: D 62 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7383 (tpp80) REVERT: D 77 TYR cc_start: 0.8154 (m-80) cc_final: 0.7629 (m-80) REVERT: D 89 SER cc_start: 0.8417 (p) cc_final: 0.8091 (t) REVERT: D 121 GLU cc_start: 0.7970 (mp0) cc_final: 0.7593 (mp0) REVERT: D 124 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7617 (ttp80) REVERT: D 128 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8474 (mtmm) REVERT: D 131 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7864 (ttm110) REVERT: C 128 LEU cc_start: 0.8074 (mp) cc_final: 0.7572 (mm) REVERT: C 135 GLU cc_start: 0.8016 (pt0) cc_final: 0.7509 (pp20) REVERT: C 151 ARG cc_start: 0.6984 (ptm160) cc_final: 0.6512 (mtm110) REVERT: C 161 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7974 (pm20) REVERT: C 239 ILE cc_start: 0.8877 (mm) cc_final: 0.8650 (mm) REVERT: C 241 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8165 (mtm180) REVERT: C 243 TYR cc_start: 0.7894 (m-80) cc_final: 0.7167 (m-80) REVERT: C 245 ARG cc_start: 0.8064 (mmp80) cc_final: 0.7673 (mmm-85) REVERT: C 247 LEU cc_start: 0.8219 (mp) cc_final: 0.7880 (tp) REVERT: C 251 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7898 (mtmm) REVERT: C 268 GLU cc_start: 0.8202 (tt0) cc_final: 0.7669 (tm-30) REVERT: C 283 TYR cc_start: 0.7920 (t80) cc_final: 0.7540 (t80) REVERT: C 289 ILE cc_start: 0.8484 (mm) cc_final: 0.8272 (mm) REVERT: C 291 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7601 (ttm) REVERT: C 310 CYS cc_start: 0.8133 (m) cc_final: 0.7576 (m) REVERT: C 315 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8188 (mmmm) REVERT: C 323 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8074 (tttt) REVERT: C 327 LEU cc_start: 0.8114 (mt) cc_final: 0.7841 (mt) REVERT: C 336 ILE cc_start: 0.8501 (tt) cc_final: 0.8284 (tt) REVERT: C 338 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7162 (tpt170) REVERT: C 341 GLU cc_start: 0.7406 (pt0) cc_final: 0.7104 (pp20) REVERT: C 401 ILE cc_start: 0.8703 (mm) cc_final: 0.8409 (pt) REVERT: C 406 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7520 (tm-30) REVERT: C 407 LEU cc_start: 0.8770 (mt) cc_final: 0.8450 (mt) REVERT: C 410 GLN cc_start: 0.7130 (mm-40) cc_final: 0.6494 (tm-30) REVERT: C 426 ASP cc_start: 0.8288 (t0) cc_final: 0.7941 (t0) REVERT: C 428 LEU cc_start: 0.8661 (tp) cc_final: 0.8345 (tp) REVERT: C 440 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7032 (ttt90) REVERT: C 447 GLU cc_start: 0.7393 (mp0) cc_final: 0.6987 (mp0) REVERT: C 451 ASN cc_start: 0.7935 (t0) cc_final: 0.7689 (t0) REVERT: C 452 GLU cc_start: 0.7409 (mp0) cc_final: 0.7196 (mp0) REVERT: C 507 ILE cc_start: 0.8338 (mt) cc_final: 0.8095 (tp) REVERT: C 520 ASN cc_start: 0.8322 (t0) cc_final: 0.8062 (t0) REVERT: C 521 PRO cc_start: 0.8496 (Cg_endo) cc_final: 0.8195 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7800 (tpt-90) cc_final: 0.7538 (tpt-90) REVERT: C 558 GLU cc_start: 0.6568 (tm-30) cc_final: 0.6237 (tm-30) REVERT: C 566 ASP cc_start: 0.6544 (t0) cc_final: 0.6215 (t0) REVERT: C 572 LYS cc_start: 0.7844 (ptpt) cc_final: 0.7248 (mtmm) REVERT: C 577 LEU cc_start: 0.8090 (mm) cc_final: 0.7388 (mm) REVERT: C 580 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 581 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7073 (mt-10) REVERT: C 584 ASN cc_start: 0.8809 (t0) cc_final: 0.8356 (t0) REVERT: C 594 GLU cc_start: 0.7176 (mp0) cc_final: 0.6863 (mp0) REVERT: C 609 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7225 (mp0) REVERT: C 644 LYS cc_start: 0.8328 (tppt) cc_final: 0.7739 (tppt) REVERT: C 645 LYS cc_start: 0.8381 (mttt) cc_final: 0.7455 (mtpp) REVERT: C 664 ASP cc_start: 0.8301 (m-30) cc_final: 0.8067 (m-30) REVERT: C 677 MET cc_start: 0.5771 (mmm) cc_final: 0.5370 (mmm) REVERT: C 710 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.7980 (ptp-170) REVERT: C 711 LYS cc_start: 0.8713 (mppt) cc_final: 0.8349 (mppt) REVERT: C 712 GLU cc_start: 0.7727 (pm20) cc_final: 0.7491 (pm20) REVERT: C 713 PHE cc_start: 0.8562 (t80) cc_final: 0.8141 (t80) REVERT: C 747 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8008 (tppt) REVERT: C 757 LEU cc_start: 0.8545 (tp) cc_final: 0.8225 (tt) REVERT: C 762 SER cc_start: 0.8173 (m) cc_final: 0.7816 (p) REVERT: C 764 ASN cc_start: 0.8071 (p0) cc_final: 0.7770 (p0) REVERT: C 766 ASP cc_start: 0.7236 (t0) cc_final: 0.6692 (t0) REVERT: C 768 GLN cc_start: 0.7877 (mp10) cc_final: 0.7023 (mp10) REVERT: C 772 GLU cc_start: 0.7518 (mp0) cc_final: 0.7043 (mp0) REVERT: C 788 ARG cc_start: 0.6692 (mmm-85) cc_final: 0.6283 (tpp80) REVERT: C 800 GLU cc_start: 0.7704 (tp30) cc_final: 0.7066 (tp30) REVERT: C 802 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7969 (mtpp) REVERT: C 804 LEU cc_start: 0.8533 (mt) cc_final: 0.7999 (mp) REVERT: C 836 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7459 (mtt90) REVERT: C 855 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7626 (ttpp) outliers start: 46 outliers final: 30 residues processed: 584 average time/residue: 0.3376 time to fit residues: 265.5275 Evaluate side-chains 581 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 542 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 118 SER 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 258 ASN Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 ASN 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 397 ASP 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 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 785 VAL 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 29 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 806 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 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 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN A 684 GLN A 801 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13904 Z= 0.188 Angle : 0.593 9.660 18776 Z= 0.297 Chirality : 0.041 0.151 2058 Planarity : 0.004 0.057 2434 Dihedral : 3.761 19.841 1844 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.55 % Allowed : 29.54 % Favored : 66.91 % 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: 0.62 (0.21), residues: 1648 helix: 0.88 (0.18), residues: 848 sheet: -2.55 (0.64), residues: 48 loop : 0.24 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 791 HIS 0.009 0.001 HIS C 738 PHE 0.027 0.001 PHE B 76 TYR 0.016 0.001 TYR D 99 ARG 0.009 0.000 ARG A 639 *********************** 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 603 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 549 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (mp) REVERT: B 41 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8094 (mmtt) REVERT: B 55 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8381 (mtt180) REVERT: B 77 TYR cc_start: 0.8095 (m-80) cc_final: 0.7834 (m-80) REVERT: B 143 CYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7140 (p) REVERT: B 144 MET cc_start: 0.7120 (mmm) cc_final: 0.6786 (mmm) REVERT: A 128 LEU cc_start: 0.8341 (mp) cc_final: 0.7948 (mt) REVERT: A 135 GLU cc_start: 0.7929 (pt0) cc_final: 0.7508 (pp20) REVERT: A 143 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8085 (mmm160) REVERT: A 153 ILE cc_start: 0.8938 (mt) cc_final: 0.8684 (tt) REVERT: A 165 GLN cc_start: 0.7696 (pm20) cc_final: 0.7311 (pm20) REVERT: A 241 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8127 (mtm-85) REVERT: A 243 TYR cc_start: 0.7845 (m-80) cc_final: 0.7295 (m-80) REVERT: A 264 SER cc_start: 0.8368 (m) cc_final: 0.8104 (p) REVERT: A 267 VAL cc_start: 0.8859 (t) cc_final: 0.8597 (p) REVERT: A 268 GLU cc_start: 0.8428 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 273 TYR cc_start: 0.7996 (m-80) cc_final: 0.7753 (m-80) REVERT: A 291 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6737 (tmm) REVERT: A 295 ASN cc_start: 0.7896 (p0) cc_final: 0.7576 (p0) REVERT: A 306 LEU cc_start: 0.8013 (tp) cc_final: 0.7443 (tp) REVERT: A 310 CYS cc_start: 0.8111 (m) cc_final: 0.7596 (m) REVERT: A 313 MET cc_start: 0.7939 (mtp) cc_final: 0.7681 (ttm) REVERT: A 315 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8186 (mmmm) REVERT: A 321 GLN cc_start: 0.8288 (mt0) cc_final: 0.8042 (mt0) REVERT: A 327 LEU cc_start: 0.7962 (mt) cc_final: 0.7653 (mt) REVERT: A 338 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7407 (tpt90) REVERT: A 340 MET cc_start: 0.7735 (tmm) cc_final: 0.7019 (tmm) REVERT: A 341 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6962 (pt0) REVERT: A 392 HIS cc_start: 0.7338 (m-70) cc_final: 0.6977 (m-70) REVERT: A 397 ASP cc_start: 0.6642 (p0) cc_final: 0.6105 (p0) REVERT: A 406 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 407 LEU cc_start: 0.8833 (mt) cc_final: 0.8496 (mt) REVERT: A 408 THR cc_start: 0.8545 (m) cc_final: 0.8280 (p) REVERT: A 411 GLU cc_start: 0.7961 (tt0) cc_final: 0.7703 (tt0) REVERT: A 429 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: A 435 LYS cc_start: 0.8233 (tmtt) cc_final: 0.7893 (tptp) REVERT: A 504 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 515 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 518 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 520 ASN cc_start: 0.8303 (t0) cc_final: 0.7844 (t0) REVERT: A 537 LEU cc_start: 0.8461 (tp) cc_final: 0.8168 (tt) REVERT: A 546 GLU cc_start: 0.7245 (tp30) cc_final: 0.6964 (tp30) REVERT: A 558 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6216 (tm-30) REVERT: A 566 ASP cc_start: 0.6589 (t0) cc_final: 0.6210 (t0) REVERT: A 577 LEU cc_start: 0.8283 (mm) cc_final: 0.7900 (mm) REVERT: A 580 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 611 GLN cc_start: 0.7889 (mp-120) cc_final: 0.7515 (mp10) REVERT: A 612 PHE cc_start: 0.8608 (m-80) cc_final: 0.8272 (m-10) REVERT: A 645 LYS cc_start: 0.8294 (mttt) cc_final: 0.7390 (mmtm) REVERT: A 649 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7774 (mtp85) REVERT: A 663 LYS cc_start: 0.8802 (pttm) cc_final: 0.8546 (pttt) REVERT: A 665 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8378 (mp) REVERT: A 710 ARG cc_start: 0.8323 (ptp-170) cc_final: 0.7884 (ptm160) REVERT: A 713 PHE cc_start: 0.8460 (t80) cc_final: 0.7983 (t80) REVERT: A 721 ILE cc_start: 0.8774 (tp) cc_final: 0.8534 (tt) REVERT: A 738 HIS cc_start: 0.6776 (t-90) cc_final: 0.6349 (t-90) REVERT: A 739 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7316 (tpp) REVERT: A 747 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8067 (tppp) REVERT: A 757 LEU cc_start: 0.8630 (tp) cc_final: 0.8376 (tt) REVERT: A 758 LEU cc_start: 0.8374 (tp) cc_final: 0.8154 (tt) REVERT: A 762 SER cc_start: 0.8015 (m) cc_final: 0.7652 (p) REVERT: A 764 ASN cc_start: 0.7978 (p0) cc_final: 0.7741 (p0) REVERT: A 768 GLN cc_start: 0.7785 (mp10) cc_final: 0.7344 (mp10) REVERT: A 772 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6992 (mp0) REVERT: A 788 ARG cc_start: 0.6703 (mmm-85) cc_final: 0.6481 (tpp-160) REVERT: A 800 GLU cc_start: 0.7867 (tp30) cc_final: 0.7366 (tp30) REVERT: A 802 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7940 (mtpp) REVERT: A 804 LEU cc_start: 0.8428 (mt) cc_final: 0.7965 (mp) REVERT: A 829 LYS cc_start: 0.8450 (tttt) cc_final: 0.7995 (ttpp) REVERT: A 836 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7535 (mtt-85) REVERT: A 841 HIS cc_start: 0.7978 (t70) cc_final: 0.7479 (t70) REVERT: A 851 GLU cc_start: 0.6881 (pm20) cc_final: 0.6616 (pm20) REVERT: A 855 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7732 (ttpp) REVERT: D 17 ARG cc_start: 0.7268 (mmt180) cc_final: 0.6930 (mmt180) REVERT: D 22 LEU cc_start: 0.7693 (tp) cc_final: 0.7395 (tp) REVERT: D 25 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8038 (mm-30) REVERT: D 26 LEU cc_start: 0.8567 (mp) cc_final: 0.8202 (mp) REVERT: D 39 TYR cc_start: 0.8172 (m-80) cc_final: 0.7703 (m-80) REVERT: D 77 TYR cc_start: 0.8173 (m-80) cc_final: 0.7650 (m-80) REVERT: D 89 SER cc_start: 0.8431 (p) cc_final: 0.8112 (t) REVERT: D 121 GLU cc_start: 0.7967 (mp0) cc_final: 0.7716 (mp0) REVERT: D 124 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7540 (ttp80) REVERT: D 128 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8467 (mtpp) REVERT: D 131 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7903 (ttm110) REVERT: D 143 CYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7008 (p) REVERT: C 123 LYS cc_start: 0.7977 (tptp) cc_final: 0.7599 (tppt) REVERT: C 128 LEU cc_start: 0.8080 (mp) cc_final: 0.7565 (mm) REVERT: C 135 GLU cc_start: 0.8056 (pt0) cc_final: 0.7599 (pp20) REVERT: C 143 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8151 (mmm160) REVERT: C 151 ARG cc_start: 0.6997 (ptm160) cc_final: 0.6516 (mtm110) REVERT: C 161 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8000 (pm20) REVERT: C 239 ILE cc_start: 0.8875 (mm) cc_final: 0.8668 (mm) REVERT: C 241 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: C 243 TYR cc_start: 0.7924 (m-80) cc_final: 0.7226 (m-80) REVERT: C 245 ARG cc_start: 0.8126 (mmp80) cc_final: 0.7714 (mmm-85) REVERT: C 247 LEU cc_start: 0.8267 (mp) cc_final: 0.7951 (tp) REVERT: C 251 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7948 (mtmm) REVERT: C 268 GLU cc_start: 0.8223 (tt0) cc_final: 0.7694 (tm-30) REVERT: C 283 TYR cc_start: 0.7927 (t80) cc_final: 0.7559 (t80) REVERT: C 289 ILE cc_start: 0.8569 (mm) cc_final: 0.8342 (mm) REVERT: C 310 CYS cc_start: 0.8029 (m) cc_final: 0.7375 (m) REVERT: C 315 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8240 (mmmm) REVERT: C 323 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8132 (tttt) REVERT: C 327 LEU cc_start: 0.8133 (mt) cc_final: 0.7864 (mt) REVERT: C 338 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7190 (tpt170) REVERT: C 341 GLU cc_start: 0.7370 (pt0) cc_final: 0.7055 (pp20) REVERT: C 401 ILE cc_start: 0.8696 (mm) cc_final: 0.8388 (pt) REVERT: C 406 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 426 ASP cc_start: 0.8161 (t0) cc_final: 0.7914 (t0) REVERT: C 428 LEU cc_start: 0.8675 (tp) cc_final: 0.8353 (tp) REVERT: C 440 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.6290 (ttt90) REVERT: C 447 GLU cc_start: 0.7419 (mp0) cc_final: 0.7029 (mp0) REVERT: C 507 ILE cc_start: 0.8374 (mt) cc_final: 0.8123 (tp) REVERT: C 520 ASN cc_start: 0.8349 (t0) cc_final: 0.8103 (t0) REVERT: C 521 PRO cc_start: 0.8491 (Cg_endo) cc_final: 0.8223 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7901 (tpt-90) cc_final: 0.7637 (tpt-90) REVERT: C 558 GLU cc_start: 0.6579 (tm-30) cc_final: 0.6245 (tm-30) REVERT: C 566 ASP cc_start: 0.6552 (t0) cc_final: 0.6247 (t0) REVERT: C 572 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7293 (mtmm) REVERT: C 577 LEU cc_start: 0.8174 (mm) cc_final: 0.7623 (mm) REVERT: C 580 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 584 ASN cc_start: 0.8806 (t0) cc_final: 0.8354 (t0) REVERT: C 594 GLU cc_start: 0.7196 (mp0) cc_final: 0.6886 (mp0) REVERT: C 609 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7077 (mp0) REVERT: C 612 PHE cc_start: 0.8561 (m-80) cc_final: 0.8217 (m-10) REVERT: C 644 LYS cc_start: 0.8375 (tppt) cc_final: 0.7781 (tppt) REVERT: C 645 LYS cc_start: 0.8431 (mttt) cc_final: 0.7524 (mtpp) REVERT: C 649 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7044 (mtm-85) REVERT: C 651 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8012 (tt) REVERT: C 677 MET cc_start: 0.5765 (mmm) cc_final: 0.5314 (mmm) REVERT: C 710 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8029 (ttm170) REVERT: C 712 GLU cc_start: 0.7758 (pm20) cc_final: 0.7507 (pm20) REVERT: C 713 PHE cc_start: 0.8572 (t80) cc_final: 0.8152 (t80) REVERT: C 747 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8045 (tppt) REVERT: C 757 LEU cc_start: 0.8560 (tp) cc_final: 0.8261 (tt) REVERT: C 762 SER cc_start: 0.8125 (m) cc_final: 0.7764 (p) REVERT: C 764 ASN cc_start: 0.8077 (p0) cc_final: 0.7724 (p0) REVERT: C 766 ASP cc_start: 0.7259 (t0) cc_final: 0.6686 (t0) REVERT: C 768 GLN cc_start: 0.7891 (mp10) cc_final: 0.7041 (mp10) REVERT: C 772 GLU cc_start: 0.7530 (mp0) cc_final: 0.7082 (mp0) REVERT: C 788 ARG cc_start: 0.6628 (mmm-85) cc_final: 0.6253 (tpp80) REVERT: C 800 GLU cc_start: 0.7791 (tp30) cc_final: 0.7115 (tp30) REVERT: C 802 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8012 (mtpp) REVERT: C 804 LEU cc_start: 0.8506 (mt) cc_final: 0.7939 (mp) REVERT: C 836 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7453 (mtt90) REVERT: C 855 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7635 (ttpp) outliers start: 54 outliers final: 37 residues processed: 573 average time/residue: 0.3227 time to fit residues: 248.0998 Evaluate side-chains 583 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 538 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 SER 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 258 ASN 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 533 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 785 VAL 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 29 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 350 LYS 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 591 THR Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 720 TYR 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 97 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN A 801 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13904 Z= 0.180 Angle : 0.616 14.533 18776 Z= 0.304 Chirality : 0.041 0.147 2058 Planarity : 0.004 0.037 2434 Dihedral : 3.751 18.507 1844 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.75 % Allowed : 30.00 % Favored : 66.25 % 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: 0.59 (0.21), residues: 1648 helix: 0.84 (0.18), residues: 846 sheet: -2.57 (0.63), residues: 48 loop : 0.25 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 328 HIS 0.008 0.001 HIS B 125 PHE 0.023 0.002 PHE D 76 TYR 0.013 0.001 TYR D 99 ARG 0.016 0.001 ARG B 124 *********************** 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 600 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 543 time to evaluate : 1.591 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: 0.8594 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 41 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8116 (mmtt) REVERT: B 55 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8361 (mtt180) REVERT: B 77 TYR cc_start: 0.8098 (m-80) cc_final: 0.7816 (m-80) REVERT: B 123 GLN cc_start: 0.8207 (tp40) cc_final: 0.7746 (tp40) REVERT: B 143 CYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7071 (p) REVERT: B 144 MET cc_start: 0.7076 (mmm) cc_final: 0.6642 (mmm) REVERT: A 123 LYS cc_start: 0.8045 (tptp) cc_final: 0.7587 (tppt) REVERT: A 128 LEU cc_start: 0.8309 (mp) cc_final: 0.7927 (mt) REVERT: A 135 GLU cc_start: 0.7874 (pt0) cc_final: 0.7486 (pp20) REVERT: A 153 ILE cc_start: 0.8945 (mt) cc_final: 0.8707 (tt) REVERT: A 165 GLN cc_start: 0.7683 (pm20) cc_final: 0.7266 (pm20) REVERT: A 241 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8129 (mtm-85) REVERT: A 243 TYR cc_start: 0.7821 (m-80) cc_final: 0.7189 (m-80) REVERT: A 247 LEU cc_start: 0.8498 (mp) cc_final: 0.8276 (mm) REVERT: A 264 SER cc_start: 0.8367 (m) cc_final: 0.8092 (p) REVERT: A 267 VAL cc_start: 0.8841 (t) cc_final: 0.8577 (p) REVERT: A 268 GLU cc_start: 0.8419 (tt0) cc_final: 0.7932 (tm-30) REVERT: A 273 TYR cc_start: 0.8030 (m-80) cc_final: 0.7734 (m-80) REVERT: A 291 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6734 (tmm) REVERT: A 306 LEU cc_start: 0.8023 (tp) cc_final: 0.7485 (tp) REVERT: A 310 CYS cc_start: 0.8106 (m) cc_final: 0.7590 (m) REVERT: A 315 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8182 (mmmm) REVERT: A 321 GLN cc_start: 0.8254 (mt0) cc_final: 0.7998 (mt0) REVERT: A 323 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8316 (ptmt) REVERT: A 338 ARG cc_start: 0.7853 (tpt90) cc_final: 0.7309 (tpt90) REVERT: A 340 MET cc_start: 0.7697 (tmm) cc_final: 0.7072 (tmm) REVERT: A 341 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6812 (mt-10) REVERT: A 344 GLN cc_start: 0.8052 (mm110) cc_final: 0.7841 (mm110) REVERT: A 392 HIS cc_start: 0.7348 (m-70) cc_final: 0.6988 (m-70) REVERT: A 397 ASP cc_start: 0.6670 (p0) cc_final: 0.6143 (p0) REVERT: A 406 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 407 LEU cc_start: 0.8821 (mt) cc_final: 0.8487 (mt) REVERT: A 408 THR cc_start: 0.8543 (m) cc_final: 0.8287 (p) REVERT: A 411 GLU cc_start: 0.7950 (tt0) cc_final: 0.7699 (tt0) REVERT: A 429 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 435 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7990 (tptp) REVERT: A 504 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7290 (mm-30) REVERT: A 515 GLN cc_start: 0.7195 (tm-30) cc_final: 0.6902 (tm-30) REVERT: A 518 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 520 ASN cc_start: 0.8291 (t0) cc_final: 0.7848 (t0) REVERT: A 537 LEU cc_start: 0.8416 (tp) cc_final: 0.8127 (tt) REVERT: A 546 GLU cc_start: 0.7260 (tp30) cc_final: 0.6935 (tp30) REVERT: A 558 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6171 (tm-30) REVERT: A 566 ASP cc_start: 0.6583 (t0) cc_final: 0.6193 (t0) REVERT: A 577 LEU cc_start: 0.8282 (mm) cc_final: 0.7803 (mm) REVERT: A 590 PHE cc_start: 0.8441 (m-80) cc_final: 0.8208 (m-80) REVERT: A 611 GLN cc_start: 0.7716 (mp-120) cc_final: 0.7204 (mp10) REVERT: A 645 LYS cc_start: 0.8247 (mttt) cc_final: 0.7430 (mmmm) REVERT: A 649 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7793 (mtp85) REVERT: A 663 LYS cc_start: 0.8786 (pttm) cc_final: 0.8536 (pttt) REVERT: A 665 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8364 (mp) REVERT: A 681 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6691 (mm-40) REVERT: A 710 ARG cc_start: 0.8253 (ptp-170) cc_final: 0.7806 (ptm160) REVERT: A 713 PHE cc_start: 0.8420 (t80) cc_final: 0.7992 (t80) REVERT: A 721 ILE cc_start: 0.8782 (tp) cc_final: 0.8540 (tt) REVERT: A 738 HIS cc_start: 0.6785 (t-90) cc_final: 0.6348 (t-90) REVERT: A 747 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8083 (tppp) REVERT: A 757 LEU cc_start: 0.8610 (tp) cc_final: 0.8356 (tt) REVERT: A 758 LEU cc_start: 0.8360 (tp) cc_final: 0.8141 (tt) REVERT: A 762 SER cc_start: 0.8001 (m) cc_final: 0.7643 (p) REVERT: A 764 ASN cc_start: 0.7964 (p0) cc_final: 0.7751 (p0) REVERT: A 768 GLN cc_start: 0.7768 (mp10) cc_final: 0.7322 (mp10) REVERT: A 772 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6980 (mp0) REVERT: A 788 ARG cc_start: 0.6711 (mmm-85) cc_final: 0.6449 (tpp-160) REVERT: A 800 GLU cc_start: 0.7845 (tp30) cc_final: 0.7325 (tp30) REVERT: A 802 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7899 (mtpt) REVERT: A 804 LEU cc_start: 0.8431 (mt) cc_final: 0.7966 (mp) REVERT: A 829 LYS cc_start: 0.8394 (tttt) cc_final: 0.8054 (ttpp) REVERT: A 836 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7529 (mtt-85) REVERT: A 841 HIS cc_start: 0.7972 (t70) cc_final: 0.7471 (t70) REVERT: A 851 GLU cc_start: 0.6859 (pm20) cc_final: 0.6580 (pm20) REVERT: A 855 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7678 (ttpp) REVERT: D 17 ARG cc_start: 0.7259 (mmt180) cc_final: 0.6917 (mmt180) REVERT: D 22 LEU cc_start: 0.7675 (tp) cc_final: 0.7359 (tp) REVERT: D 25 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 26 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8188 (mp) REVERT: D 39 TYR cc_start: 0.8151 (m-80) cc_final: 0.7666 (m-80) REVERT: D 77 TYR cc_start: 0.8183 (m-80) cc_final: 0.7625 (m-80) REVERT: D 89 SER cc_start: 0.8427 (p) cc_final: 0.8116 (t) REVERT: D 121 GLU cc_start: 0.7979 (mp0) cc_final: 0.7714 (mp0) REVERT: D 124 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7461 (ttp80) REVERT: D 128 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8456 (mtpp) REVERT: D 131 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7911 (ttm110) REVERT: D 143 CYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6995 (p) REVERT: C 123 LYS cc_start: 0.7974 (tptp) cc_final: 0.7602 (tppt) REVERT: C 128 LEU cc_start: 0.8051 (mp) cc_final: 0.7532 (mm) REVERT: C 135 GLU cc_start: 0.8032 (pt0) cc_final: 0.7585 (pp20) REVERT: C 151 ARG cc_start: 0.7004 (ptm160) cc_final: 0.6566 (mtm110) REVERT: C 161 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8001 (pm20) REVERT: C 241 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8180 (mtm180) REVERT: C 243 TYR cc_start: 0.7915 (m-80) cc_final: 0.7221 (m-80) REVERT: C 245 ARG cc_start: 0.8125 (mmp80) cc_final: 0.7693 (mmm-85) REVERT: C 247 LEU cc_start: 0.8275 (mp) cc_final: 0.7788 (tp) REVERT: C 251 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7938 (mtmm) REVERT: C 268 GLU cc_start: 0.8217 (tt0) cc_final: 0.7692 (tm-30) REVERT: C 283 TYR cc_start: 0.7876 (t80) cc_final: 0.7538 (t80) REVERT: C 289 ILE cc_start: 0.8553 (mm) cc_final: 0.8345 (mm) REVERT: C 295 ASN cc_start: 0.8353 (m110) cc_final: 0.7857 (m110) REVERT: C 310 CYS cc_start: 0.8091 (m) cc_final: 0.7521 (m) REVERT: C 315 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8204 (mmmm) REVERT: C 323 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8114 (tttt) REVERT: C 327 LEU cc_start: 0.8119 (mt) cc_final: 0.7851 (mt) REVERT: C 338 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7312 (tpp-160) REVERT: C 341 GLU cc_start: 0.7416 (pt0) cc_final: 0.7118 (pp20) REVERT: C 350 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8203 (mmmt) REVERT: C 394 GLU cc_start: 0.7308 (tp30) cc_final: 0.6722 (tp30) REVERT: C 406 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 426 ASP cc_start: 0.8236 (t0) cc_final: 0.7920 (t0) REVERT: C 428 LEU cc_start: 0.8674 (tp) cc_final: 0.8369 (tp) REVERT: C 440 ARG cc_start: 0.7490 (mmm-85) cc_final: 0.6447 (ttt90) REVERT: C 447 GLU cc_start: 0.7407 (mp0) cc_final: 0.7028 (mp0) REVERT: C 507 ILE cc_start: 0.8375 (mt) cc_final: 0.8088 (tp) REVERT: C 521 PRO cc_start: 0.8494 (Cg_endo) cc_final: 0.8248 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7870 (tpt-90) cc_final: 0.7589 (tpt-90) REVERT: C 558 GLU cc_start: 0.6583 (tm-30) cc_final: 0.6230 (tm-30) REVERT: C 566 ASP cc_start: 0.6572 (t0) cc_final: 0.6282 (t0) REVERT: C 572 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7261 (mtmm) REVERT: C 577 LEU cc_start: 0.8141 (mm) cc_final: 0.7603 (mm) REVERT: C 580 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 584 ASN cc_start: 0.8803 (t0) cc_final: 0.8378 (t0) REVERT: C 594 GLU cc_start: 0.7196 (mp0) cc_final: 0.6884 (mp0) REVERT: C 609 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7057 (mp0) REVERT: C 644 LYS cc_start: 0.8375 (tppt) cc_final: 0.7767 (tppt) REVERT: C 645 LYS cc_start: 0.8425 (mttt) cc_final: 0.7465 (mmmm) REVERT: C 649 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7172 (mtm-85) REVERT: C 651 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8001 (tt) REVERT: C 677 MET cc_start: 0.5723 (mmm) cc_final: 0.5288 (mmm) REVERT: C 710 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.8074 (ttm170) REVERT: C 712 GLU cc_start: 0.7775 (pm20) cc_final: 0.7522 (pm20) REVERT: C 713 PHE cc_start: 0.8549 (t80) cc_final: 0.8152 (t80) REVERT: C 720 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.7076 (t80) REVERT: C 747 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8051 (tppt) REVERT: C 757 LEU cc_start: 0.8494 (tp) cc_final: 0.8247 (tt) REVERT: C 762 SER cc_start: 0.8127 (m) cc_final: 0.7767 (p) REVERT: C 764 ASN cc_start: 0.8063 (p0) cc_final: 0.7730 (p0) REVERT: C 766 ASP cc_start: 0.7238 (t0) cc_final: 0.6663 (t0) REVERT: C 768 GLN cc_start: 0.7881 (mp10) cc_final: 0.7019 (mp10) REVERT: C 772 GLU cc_start: 0.7517 (mp0) cc_final: 0.7066 (mp0) REVERT: C 788 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.6252 (tpp80) REVERT: C 800 GLU cc_start: 0.7768 (tp30) cc_final: 0.7003 (tp30) REVERT: C 802 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8000 (mtpp) REVERT: C 804 LEU cc_start: 0.8466 (mt) cc_final: 0.7786 (mp) REVERT: C 836 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7440 (mtt90) REVERT: C 855 LYS cc_start: 0.7893 (ttpp) cc_final: 0.7625 (ttpp) outliers start: 57 outliers final: 35 residues processed: 571 average time/residue: 0.3227 time to fit residues: 246.1330 Evaluate side-chains 584 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 538 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 SER 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 258 ASN 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 533 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 734 ARG Chi-restraints excluded: chain A residue 785 VAL 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 60 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 350 LYS 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 591 THR 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 651 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 797 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 801 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13904 Z= 0.213 Angle : 0.647 13.232 18776 Z= 0.320 Chirality : 0.042 0.144 2058 Planarity : 0.004 0.033 2434 Dihedral : 3.847 19.315 1844 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.36 % Allowed : 30.92 % Favored : 65.72 % 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: 0.58 (0.21), residues: 1648 helix: 0.82 (0.18), residues: 846 sheet: -2.59 (0.64), residues: 48 loop : 0.27 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 328 HIS 0.007 0.001 HIS B 125 PHE 0.030 0.002 PHE D 76 TYR 0.015 0.001 TYR A 494 ARG 0.013 0.001 ARG B 124 *********************** 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 606 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 555 time to evaluate : 1.503 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: 0.8601 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 41 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8133 (mmtt) REVERT: B 77 TYR cc_start: 0.8105 (m-80) cc_final: 0.7824 (m-80) REVERT: B 123 GLN cc_start: 0.8168 (tp40) cc_final: 0.7719 (tp40) REVERT: B 143 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7227 (p) REVERT: B 144 MET cc_start: 0.7159 (mmm) cc_final: 0.6752 (mmm) REVERT: A 123 LYS cc_start: 0.8108 (tptp) cc_final: 0.7666 (tppt) REVERT: A 128 LEU cc_start: 0.8330 (mp) cc_final: 0.7931 (mt) REVERT: A 135 GLU cc_start: 0.7879 (pt0) cc_final: 0.7514 (pp20) REVERT: A 143 ARG cc_start: 0.8409 (mmm160) cc_final: 0.8085 (mmm160) REVERT: A 153 ILE cc_start: 0.8961 (mt) cc_final: 0.8724 (tt) REVERT: A 241 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.8150 (mtm-85) REVERT: A 243 TYR cc_start: 0.7858 (m-80) cc_final: 0.7253 (m-80) REVERT: A 245 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7652 (mmp80) REVERT: A 264 SER cc_start: 0.8399 (m) cc_final: 0.8112 (p) REVERT: A 267 VAL cc_start: 0.8844 (t) cc_final: 0.8588 (p) REVERT: A 268 GLU cc_start: 0.8425 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 273 TYR cc_start: 0.8024 (m-80) cc_final: 0.7753 (m-80) REVERT: A 291 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6664 (tmm) REVERT: A 294 ARG cc_start: 0.7707 (ptt90) cc_final: 0.7476 (ptt90) REVERT: A 310 CYS cc_start: 0.8036 (m) cc_final: 0.7444 (m) REVERT: A 315 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8116 (mmmm) REVERT: A 321 GLN cc_start: 0.8309 (mt0) cc_final: 0.8052 (mt0) REVERT: A 338 ARG cc_start: 0.7838 (tpt90) cc_final: 0.7378 (tpt90) REVERT: A 340 MET cc_start: 0.7733 (tmm) cc_final: 0.7082 (tmm) REVERT: A 341 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6463 (mt-10) REVERT: A 392 HIS cc_start: 0.7379 (m-70) cc_final: 0.7007 (m-70) REVERT: A 397 ASP cc_start: 0.6683 (p0) cc_final: 0.6180 (p0) REVERT: A 406 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7437 (tm-30) REVERT: A 407 LEU cc_start: 0.8805 (mt) cc_final: 0.8478 (mt) REVERT: A 408 THR cc_start: 0.8569 (m) cc_final: 0.8305 (p) REVERT: A 411 GLU cc_start: 0.7975 (tt0) cc_final: 0.7731 (tt0) REVERT: A 429 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: A 435 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7893 (tptp) REVERT: A 504 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 515 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6976 (tm-30) REVERT: A 518 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7111 (tm-30) REVERT: A 520 ASN cc_start: 0.8323 (t0) cc_final: 0.7867 (t0) REVERT: A 537 LEU cc_start: 0.8398 (tp) cc_final: 0.8089 (tt) REVERT: A 542 MET cc_start: 0.7276 (ptp) cc_final: 0.6811 (ptp) REVERT: A 546 GLU cc_start: 0.7297 (tp30) cc_final: 0.6989 (tp30) REVERT: A 558 GLU cc_start: 0.6417 (tm-30) cc_final: 0.6178 (tm-30) REVERT: A 566 ASP cc_start: 0.6532 (t0) cc_final: 0.6177 (t0) REVERT: A 577 LEU cc_start: 0.8192 (mm) cc_final: 0.7703 (mm) REVERT: A 590 PHE cc_start: 0.8394 (m-80) cc_final: 0.8120 (m-80) REVERT: A 611 GLN cc_start: 0.7829 (mp-120) cc_final: 0.7324 (mp10) REVERT: A 645 LYS cc_start: 0.8227 (mttt) cc_final: 0.7432 (mmmm) REVERT: A 649 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7771 (mtp85) REVERT: A 653 ASP cc_start: 0.7328 (m-30) cc_final: 0.6883 (p0) REVERT: A 663 LYS cc_start: 0.8782 (pttm) cc_final: 0.8473 (pttp) REVERT: A 665 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 694 TYR cc_start: 0.7627 (t80) cc_final: 0.7408 (t80) REVERT: A 710 ARG cc_start: 0.8240 (ptp-170) cc_final: 0.7800 (ptm160) REVERT: A 712 GLU cc_start: 0.7728 (pm20) cc_final: 0.7406 (pm20) REVERT: A 713 PHE cc_start: 0.8436 (t80) cc_final: 0.8002 (t80) REVERT: A 717 TYR cc_start: 0.8322 (t80) cc_final: 0.8029 (t80) REVERT: A 721 ILE cc_start: 0.8738 (tp) cc_final: 0.8506 (tt) REVERT: A 738 HIS cc_start: 0.6828 (t-90) cc_final: 0.6371 (t-90) REVERT: A 747 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8144 (tppp) REVERT: A 757 LEU cc_start: 0.8643 (tp) cc_final: 0.8397 (tt) REVERT: A 762 SER cc_start: 0.8058 (m) cc_final: 0.7682 (p) REVERT: A 764 ASN cc_start: 0.7951 (p0) cc_final: 0.7744 (p0) REVERT: A 768 GLN cc_start: 0.7798 (mp10) cc_final: 0.7341 (mp10) REVERT: A 772 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7044 (mp0) REVERT: A 788 ARG cc_start: 0.6766 (mmm-85) cc_final: 0.6479 (tpp-160) REVERT: A 800 GLU cc_start: 0.7885 (tp30) cc_final: 0.7652 (tp30) REVERT: A 802 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7807 (mtpp) REVERT: A 804 LEU cc_start: 0.8451 (mt) cc_final: 0.8120 (mt) REVERT: A 829 LYS cc_start: 0.8439 (tttt) cc_final: 0.8117 (ttpp) REVERT: A 841 HIS cc_start: 0.7939 (t70) cc_final: 0.7429 (t70) REVERT: A 855 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7680 (ttpp) REVERT: D 17 ARG cc_start: 0.7292 (mmt180) cc_final: 0.6951 (mmt180) REVERT: D 22 LEU cc_start: 0.7698 (tp) cc_final: 0.7392 (tp) REVERT: D 25 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8021 (mm-30) REVERT: D 26 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8201 (mp) REVERT: D 39 TYR cc_start: 0.8139 (m-80) cc_final: 0.7637 (m-80) REVERT: D 77 TYR cc_start: 0.8158 (m-80) cc_final: 0.7575 (m-80) REVERT: D 89 SER cc_start: 0.8452 (p) cc_final: 0.8128 (t) REVERT: D 121 GLU cc_start: 0.8069 (mp0) cc_final: 0.7701 (mp0) REVERT: D 124 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7481 (ttp80) REVERT: D 131 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7958 (ttm110) REVERT: D 143 CYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7016 (p) REVERT: C 123 LYS cc_start: 0.7998 (tptp) cc_final: 0.7617 (tppt) REVERT: C 128 LEU cc_start: 0.8082 (mp) cc_final: 0.7692 (mp) REVERT: C 135 GLU cc_start: 0.8072 (pt0) cc_final: 0.7653 (pp20) REVERT: C 161 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8019 (pm20) REVERT: C 241 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.8239 (mtm180) REVERT: C 243 TYR cc_start: 0.7908 (m-80) cc_final: 0.7173 (m-80) REVERT: C 245 ARG cc_start: 0.8157 (mmp80) cc_final: 0.7741 (mmm-85) REVERT: C 247 LEU cc_start: 0.8342 (mp) cc_final: 0.7832 (tp) REVERT: C 268 GLU cc_start: 0.8215 (tt0) cc_final: 0.7737 (tm-30) REVERT: C 283 TYR cc_start: 0.7886 (t80) cc_final: 0.7539 (t80) REVERT: C 295 ASN cc_start: 0.8367 (m110) cc_final: 0.7899 (m110) REVERT: C 310 CYS cc_start: 0.8045 (m) cc_final: 0.7517 (m) REVERT: C 315 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8218 (mmmm) REVERT: C 321 GLN cc_start: 0.8270 (mt0) cc_final: 0.8033 (mt0) REVERT: C 323 LYS cc_start: 0.8525 (ptmt) cc_final: 0.8100 (tttt) REVERT: C 327 LEU cc_start: 0.8132 (mt) cc_final: 0.7882 (mt) REVERT: C 338 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7301 (tpt-90) REVERT: C 394 GLU cc_start: 0.7317 (tp30) cc_final: 0.6747 (tp30) REVERT: C 406 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 426 ASP cc_start: 0.8224 (t0) cc_final: 0.7911 (t0) REVERT: C 428 LEU cc_start: 0.8685 (tp) cc_final: 0.8375 (tp) REVERT: C 447 GLU cc_start: 0.7438 (mp0) cc_final: 0.7066 (mp0) REVERT: C 487 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8248 (t) REVERT: C 507 ILE cc_start: 0.8373 (mt) cc_final: 0.8115 (tp) REVERT: C 518 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6973 (pp30) REVERT: C 520 ASN cc_start: 0.8383 (t0) cc_final: 0.7991 (t0) REVERT: C 539 ARG cc_start: 0.7859 (tpt-90) cc_final: 0.7558 (tpt-90) REVERT: C 558 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6256 (tm-30) REVERT: C 566 ASP cc_start: 0.6558 (t0) cc_final: 0.6263 (t0) REVERT: C 572 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7315 (mtmm) REVERT: C 577 LEU cc_start: 0.8198 (mm) cc_final: 0.7694 (mm) REVERT: C 580 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 584 ASN cc_start: 0.8820 (t0) cc_final: 0.8379 (t0) REVERT: C 594 GLU cc_start: 0.7212 (mp0) cc_final: 0.6903 (mp0) REVERT: C 609 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7076 (mp0) REVERT: C 644 LYS cc_start: 0.8393 (tppt) cc_final: 0.7770 (tppt) REVERT: C 645 LYS cc_start: 0.8409 (mttt) cc_final: 0.7481 (mmmm) REVERT: C 649 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.6911 (mtm-85) REVERT: C 677 MET cc_start: 0.5728 (mmm) cc_final: 0.5265 (mmm) REVERT: C 710 ARG cc_start: 0.8483 (ttp-170) cc_final: 0.8044 (ttm170) REVERT: C 712 GLU cc_start: 0.7768 (pm20) cc_final: 0.7483 (pm20) REVERT: C 713 PHE cc_start: 0.8539 (t80) cc_final: 0.8133 (t80) REVERT: C 720 TYR cc_start: 0.7773 (t80) cc_final: 0.7086 (t80) REVERT: C 757 LEU cc_start: 0.8566 (tp) cc_final: 0.8267 (tt) REVERT: C 762 SER cc_start: 0.8137 (m) cc_final: 0.7771 (p) REVERT: C 764 ASN cc_start: 0.8034 (p0) cc_final: 0.7745 (p0) REVERT: C 766 ASP cc_start: 0.7249 (t0) cc_final: 0.6914 (t0) REVERT: C 768 GLN cc_start: 0.7913 (mp10) cc_final: 0.7192 (mp10) REVERT: C 772 GLU cc_start: 0.7523 (mp0) cc_final: 0.7105 (mp0) REVERT: C 800 GLU cc_start: 0.7774 (tp30) cc_final: 0.7435 (tp30) REVERT: C 802 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7987 (mtpp) REVERT: C 803 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7420 (mtt180) REVERT: C 804 LEU cc_start: 0.8475 (mt) cc_final: 0.8114 (mt) REVERT: C 836 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7507 (mtt90) REVERT: C 855 LYS cc_start: 0.7909 (ttpp) cc_final: 0.7638 (ttpp) outliers start: 51 outliers final: 35 residues processed: 580 average time/residue: 0.3263 time to fit residues: 253.9783 Evaluate side-chains 588 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 545 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 SER 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 258 ASN 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 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG 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 60 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 591 THR 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 785 VAL Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 797 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13904 Z= 0.284 Angle : 0.683 12.813 18776 Z= 0.349 Chirality : 0.044 0.216 2058 Planarity : 0.004 0.032 2434 Dihedral : 4.085 19.846 1844 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.29 % Allowed : 31.32 % Favored : 65.39 % 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: 0.38 (0.21), residues: 1648 helix: 0.64 (0.18), residues: 850 sheet: -2.01 (0.55), residues: 72 loop : 0.22 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 328 HIS 0.007 0.001 HIS B 125 PHE 0.031 0.002 PHE C 343 TYR 0.016 0.001 TYR A 494 ARG 0.011 0.001 ARG B 124 ********************** 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 600 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 550 time to evaluate : 1.594 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 26 LEU cc_start: 0.8582 (mp) cc_final: 0.8287 (mp) REVERT: B 41 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8013 (mmtt) REVERT: B 77 TYR cc_start: 0.8170 (m-80) cc_final: 0.7921 (m-80) REVERT: B 123 GLN cc_start: 0.8150 (tp40) cc_final: 0.7608 (tp-100) REVERT: B 143 CYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7095 (p) REVERT: B 144 MET cc_start: 0.7239 (mmm) cc_final: 0.6856 (mmm) REVERT: A 123 LYS cc_start: 0.8132 (tptp) cc_final: 0.7719 (tppt) REVERT: A 128 LEU cc_start: 0.8356 (mp) cc_final: 0.7865 (mm) REVERT: A 135 GLU cc_start: 0.7965 (pt0) cc_final: 0.7577 (pp20) REVERT: A 143 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8087 (mmm160) REVERT: A 153 ILE cc_start: 0.8969 (mt) cc_final: 0.8768 (tt) REVERT: A 241 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8165 (mtm-85) REVERT: A 243 TYR cc_start: 0.7921 (m-80) cc_final: 0.7359 (m-80) REVERT: A 245 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7742 (mmp80) REVERT: A 264 SER cc_start: 0.8407 (m) cc_final: 0.8116 (p) REVERT: A 267 VAL cc_start: 0.8922 (t) cc_final: 0.8680 (p) REVERT: A 268 GLU cc_start: 0.8446 (tt0) cc_final: 0.8035 (tm-30) REVERT: A 273 TYR cc_start: 0.8042 (m-80) cc_final: 0.7768 (m-80) REVERT: A 291 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6695 (tmm) REVERT: A 295 ASN cc_start: 0.8136 (p0) cc_final: 0.7631 (p0) REVERT: A 310 CYS cc_start: 0.7973 (m) cc_final: 0.7508 (m) REVERT: A 315 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8237 (mmmm) REVERT: A 321 GLN cc_start: 0.8300 (mt0) cc_final: 0.8050 (mt0) REVERT: A 323 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8154 (tttt) REVERT: A 338 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7362 (tpt90) REVERT: A 340 MET cc_start: 0.7631 (tmm) cc_final: 0.7015 (tmm) REVERT: A 341 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 388 VAL cc_start: 0.7998 (t) cc_final: 0.7740 (p) REVERT: A 392 HIS cc_start: 0.7434 (m-70) cc_final: 0.7038 (m-70) REVERT: A 397 ASP cc_start: 0.6675 (p0) cc_final: 0.6206 (p0) REVERT: A 406 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 407 LEU cc_start: 0.8805 (mt) cc_final: 0.8465 (mt) REVERT: A 408 THR cc_start: 0.8623 (m) cc_final: 0.8373 (p) REVERT: A 411 GLU cc_start: 0.7999 (tt0) cc_final: 0.7776 (tt0) REVERT: A 429 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: A 435 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7901 (tptp) REVERT: A 515 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6972 (tm-30) REVERT: A 518 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 520 ASN cc_start: 0.8348 (t0) cc_final: 0.7884 (t0) REVERT: A 537 LEU cc_start: 0.8385 (tp) cc_final: 0.8102 (tt) REVERT: A 539 ARG cc_start: 0.7603 (tpt-90) cc_final: 0.7016 (mtp85) REVERT: A 542 MET cc_start: 0.7296 (ptp) cc_final: 0.6849 (ptp) REVERT: A 546 GLU cc_start: 0.7330 (tp30) cc_final: 0.7000 (tp30) REVERT: A 577 LEU cc_start: 0.8199 (mm) cc_final: 0.7917 (mm) REVERT: A 590 PHE cc_start: 0.8305 (m-80) cc_final: 0.8049 (m-80) REVERT: A 611 GLN cc_start: 0.7929 (mp-120) cc_final: 0.7360 (mp10) REVERT: A 625 ASN cc_start: 0.8163 (m-40) cc_final: 0.7907 (m-40) REVERT: A 645 LYS cc_start: 0.8167 (mttt) cc_final: 0.7350 (mmmm) REVERT: A 649 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7750 (mtp85) REVERT: A 653 ASP cc_start: 0.7427 (m-30) cc_final: 0.7035 (p0) REVERT: A 665 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8355 (mp) REVERT: A 713 PHE cc_start: 0.8415 (t80) cc_final: 0.8021 (t80) REVERT: A 735 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7795 (ttp80) REVERT: A 738 HIS cc_start: 0.6883 (t-90) cc_final: 0.6431 (t-90) REVERT: A 747 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8080 (tppp) REVERT: A 757 LEU cc_start: 0.8637 (tp) cc_final: 0.8384 (tt) REVERT: A 762 SER cc_start: 0.8068 (m) cc_final: 0.7664 (p) REVERT: A 768 GLN cc_start: 0.7825 (mp10) cc_final: 0.7298 (mp10) REVERT: A 772 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7092 (mp0) REVERT: A 788 ARG cc_start: 0.6917 (mmm-85) cc_final: 0.6652 (tpp-160) REVERT: A 800 GLU cc_start: 0.7892 (tp30) cc_final: 0.7649 (tp30) REVERT: A 802 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7823 (mtpp) REVERT: A 804 LEU cc_start: 0.8469 (mt) cc_final: 0.8142 (mt) REVERT: A 829 LYS cc_start: 0.8485 (tttt) cc_final: 0.8147 (ttpp) REVERT: A 836 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7481 (mtt90) REVERT: A 841 HIS cc_start: 0.7922 (t70) cc_final: 0.7408 (t70) REVERT: A 855 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7777 (ttpp) REVERT: D 17 ARG cc_start: 0.7305 (mmt180) cc_final: 0.7015 (mmt180) REVERT: D 22 LEU cc_start: 0.7721 (tp) cc_final: 0.7415 (tp) REVERT: D 25 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8133 (mm-30) REVERT: D 26 LEU cc_start: 0.8601 (mp) cc_final: 0.8255 (mp) REVERT: D 39 TYR cc_start: 0.8177 (m-80) cc_final: 0.7587 (m-80) REVERT: D 46 ARG cc_start: 0.7653 (mmp-170) cc_final: 0.7015 (mmt180) REVERT: D 77 TYR cc_start: 0.8155 (m-80) cc_final: 0.7614 (m-80) REVERT: D 89 SER cc_start: 0.8409 (p) cc_final: 0.7968 (t) REVERT: D 101 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8439 (ttmm) REVERT: D 115 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8463 (ptmm) REVERT: D 121 GLU cc_start: 0.8116 (mp0) cc_final: 0.7644 (mp0) REVERT: D 124 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7759 (ttp80) REVERT: D 128 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8471 (mtmm) REVERT: D 131 ARG cc_start: 0.8409 (ttm110) cc_final: 0.7796 (ttm110) REVERT: D 143 CYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7017 (p) REVERT: C 123 LYS cc_start: 0.8116 (tptp) cc_final: 0.7670 (tppt) REVERT: C 128 LEU cc_start: 0.8120 (mp) cc_final: 0.7588 (mm) REVERT: C 135 GLU cc_start: 0.8125 (pt0) cc_final: 0.7703 (pp20) REVERT: C 161 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8069 (pm20) REVERT: C 241 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: C 243 TYR cc_start: 0.7925 (m-80) cc_final: 0.7262 (m-80) REVERT: C 245 ARG cc_start: 0.8166 (mmp80) cc_final: 0.7727 (mmm-85) REVERT: C 247 LEU cc_start: 0.8423 (mp) cc_final: 0.7929 (tp) REVERT: C 268 GLU cc_start: 0.8239 (tt0) cc_final: 0.7789 (tm-30) REVERT: C 289 ILE cc_start: 0.8586 (mm) cc_final: 0.8166 (mm) REVERT: C 295 ASN cc_start: 0.8422 (m110) cc_final: 0.7982 (m110) REVERT: C 310 CYS cc_start: 0.8037 (m) cc_final: 0.7457 (m) REVERT: C 315 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8268 (mmmm) REVERT: C 323 LYS cc_start: 0.8535 (ptmt) cc_final: 0.8119 (tttt) REVERT: C 327 LEU cc_start: 0.8158 (mt) cc_final: 0.7906 (mt) REVERT: C 338 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7367 (tpt-90) REVERT: C 340 MET cc_start: 0.7314 (tmm) cc_final: 0.6669 (tmm) REVERT: C 341 GLU cc_start: 0.7559 (pt0) cc_final: 0.6763 (pt0) REVERT: C 347 ILE cc_start: 0.8854 (mt) cc_final: 0.8554 (tt) REVERT: C 350 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8239 (mmmt) REVERT: C 406 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7650 (tp30) REVERT: C 426 ASP cc_start: 0.8103 (t0) cc_final: 0.7823 (t0) REVERT: C 428 LEU cc_start: 0.8698 (tp) cc_final: 0.8359 (tp) REVERT: C 440 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.6316 (ttt90) REVERT: C 487 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8353 (t) REVERT: C 520 ASN cc_start: 0.8419 (t0) cc_final: 0.8152 (t0) REVERT: C 521 PRO cc_start: 0.8500 (Cg_endo) cc_final: 0.8269 (Cg_exo) REVERT: C 539 ARG cc_start: 0.7775 (tpt-90) cc_final: 0.7508 (tpt-90) REVERT: C 558 GLU cc_start: 0.6593 (tm-30) cc_final: 0.6296 (tm-30) REVERT: C 566 ASP cc_start: 0.6521 (t0) cc_final: 0.6249 (t0) REVERT: C 572 LYS cc_start: 0.7987 (ptpt) cc_final: 0.7444 (mtmm) REVERT: C 577 LEU cc_start: 0.8343 (mm) cc_final: 0.7926 (mm) REVERT: C 580 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7600 (mt-10) REVERT: C 584 ASN cc_start: 0.8870 (t0) cc_final: 0.8456 (t0) REVERT: C 594 GLU cc_start: 0.7252 (mp0) cc_final: 0.6941 (mp0) REVERT: C 609 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7076 (mp0) REVERT: C 642 MET cc_start: 0.8091 (mmp) cc_final: 0.7880 (mmp) REVERT: C 644 LYS cc_start: 0.8450 (tppt) cc_final: 0.7793 (tppt) REVERT: C 649 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.6975 (mtm-85) REVERT: C 651 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 677 MET cc_start: 0.5778 (mmm) cc_final: 0.5295 (mmm) REVERT: C 710 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.7999 (ttm170) REVERT: C 712 GLU cc_start: 0.7844 (pm20) cc_final: 0.7578 (pm20) REVERT: C 713 PHE cc_start: 0.8518 (t80) cc_final: 0.8170 (t80) REVERT: C 720 TYR cc_start: 0.7730 (t80) cc_final: 0.7067 (t80) REVERT: C 757 LEU cc_start: 0.8556 (tp) cc_final: 0.8304 (tt) REVERT: C 762 SER cc_start: 0.8144 (m) cc_final: 0.7778 (p) REVERT: C 764 ASN cc_start: 0.7980 (p0) cc_final: 0.7707 (p0) REVERT: C 766 ASP cc_start: 0.7310 (t0) cc_final: 0.6602 (t0) REVERT: C 768 GLN cc_start: 0.7883 (mp10) cc_final: 0.7469 (mp10) REVERT: C 800 GLU cc_start: 0.7802 (tp30) cc_final: 0.7370 (tp30) REVERT: C 802 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7947 (mtpp) REVERT: C 803 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7441 (mtt180) REVERT: C 804 LEU cc_start: 0.8520 (mt) cc_final: 0.7993 (mp) REVERT: C 836 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7490 (mtt90) REVERT: C 855 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7661 (ttpp) outliers start: 50 outliers final: 34 residues processed: 573 average time/residue: 0.3312 time to fit residues: 253.5675 Evaluate side-chains 584 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 541 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 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 533 ILE Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 734 ARG 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 29 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 350 LYS Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 615 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 795 HIS Chi-restraints excluded: chain C residue 797 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 133 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097524 restraints weight = 27213.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101129 restraints weight = 13418.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103494 restraints weight = 7931.539| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13904 Z= 0.194 Angle : 0.662 12.020 18776 Z= 0.330 Chirality : 0.042 0.206 2058 Planarity : 0.004 0.031 2434 Dihedral : 3.875 16.803 1844 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.96 % Allowed : 31.84 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1648 helix: 0.71 (0.19), residues: 844 sheet: -2.01 (0.55), residues: 72 loop : 0.23 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 328 HIS 0.009 0.001 HIS C 738 PHE 0.026 0.002 PHE D 76 TYR 0.017 0.001 TYR C 659 ARG 0.012 0.001 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.95 seconds wall clock time: 77 minutes 36.00 seconds (4656.00 seconds total)